Diff for /imach/src/imach.c between versions 1.50 and 1.126

version 1.50, 2002/06/26 23:25:02 version 1.126, 2006/04/28 17:23:28
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.126  2006/04/28 17:23:28  brouard
      (Module): Yes the sum of survivors was wrong since
   This program computes Healthy Life Expectancies from    imach-114 because nhstepm was no more computed in the age
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    loop. Now we define nhstepma in the age loop.
   first survey ("cross") where individuals from different ages are    Version 0.98h
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.125  2006/04/04 15:20:31  lievre
   second wave of interviews ("longitudinal") which measure each change    Errors in calculation of health expectancies. Age was not initialized.
   (if any) in individual health status.  Health expectancies are    Forecasting file added.
   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 1.124  2006/03/22 17:13:53  lievre
   Maximum Likelihood of the parameters involved in the model.  The    Parameters are printed with %lf instead of %f (more numbers after the comma).
   simplest model is the multinomial logistic model where pij is the    The log-likelihood is printed in the log file
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.123  2006/03/20 10:52:43  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    * imach.c (Module): <title> changed, corresponds to .htm file
   'age' is age and 'sex' is a covariate. If you want to have a more    name. <head> headers where missing.
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    * imach.c (Module): Weights can have a decimal point as for
   you to do it.  More covariates you add, slower the    English (a comma might work with a correct LC_NUMERIC environment,
   convergence.    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
   The advantage of this computer programme, compared to a simple    1.
   multinomial logistic model, is clear when the delay between waves is not    Version 0.98g
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.122  2006/03/20 09:45:41  brouard
   account using an interpolation or extrapolation.      (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
   hPijx is the probability to be observed in state i at age x+h    otherwise the weight is truncated).
   conditional to the observed state i at age x. The delay 'h' can be    Modification of warning when the covariates values are not 0 or
   split into an exact number (nh*stepm) of unobserved intermediate    1.
   states. This elementary transition (by month or quarter trimester,    Version 0.98g
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.121  2006/03/16 17:45:01  lievre
   and the contribution of each individual to the likelihood is simply    * imach.c (Module): Comments concerning covariates added
   hPijx.  
     * imach.c (Module): refinements in the computation of lli if
   Also this programme outputs the covariance matrix of the parameters but also    status=-2 in order to have more reliable computation if stepm is
   of the life expectancies. It also computes the prevalence limits.    not 1 month. Version 0.98f
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.120  2006/03/16 15:10:38  lievre
            Institut national d'études démographiques, Paris.    (Module): refinements in the computation of lli if
   This software have been partly granted by Euro-REVES, a concerted action    status=-2 in order to have more reliable computation if stepm is
   from the European Union.    not 1 month. Version 0.98f
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.119  2006/03/15 17:42:26  brouard
   can be accessed at http://euroreves.ined.fr/imach .    (Module): Bug if status = -2, the loglikelihood was
   **********************************************************************/    computed as likelihood omitting the logarithm. Version O.98e
    
 #include <math.h>    Revision 1.118  2006/03/14 18:20:07  brouard
 #include <stdio.h>    (Module): varevsij Comments added explaining the second
 #include <stdlib.h>    table of variances if popbased=1 .
 #include <unistd.h>    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 #define MAXLINE 256    (Module): Version 0.98d
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.117  2006/03/14 17:16:22  brouard
 #define FILENAMELENGTH 80    (Module): varevsij Comments added explaining the second
 /*#define DEBUG*/    table of variances if popbased=1 .
 #define windows    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): Function pstamp added
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    (Module): Version 0.98d
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.116  2006/03/06 10:29:27  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.115  2006/02/27 12:17:45  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): One freematrix added in mlikeli! 0.98c
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.114  2006/02/26 12:57:58  brouard
 #define YEARM 12. /* Number of months per year */    (Module): Some improvements in processing parameter
 #define AGESUP 130    filename with strsep.
 #define AGEBASE 40  
 #ifdef windows    Revision 1.113  2006/02/24 14:20:24  brouard
 #define DIRSEPARATOR '\\'    (Module): Memory leaks checks with valgrind and:
 #define ODIRSEPARATOR '/'    datafile was not closed, some imatrix were not freed and on matrix
 #else    allocation too.
 #define DIRSEPARATOR '/'  
 #define ODIRSEPARATOR '\\'    Revision 1.112  2006/01/30 09:55:26  brouard
 #endif    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Revision 1.111  2006/01/25 20:38:18  brouard
 int erreur; /* Error number */    (Module): Lots of cleaning and bugs added (Gompertz)
 int nvar;    (Module): Comments can be added in data file. Missing date values
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    can be a simple dot '.'.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.110  2006/01/25 00:51:50  brouard
 int ndeath=1; /* Number of dead states */    (Module): Lots of cleaning and bugs added (Gompertz)
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.108  2006/01/19 18:05:42  lievre
 int jmin, jmax; /* min, max spacing between 2 waves */    Gnuplot problem appeared...
 int mle, weightopt;    To be fixed
 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 1.107  2006/01/19 16:20:37  brouard
 double jmean; /* Mean space between 2 waves */    Test existence of gnuplot in imach path
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.106  2006/01/19 13:24:36  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Some cleaning and links added in html output
 FILE *ficlog;  
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    Revision 1.105  2006/01/05 20:23:19  lievre
 FILE *ficresprobmorprev;    *** empty log message ***
 FILE *fichtm; /* Html File */  
 FILE *ficreseij;    Revision 1.104  2005/09/30 16:11:43  lievre
 char filerese[FILENAMELENGTH];    (Module): sump fixed, loop imx fixed, and simplifications.
 FILE  *ficresvij;    (Module): If the status is missing at the last wave but we know
 char fileresv[FILENAMELENGTH];    that the person is alive, then we can code his/her status as -2
 FILE  *ficresvpl;    (instead of missing=-1 in earlier versions) and his/her
 char fileresvpl[FILENAMELENGTH];    contributions to the likelihood is 1 - Prob of dying from last
 char title[MAXLINE];    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    the healthy state at last known wave). Version is 0.98
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  
     Revision 1.103  2005/09/30 15:54:49  lievre
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    (Module): sump fixed, loop imx fixed, and simplifications.
 char filelog[FILENAMELENGTH]; /* Log file */  
 char filerest[FILENAMELENGTH];    Revision 1.102  2004/09/15 17:31:30  brouard
 char fileregp[FILENAMELENGTH];    Add the possibility to read data file including tab characters.
 char popfile[FILENAMELENGTH];  
     Revision 1.101  2004/09/15 10:38:38  brouard
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Fix on curr_time
   
 #define NR_END 1    Revision 1.100  2004/07/12 18:29:06  brouard
 #define FREE_ARG char*    Add version for Mac OS X. Just define UNIX in Makefile
 #define FTOL 1.0e-10  
     Revision 1.99  2004/06/05 08:57:40  brouard
 #define NRANSI    *** empty log message ***
 #define ITMAX 200  
     Revision 1.98  2004/05/16 15:05:56  brouard
 #define TOL 2.0e-4    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 #define CGOLD 0.3819660    state at each age, but using a Gompertz model: log u =a + b*age .
 #define ZEPS 1.0e-10    This is the basic analysis of mortality and should be done before any
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
 #define GOLD 1.618034    from other sources like vital statistic data.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    The same imach parameter file can be used but the option for mle should be -3.
   
 static double maxarg1,maxarg2;    Agnès, who wrote this part of the code, tried to keep most of the
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    former routines in order to include the new code within the former code.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      The output is very simple: only an estimate of the intercept and of
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    the slope with 95% confident intervals.
 #define rint(a) floor(a+0.5)  
     Current limitations:
 static double sqrarg;    A) Even if you enter covariates, i.e. with the
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    B) There is no computation of Life Expectancy nor Life Table.
   
 int imx;    Revision 1.97  2004/02/20 13:25:42  lievre
 int stepm;    Version 0.96d. Population forecasting command line is (temporarily)
 /* Stepm, step in month: minimum step interpolation*/    suppressed.
   
 int estepm;    Revision 1.96  2003/07/15 15:38:55  brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.95  2003/07/08 07:54:34  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    * imach.c (Repository):
 double **pmmij, ***probs, ***mobaverage;    (Repository): Using imachwizard code to output a more meaningful covariance
 double dateintmean=0;    matrix (cov(a12,c31) instead of numbers.
   
 double *weight;    Revision 1.94  2003/06/27 13:00:02  brouard
 int **s; /* Status */    Just cleaning
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    exist so I changed back to asctime which exists.
 double ftolhess; /* Tolerance for computing hessian */    (Module): Version 0.96b
   
 /**************** split *************************/    Revision 1.92  2003/06/25 16:30:45  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
    l1 = strlen( path );                 /* length of path */    (Repository): Elapsed time after each iteration is now output. It
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    helps to forecast when convergence will be reached. Elapsed time
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    is stamped in powell.  We created a new html file for the graphs
    if ( s == NULL ) {                   /* no directory, so use current */    concerning matrix of covariance. It has extension -cov.htm.
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    Revision 1.90  2003/06/24 12:34:15  brouard
 #if     defined(__bsd__)                /* get current working directory */    (Module): Some bugs corrected for windows. Also, when
       extern char       *getwd( );    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.89  2003/06/24 12:30:52  brouard
       extern char       *getcwd( );    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    of the covariance matrix to be input.
 #endif  
          return( GLOCK_ERROR_GETCWD );    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.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.87  2003/06/18 12:26:01  brouard
       s++;                              /* after this, the filename */    Version 0.96
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.86  2003/06/17 20:04:08  brouard
       strcpy( name, s );                /* save file name */    (Module): Change position of html and gnuplot routines and added
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    routine fileappend.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.85  2003/06/17 13:12:43  brouard
    l1 = strlen( dirc );                 /* length of directory */    * imach.c (Repository): Check when date of death was earlier that
 #ifdef windows    current date of interview. It may happen when the death was just
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    prior to the death. In this case, dh was negative and likelihood
 #else    was wrong (infinity). We still send an "Error" but patch by
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    assuming that the date of death was just one stepm after the
 #endif    interview.
    s = strrchr( name, '.' );            /* find last / */    (Repository): Because some people have very long ID (first column)
    s++;    we changed int to long in num[] and we added a new lvector for
    strcpy(ext,s);                       /* save extension */    memory allocation. But we also truncated to 8 characters (left
    l1= strlen( name);    truncation)
    l2= strlen( s)+1;    (Repository): No more line truncation errors.
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.84  2003/06/13 21:44:43  brouard
    return( 0 );                         /* we're done */    * imach.c (Repository): Replace "freqsummary" at a correct
 }    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
     parcimony.
 /******************************************/    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 void replace(char *s, char*t)    Revision 1.83  2003/06/10 13:39:11  lievre
 {    *** empty log message ***
   int i;  
   int lg=20;    Revision 1.82  2003/06/05 15:57:20  brouard
   i=0;    Add log in  imach.c and  fullversion number is now printed.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  */
     (s[i] = t[i]);  /*
     if (t[i]== '\\') s[i]='/';     Interpolated Markov Chain
   }  
 }    Short summary of the programme:
     
 int nbocc(char *s, char occ)    This program computes Healthy Life Expectancies from
 {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   int i,j=0;    first survey ("cross") where individuals from different ages are
   int lg=20;    interviewed on their health status or degree of disability (in the
   i=0;    case of a health survey which is our main interest) -2- at least a
   lg=strlen(s);    second wave of interviews ("longitudinal") which measure each change
   for(i=0; i<= lg; i++) {    (if any) in individual health status.  Health expectancies are
   if  (s[i] == occ ) j++;    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
   return j;    Maximum Likelihood of the parameters involved in the model.  The
 }    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 void cutv(char *u,char *v, char*t, char occ)    conditional to be observed in state i at the first wave. Therefore
 {    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   /* cuts string t into u and v where u is ended by char occ excluding it    'age' is age and 'sex' is a covariate. If you want to have a more
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    complex model than "constant and age", you should modify the program
      gives u="abcedf" and v="ghi2j" */    where the markup *Covariates have to be included here again* invites
   int i,lg,j,p=0;    you to do it.  More covariates you add, slower the
   i=0;    convergence.
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    The advantage of this computer programme, compared to a simple
   }    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
   lg=strlen(t);    intermediate interview, the information is lost, but taken into
   for(j=0; j<p; j++) {    account using an interpolation or extrapolation.  
     (u[j] = t[j]);  
   }    hPijx is the probability to be observed in state i at age x+h
      u[p]='\0';    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
    for(j=0; j<= lg; j++) {    states. This elementary transition (by month, quarter,
     if (j>=(p+1))(v[j-p-1] = t[j]);    semester or year) is modelled as a multinomial logistic.  The hPx
   }    matrix is simply the matrix product of nh*stepm elementary matrices
 }    and the contribution of each individual to the likelihood is simply
     hPijx.
 /********************** nrerror ********************/  
     Also this programme outputs the covariance matrix of the parameters but also
 void nrerror(char error_text[])    of the life expectancies. It also computes the period (stable) prevalence. 
 {    
   fprintf(stderr,"ERREUR ...\n");    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   fprintf(stderr,"%s\n",error_text);             Institut national d'études démographiques, Paris.
   exit(1);    This software have been partly granted by Euro-REVES, a concerted action
 }    from the European Union.
 /*********************** vector *******************/    It is copyrighted identically to a GNU software product, ie programme and
 double *vector(int nl, int nh)    software can be distributed freely for non commercial use. Latest version
 {    can be accessed at http://euroreves.ined.fr/imach .
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   if (!v) nrerror("allocation failure in vector");    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   return v-nl+NR_END;    
 }    **********************************************************************/
   /*
 /************************ free vector ******************/    main
 void free_vector(double*v, int nl, int nh)    read parameterfile
 {    read datafile
   free((FREE_ARG)(v+nl-NR_END));    concatwav
 }    freqsummary
     if (mle >= 1)
 /************************ivector *******************************/      mlikeli
 int *ivector(long nl,long nh)    print results files
 {    if mle==1 
   int *v;       computes hessian
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    read end of parameter file: agemin, agemax, bage, fage, estepm
   if (!v) nrerror("allocation failure in ivector");        begin-prev-date,...
   return v-nl+NR_END;    open gnuplot file
 }    open html file
     period (stable) prevalence
 /******************free ivector **************************/     for age prevalim()
 void free_ivector(int *v, long nl, long nh)    h Pij x
 {    variance of p varprob
   free((FREE_ARG)(v+nl-NR_END));    forecasting if prevfcast==1 prevforecast call prevalence()
 }    health expectancies
     Variance-covariance of DFLE
 /******************* imatrix *******************************/    prevalence()
 int **imatrix(long nrl, long nrh, long ncl, long nch)     movingaverage()
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    varevsij() 
 {    if popbased==1 varevsij(,popbased)
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    total life expectancies
   int **m;    Variance of period (stable) prevalence
     end
   /* allocate pointers to rows */  */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  
   m -= nrl;   
    #include <math.h>
    #include <stdio.h>
   /* allocate rows and set pointers to them */  #include <stdlib.h>
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #include <string.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <unistd.h>
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  #include <limits.h>
    #include <sys/types.h>
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #include <sys/stat.h>
    #include <errno.h>
   /* return pointer to array of pointers to rows */  extern int errno;
   return m;  
 }  /* #include <sys/time.h> */
   #include <time.h>
 /****************** free_imatrix *************************/  #include "timeval.h"
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  /* #include <libintl.h> */
       long nch,ncl,nrh,nrl;  /* #define _(String) gettext (String) */
      /* free an int matrix allocated by imatrix() */  
 {  #define MAXLINE 256
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  #define GNUPLOTPROGRAM "gnuplot"
 }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  #define NINTERVMAX 8
   m += NR_END;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   m -= nrl;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define MAXN 20000
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define YEARM 12. /* Number of months per year */
   m[nrl] += NR_END;  #define AGESUP 130
   m[nrl] -= ncl;  #define AGEBASE 40
   #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #ifdef UNIX
   return m;  #define DIRSEPARATOR '/'
 }  #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 /*************************free matrix ************************/  #else
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #define DIRSEPARATOR '\\'
 {  #define CHARSEPARATOR "\\"
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define ODIRSEPARATOR '/'
   free((FREE_ARG)(m+nrl-NR_END));  #endif
 }  
   /* $Id$ */
 /******************* ma3x *******************************/  /* $State$ */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  char version[]="Imach version 0.98h, April 2006, INED-EUROREVES-Institut de longevite ";
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  char fullversion[]="$Revision$ $Date$"; 
   double ***m;  char strstart[80];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   if (!m) nrerror("allocation failure 1 in matrix()");  int nvar;
   m += NR_END;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m -= nrl;  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int ndeath=1; /* Number of dead states */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   m[nrl] += NR_END;  int popbased=0;
   m[nrl] -= ncl;  
   int *wav; /* Number of waves for this individuual 0 is possible */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  int gipmx, gsw; /* Global variables on the number of contributions 
   m[nrl][ncl] += NR_END;                     to the likelihood and the sum of weights (done by funcone)*/
   m[nrl][ncl] -= nll;  int mle, weightopt;
   for (j=ncl+1; j<=nch; j++)  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     m[nrl][j]=m[nrl][j-1]+nlay;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   for (i=nrl+1; i<=nrh; i++) {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  double jmean; /* Mean space between 2 waves */
     for (j=ncl+1; j<=nch; j++)  double **oldm, **newm, **savm; /* Working pointers to matrices */
       m[i][j]=m[i][j-1]+nlay;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   }  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   return m;  FILE *ficlog, *ficrespow;
 }  int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
 /*************************free ma3x ************************/  long ipmx; /* Number of contributions */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  double sw; /* Sum of weights */
 {  char filerespow[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  FILE *ficresilk;
   free((FREE_ARG)(m+nrl-NR_END));  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 }  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
 /***************** f1dim *************************/  FILE *ficreseij;
 extern int ncom;  char filerese[FILENAMELENGTH];
 extern double *pcom,*xicom;  FILE *ficresstdeij;
 extern double (*nrfunc)(double []);  char fileresstde[FILENAMELENGTH];
    FILE *ficrescveij;
 double f1dim(double x)  char filerescve[FILENAMELENGTH];
 {  FILE  *ficresvij;
   int j;  char fileresv[FILENAMELENGTH];
   double f;  FILE  *ficresvpl;
   double *xt;  char fileresvpl[FILENAMELENGTH];
    char title[MAXLINE];
   xt=vector(1,ncom);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   f=(*nrfunc)(xt);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   free_vector(xt,1,ncom);  char command[FILENAMELENGTH];
   return f;  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  char filelog[FILENAMELENGTH]; /* Log file */
 {  char filerest[FILENAMELENGTH];
   int iter;  char fileregp[FILENAMELENGTH];
   double a,b,d,etemp;  char popfile[FILENAMELENGTH];
   double fu,fv,fw,fx;  
   double ftemp;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
    struct timezone tzp;
   a=(ax < cx ? ax : cx);  extern int gettimeofday();
   b=(ax > cx ? ax : cx);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   x=w=v=bx;  long time_value;
   fw=fv=fx=(*f)(x);  extern long time();
   for (iter=1;iter<=ITMAX;iter++) {  char strcurr[80], strfor[80];
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  char *endptr;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  long lval;
     printf(".");fflush(stdout);  double dval;
     fprintf(ficlog,".");fflush(ficlog);  
 #ifdef DEBUG  #define NR_END 1
     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);  #define FREE_ARG char*
     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);  #define FTOL 1.0e-10
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  #define NRANSI 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #define ITMAX 200 
       *xmin=x;  
       return fx;  #define TOL 2.0e-4 
     }  
     ftemp=fu;  #define CGOLD 0.3819660 
     if (fabs(e) > tol1) {  #define ZEPS 1.0e-10 
       r=(x-w)*(fx-fv);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  #define GOLD 1.618034 
       q=2.0*(q-r);  #define GLIMIT 100.0 
       if (q > 0.0) p = -p;  #define TINY 1.0e-20 
       q=fabs(q);  
       etemp=e;  static double maxarg1,maxarg2;
       e=d;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    
       else {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         d=p/q;  #define rint(a) floor(a+0.5)
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  static double sqrarg;
           d=SIGN(tol1,xm-x);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     } else {  int agegomp= AGEGOMP;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  int imx; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  int stepm=1;
     fu=(*f)(u);  /* Stepm, step in month: minimum step interpolation*/
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  int estepm;
       SHFT(v,w,x,u)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
         SHFT(fv,fw,fx,fu)  
         } else {  int m,nb;
           if (u < x) a=u; else b=u;  long *num;
           if (fu <= fw || w == x) {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
             v=w;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
             w=u;  double **pmmij, ***probs;
             fv=fw;  double *ageexmed,*agecens;
             fw=fu;  double dateintmean=0;
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  double *weight;
             fv=fu;  int **s; /* Status */
           }  double *agedc, **covar, idx;
         }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   }  double *lsurv, *lpop, *tpop;
   nrerror("Too many iterations in brent");  
   *xmin=x;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   return fx;  double ftolhess; /* Tolerance for computing hessian */
 }  
   /**************** split *************************/
 /****************** mnbrak ***********************/  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
             double (*func)(double))       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 {    */ 
   double ulim,u,r,q, dum;    char  *ss;                            /* pointer */
   double fu;    int   l1, l2;                         /* length counters */
    
   *fa=(*func)(*ax);    l1 = strlen(path );                   /* length of path */
   *fb=(*func)(*bx);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   if (*fb > *fa) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     SHFT(dum,*ax,*bx,dum)    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       SHFT(dum,*fb,*fa,dum)      strcpy( name, path );               /* we got the fullname name because no directory */
       }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   *cx=(*bx)+GOLD*(*bx-*ax);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   *fc=(*func)(*cx);      /* get current working directory */
   while (*fb > *fc) {      /*    extern  char* getcwd ( char *buf , int len);*/
     r=(*bx-*ax)*(*fb-*fc);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     q=(*bx-*cx)*(*fb-*fa);        return( GLOCK_ERROR_GETCWD );
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      }
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      /* got dirc from getcwd*/
     ulim=(*bx)+GLIMIT*(*cx-*bx);      printf(" DIRC = %s \n",dirc);
     if ((*bx-u)*(u-*cx) > 0.0) {    } else {                              /* strip direcotry from path */
       fu=(*func)(u);      ss++;                               /* after this, the filename */
     } else if ((*cx-u)*(u-ulim) > 0.0) {      l2 = strlen( ss );                  /* length of filename */
       fu=(*func)(u);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       if (fu < *fc) {      strcpy( name, ss );         /* save file name */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      strncpy( dirc, path, l1 - l2 );     /* now the directory */
           SHFT(*fb,*fc,fu,(*func)(u))      dirc[l1-l2] = 0;                    /* add zero */
           }      printf(" DIRC2 = %s \n",dirc);
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    }
       u=ulim;    /* We add a separator at the end of dirc if not exists */
       fu=(*func)(u);    l1 = strlen( dirc );                  /* length of directory */
     } else {    if( dirc[l1-1] != DIRSEPARATOR ){
       u=(*cx)+GOLD*(*cx-*bx);      dirc[l1] =  DIRSEPARATOR;
       fu=(*func)(u);      dirc[l1+1] = 0; 
     }      printf(" DIRC3 = %s \n",dirc);
     SHFT(*ax,*bx,*cx,u)    }
       SHFT(*fa,*fb,*fc,fu)    ss = strrchr( name, '.' );            /* find last / */
       }    if (ss >0){
 }      ss++;
       strcpy(ext,ss);                     /* save extension */
 /*************** linmin ************************/      l1= strlen( name);
       l2= strlen(ss)+1;
 int ncom;      strncpy( finame, name, l1-l2);
 double *pcom,*xicom;      finame[l1-l2]= 0;
 double (*nrfunc)(double []);    }
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    return( 0 );                          /* we're done */
 {  }
   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,  
               double *fc, double (*func)(double));  void replace_back_to_slash(char *s, char*t)
   int j;  {
   double xx,xmin,bx,ax;    int i;
   double fx,fb,fa;    int lg=0;
      i=0;
   ncom=n;    lg=strlen(t);
   pcom=vector(1,n);    for(i=0; i<= lg; i++) {
   xicom=vector(1,n);      (s[i] = t[i]);
   nrfunc=func;      if (t[i]== '\\') s[i]='/';
   for (j=1;j<=n;j++) {    }
     pcom[j]=p[j];  }
     xicom[j]=xi[j];  
   }  int nbocc(char *s, char occ)
   ax=0.0;  {
   xx=1.0;    int i,j=0;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    int lg=20;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    i=0;
 #ifdef DEBUG    lg=strlen(s);
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    for(i=0; i<= lg; i++) {
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    if  (s[i] == occ ) j++;
 #endif    }
   for (j=1;j<=n;j++) {    return j;
     xi[j] *= xmin;  }
     p[j] += xi[j];  
   }  void cutv(char *u,char *v, char*t, char occ)
   free_vector(xicom,1,n);  {
   free_vector(pcom,1,n);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
 }       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
        gives u="abcedf" and v="ghi2j" */
 /*************** powell ************************/    int i,lg,j,p=0;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    i=0;
             double (*func)(double []))    for(j=0; j<=strlen(t)-1; j++) {
 {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   void linmin(double p[], double xi[], int n, double *fret,    }
               double (*func)(double []));  
   int i,ibig,j;    lg=strlen(t);
   double del,t,*pt,*ptt,*xit;    for(j=0; j<p; j++) {
   double fp,fptt;      (u[j] = t[j]);
   double *xits;    }
   pt=vector(1,n);       u[p]='\0';
   ptt=vector(1,n);  
   xit=vector(1,n);     for(j=0; j<= lg; j++) {
   xits=vector(1,n);      if (j>=(p+1))(v[j-p-1] = t[j]);
   *fret=(*func)(p);    }
   for (j=1;j<=n;j++) pt[j]=p[j];  }
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  /********************** nrerror ********************/
     ibig=0;  
     del=0.0;  void nrerror(char error_text[])
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  {
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    fprintf(stderr,"ERREUR ...\n");
     for (i=1;i<=n;i++)    fprintf(stderr,"%s\n",error_text);
       printf(" %d %.12f",i, p[i]);    exit(EXIT_FAILURE);
     fprintf(ficlog," %d %.12f",i, p[i]);  }
     printf("\n");  /*********************** vector *******************/
     fprintf(ficlog,"\n");  double *vector(int nl, int nh)
     for (i=1;i<=n;i++) {  {
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    double *v;
       fptt=(*fret);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!v) nrerror("allocation failure in vector");
       printf("fret=%lf \n",*fret);    return v-nl+NR_END;
       fprintf(ficlog,"fret=%lf \n",*fret);  }
 #endif  
       printf("%d",i);fflush(stdout);  /************************ free vector ******************/
       fprintf(ficlog,"%d",i);fflush(ficlog);  void free_vector(double*v, int nl, int nh)
       linmin(p,xit,n,fret,func);  {
       if (fabs(fptt-(*fret)) > del) {    free((FREE_ARG)(v+nl-NR_END));
         del=fabs(fptt-(*fret));  }
         ibig=i;  
       }  /************************ivector *******************************/
 #ifdef DEBUG  int *ivector(long nl,long nh)
       printf("%d %.12e",i,(*fret));  {
       fprintf(ficlog,"%d %.12e",i,(*fret));    int *v;
       for (j=1;j<=n;j++) {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    if (!v) nrerror("allocation failure in ivector");
         printf(" x(%d)=%.12e",j,xit[j]);    return v-nl+NR_END;
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  }
       }  
       for(j=1;j<=n;j++) {  /******************free ivector **************************/
         printf(" p=%.12e",p[j]);  void free_ivector(int *v, long nl, long nh)
         fprintf(ficlog," p=%.12e",p[j]);  {
       }    free((FREE_ARG)(v+nl-NR_END));
       printf("\n");  }
       fprintf(ficlog,"\n");  
 #endif  /************************lvector *******************************/
     }  long *lvector(long nl,long nh)
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  {
 #ifdef DEBUG    long *v;
       int k[2],l;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       k[0]=1;    if (!v) nrerror("allocation failure in ivector");
       k[1]=-1;    return v-nl+NR_END;
       printf("Max: %.12e",(*func)(p));  }
       fprintf(ficlog,"Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++) {  /******************free lvector **************************/
         printf(" %.12e",p[j]);  void free_lvector(long *v, long nl, long nh)
         fprintf(ficlog," %.12e",p[j]);  {
       }    free((FREE_ARG)(v+nl-NR_END));
       printf("\n");  }
       fprintf(ficlog,"\n");  
       for(l=0;l<=1;l++) {  /******************* imatrix *******************************/
         for (j=1;j<=n;j++) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
           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]);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         }    int **m; 
         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)));    /* allocate pointers to rows */ 
       }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 #endif    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
     m -= nrl; 
       free_vector(xit,1,n);    
       free_vector(xits,1,n);    
       free_vector(ptt,1,n);    /* allocate rows and set pointers to them */ 
       free_vector(pt,1,n);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       return;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     }    m[nrl] += NR_END; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    m[nrl] -= ncl; 
     for (j=1;j<=n;j++) {    
       ptt[j]=2.0*p[j]-pt[j];    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       xit[j]=p[j]-pt[j];    
       pt[j]=p[j];    /* return pointer to array of pointers to rows */ 
     }    return m; 
     fptt=(*func)(ptt);  } 
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  /****************** free_imatrix *************************/
       if (t < 0.0) {  void free_imatrix(m,nrl,nrh,ncl,nch)
         linmin(p,xit,n,fret,func);        int **m;
         for (j=1;j<=n;j++) {        long nch,ncl,nrh,nrl; 
           xi[j][ibig]=xi[j][n];       /* free an int matrix allocated by imatrix() */ 
           xi[j][n]=xit[j];  { 
         }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 #ifdef DEBUG    free((FREE_ARG) (m+nrl-NR_END)); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  } 
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++){  /******************* matrix *******************************/
           printf(" %.12e",xit[j]);  double **matrix(long nrl, long nrh, long ncl, long nch)
           fprintf(ficlog," %.12e",xit[j]);  {
         }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         printf("\n");    double **m;
         fprintf(ficlog,"\n");  
 #endif    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
   }    m -= nrl;
 }  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /**** Prevalence limit ****************/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    m[nrl] -= ncl;
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
      matrix by transitions matrix until convergence is reached */    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   int i, ii,j,k;     */
   double min, max, maxmin, maxmax,sumnew=0.;  }
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  /*************************free matrix ************************/
   double **newm;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double agefin, delaymax=50 ; /* Max number of years to converge */  {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (ii=1;ii<=nlstate+ndeath;ii++)    free((FREE_ARG)(m+nrl-NR_END));
     for (j=1;j<=nlstate+ndeath;j++){  }
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
    cov[1]=1.;  {
      long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double ***m;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     /* Covariates have to be included here again */    if (!m) nrerror("allocation failure 1 in matrix()");
      cov[2]=agefin;    m += NR_END;
      m -= nrl;
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         /*      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 (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       }    m[nrl] += NR_END;
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    m[nrl] -= ncl;
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    m[nrl][ncl] += NR_END;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
     savm=oldm;      m[nrl][j]=m[nrl][j-1]+nlay;
     oldm=newm;    
     maxmax=0.;    for (i=nrl+1; i<=nrh; i++) {
     for(j=1;j<=nlstate;j++){      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       min=1.;      for (j=ncl+1; j<=nch; j++) 
       max=0.;        m[i][j]=m[i][j-1]+nlay;
       for(i=1; i<=nlstate; i++) {    }
         sumnew=0;    return m; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         prlim[i][j]= newm[i][j]/(1-sumnew);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         max=FMAX(max,prlim[i][j]);    */
         min=FMIN(min,prlim[i][j]);  }
       }  
       maxmin=max-min;  /*************************free ma3x ************************/
       maxmax=FMAX(maxmax,maxmin);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     }  {
     if(maxmax < ftolpl){    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       return prlim;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     }    free((FREE_ARG)(m+nrl-NR_END));
   }  }
 }  
   /*************** function subdirf ***********/
 /*************** transition probabilities ***************/  char *subdirf(char fileres[])
   {
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    /* Caution optionfilefiname is hidden */
 {    strcpy(tmpout,optionfilefiname);
   double s1, s2;    strcat(tmpout,"/"); /* Add to the right */
   /*double t34;*/    strcat(tmpout,fileres);
   int i,j,j1, nc, ii, jj;    return tmpout;
   }
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){  /*************** function subdirf2 ***********/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  char *subdirf2(char fileres[], char *preop)
         /*s2 += param[i][j][nc]*cov[nc];*/  {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    /* Caution optionfilefiname is hidden */
       }    strcpy(tmpout,optionfilefiname);
       ps[i][j]=s2;    strcat(tmpout,"/");
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    strcat(tmpout,preop);
     }    strcat(tmpout,fileres);
     for(j=i+1; j<=nlstate+ndeath;j++){    return tmpout;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  }
         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);*/  /*************** function subdirf3 ***********/
       }  char *subdirf3(char fileres[], char *preop, char *preop2)
       ps[i][j]=s2;  {
     }    
   }    /* Caution optionfilefiname is hidden */
     /*ps[3][2]=1;*/    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
   for(i=1; i<= nlstate; i++){    strcat(tmpout,preop);
      s1=0;    strcat(tmpout,preop2);
     for(j=1; j<i; j++)    strcat(tmpout,fileres);
       s1+=exp(ps[i][j]);    return tmpout;
     for(j=i+1; j<=nlstate+ndeath; j++)  }
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);  /***************** f1dim *************************/
     for(j=1; j<i; j++)  extern int ncom; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  extern double *pcom,*xicom;
     for(j=i+1; j<=nlstate+ndeath; j++)  extern double (*nrfunc)(double []); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];   
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  double f1dim(double x) 
   } /* end i */  { 
     int j; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    double f;
     for(jj=1; jj<= nlstate+ndeath; jj++){    double *xt; 
       ps[ii][jj]=0;   
       ps[ii][ii]=1;    xt=vector(1,ncom); 
     }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   }    f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
     return f; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  } 
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  /*****************brent *************************/
    }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     printf("\n ");  { 
     }    int iter; 
     printf("\n ");printf("%lf ",cov[2]);*/    double a,b,d,etemp;
 /*    double fu,fv,fw,fx;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    double ftemp;
   goto end;*/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     return ps;    double e=0.0; 
 }   
     a=(ax < cx ? ax : cx); 
 /**************** Product of 2 matrices ******************/    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    fw=fv=fx=(*f)(x); 
 {    for (iter=1;iter<=ITMAX;iter++) { 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      xm=0.5*(a+b); 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   /* in, b, out are matrice of pointers which should have been initialized      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
      before: only the contents of out is modified. The function returns      printf(".");fflush(stdout);
      a pointer to pointers identical to out */      fprintf(ficlog,".");fflush(ficlog);
   long i, j, k;  #ifdef DEBUG
   for(i=nrl; i<= nrh; 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);
     for(k=ncolol; k<=ncoloh; k++)      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         out[i][k] +=in[i][j]*b[j][k];  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   return out;        *xmin=x; 
 }        return fx; 
       } 
       ftemp=fu;
 /************* Higher Matrix Product ***************/      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        q=(x-v)*(fx-fw); 
 {        p=(x-v)*q-(x-w)*r; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        q=2.0*(q-r); 
      duration (i.e. until        if (q > 0.0) p = -p; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        q=fabs(q); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        etemp=e; 
      (typically every 2 years instead of every month which is too big).        e=d; 
      Model is determined by parameters x and covariates have to be        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
      included manually here.          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
      */          d=p/q; 
           u=x+d; 
   int i, j, d, h, k;          if (u-a < tol2 || b-u < tol2) 
   double **out, cov[NCOVMAX];            d=SIGN(tol1,xm-x); 
   double **newm;        } 
       } else { 
   /* Hstepm could be zero and should return the unit matrix */        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (i=1;i<=nlstate+ndeath;i++)      } 
     for (j=1;j<=nlstate+ndeath;j++){      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      fu=(*f)(u); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      if (fu <= fx) { 
     }        if (u >= x) a=x; else b=x; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        SHFT(v,w,x,u) 
   for(h=1; h <=nhstepm; h++){          SHFT(fv,fw,fx,fu) 
     for(d=1; d <=hstepm; d++){          } else { 
       newm=savm;            if (u < x) a=u; else b=u; 
       /* Covariates have to be included here again */            if (fu <= fw || w == x) { 
       cov[1]=1.;              v=w; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;              w=u; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];              fv=fw; 
       for (k=1; k<=cptcovage;k++)              fw=fu; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            } else if (fu <= fv || v == x || v == w) { 
       for (k=1; k<=cptcovprod;k++)              v=u; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              fv=fu; 
             } 
           } 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    } 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    nrerror("Too many iterations in brent"); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    *xmin=x; 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    return fx; 
       savm=oldm;  } 
       oldm=newm;  
     }  /****************** mnbrak ***********************/
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         po[i][j][h]=newm[i][j];              double (*func)(double)) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  { 
          */    double ulim,u,r,q, dum;
       }    double fu; 
   } /* end h */   
   return po;    *fa=(*func)(*ax); 
 }    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
 /*************** log-likelihood *************/        SHFT(dum,*fb,*fa,dum) 
 double func( double *x)        } 
 {    *cx=(*bx)+GOLD*(*bx-*ax); 
   int i, ii, j, k, mi, d, kk;    *fc=(*func)(*cx); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    while (*fb > *fc) { 
   double **out;      r=(*bx-*ax)*(*fb-*fc); 
   double sw; /* Sum of weights */      q=(*bx-*cx)*(*fb-*fa); 
   double lli; /* Individual log likelihood */      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   long ipmx;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   /*extern weight */      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   /* We are differentiating ll according to initial status */      if ((*bx-u)*(u-*cx) > 0.0) { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        fu=(*func)(u); 
   /*for(i=1;i<imx;i++)      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     printf(" %d\n",s[4][i]);        fu=(*func)(u); 
   */        if (fu < *fc) { 
   cov[1]=1.;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
   for(k=1; k<=nlstate; k++) ll[k]=0.;            } 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        u=ulim; 
     for(mi=1; mi<= wav[i]-1; mi++){        fu=(*func)(u); 
       for (ii=1;ii<=nlstate+ndeath;ii++)      } else { 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        u=(*cx)+GOLD*(*cx-*bx); 
       for(d=0; d<dh[mi][i]; d++){        fu=(*func)(u); 
         newm=savm;      } 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      SHFT(*ax,*bx,*cx,u) 
         for (kk=1; kk<=cptcovage;kk++) {        SHFT(*fa,*fb,*fc,fu) 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        } 
         }  } 
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  /*************** linmin ************************/
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;  int ncom; 
         oldm=newm;  double *pcom,*xicom;
          double (*nrfunc)(double []); 
           
       } /* end mult */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
        { 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    double brent(double ax, double bx, double cx, 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/                 double (*f)(double), double tol, double *xmin); 
       ipmx +=1;    double f1dim(double x); 
       sw += weight[i];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;                double *fc, double (*func)(double)); 
     } /* end of wave */    int j; 
   } /* end of individual */    double xx,xmin,bx,ax; 
     double fx,fb,fa;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];   
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    ncom=n; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    pcom=vector(1,n); 
   return -l;    xicom=vector(1,n); 
 }    nrfunc=func; 
     for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
 /*********** Maximum Likelihood Estimation ***************/      xicom[j]=xi[j]; 
     } 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    ax=0.0; 
 {    xx=1.0; 
   int i,j, iter;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   double **xi,*delti;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   double fret;  #ifdef DEBUG
   xi=matrix(1,npar,1,npar);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (i=1;i<=npar;i++)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for (j=1;j<=npar;j++)  #endif
       xi[i][j]=(i==j ? 1.0 : 0.0);    for (j=1;j<=n;j++) { 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");      xi[j] *= xmin; 
   powell(p,xi,npar,ftol,&iter,&fret,func);      p[j] += xi[j]; 
     } 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    free_vector(xicom,1,n); 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    free_vector(pcom,1,n); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  } 
   
 }  char *asc_diff_time(long time_sec, char ascdiff[])
   {
 /**** Computes Hessian and covariance matrix ***/    long sec_left, days, hours, minutes;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    days = (time_sec) / (60*60*24);
 {    sec_left = (time_sec) % (60*60*24);
   double  **a,**y,*x,pd;    hours = (sec_left) / (60*60) ;
   double **hess;    sec_left = (sec_left) %(60*60);
   int i, j,jk;    minutes = (sec_left) /60;
   int *indx;    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   double hessii(double p[], double delta, int theta, double delti[]);    return ascdiff;
   double hessij(double p[], double delti[], int i, int j);  }
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   hess=matrix(1,npar,1,npar);              double (*func)(double [])) 
   { 
   printf("\nCalculation of the hessian matrix. Wait...\n");    void linmin(double p[], double xi[], int n, double *fret, 
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");                double (*func)(double [])); 
   for (i=1;i<=npar;i++){    int i,ibig,j; 
     printf("%d",i);fflush(stdout);    double del,t,*pt,*ptt,*xit;
     fprintf(ficlog,"%d",i);fflush(ficlog);    double fp,fptt;
     hess[i][i]=hessii(p,ftolhess,i,delti);    double *xits;
     /*printf(" %f ",p[i]);*/    int niterf, itmp;
     /*printf(" %lf ",hess[i][i]);*/  
   }    pt=vector(1,n); 
      ptt=vector(1,n); 
   for (i=1;i<=npar;i++) {    xit=vector(1,n); 
     for (j=1;j<=npar;j++)  {    xits=vector(1,n); 
       if (j>i) {    *fret=(*func)(p); 
         printf(".%d%d",i,j);fflush(stdout);    for (j=1;j<=n;j++) pt[j]=p[j]; 
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    for (*iter=1;;++(*iter)) { 
         hess[i][j]=hessij(p,delti,i,j);      fp=(*fret); 
         hess[j][i]=hess[i][j];          ibig=0; 
         /*printf(" %lf ",hess[i][j]);*/      del=0.0; 
       }      last_time=curr_time;
     }      (void) gettimeofday(&curr_time,&tzp);
   }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   printf("\n");      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
   fprintf(ficlog,"\n");  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
      for (i=1;i<=n;i++) {
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        printf(" %d %.12f",i, p[i]);
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");        fprintf(ficlog," %d %.12lf",i, p[i]);
          fprintf(ficrespow," %.12lf", p[i]);
   a=matrix(1,npar,1,npar);      }
   y=matrix(1,npar,1,npar);      printf("\n");
   x=vector(1,npar);      fprintf(ficlog,"\n");
   indx=ivector(1,npar);      fprintf(ficrespow,"\n");fflush(ficrespow);
   for (i=1;i<=npar;i++)      if(*iter <=3){
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        tm = *localtime(&curr_time.tv_sec);
   ludcmp(a,npar,indx,&pd);        strcpy(strcurr,asctime(&tm));
   /*       asctime_r(&tm,strcurr); */
   for (j=1;j<=npar;j++) {        forecast_time=curr_time; 
     for (i=1;i<=npar;i++) x[i]=0;        itmp = strlen(strcurr);
     x[j]=1;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     lubksb(a,npar,indx,x);          strcurr[itmp-1]='\0';
     for (i=1;i<=npar;i++){        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       matcov[i][j]=x[i];        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     }        for(niterf=10;niterf<=30;niterf+=10){
   }          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   printf("\n#Hessian matrix#\n");  /*      asctime_r(&tmf,strfor); */
   fprintf(ficlog,"\n#Hessian matrix#\n");          strcpy(strfor,asctime(&tmf));
   for (i=1;i<=npar;i++) {          itmp = strlen(strfor);
     for (j=1;j<=npar;j++) {          if(strfor[itmp-1]=='\n')
       printf("%.3e ",hess[i][j]);          strfor[itmp-1]='\0';
       fprintf(ficlog,"%.3e ",hess[i][j]);          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(forecast_time.tv_sec-curr_time.tv_sec,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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     printf("\n");        }
     fprintf(ficlog,"\n");      }
   }      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   /* Recompute Inverse */        fptt=(*fret); 
   for (i=1;i<=npar;i++)  #ifdef DEBUG
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        printf("fret=%lf \n",*fret);
   ludcmp(a,npar,indx,&pd);        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
   /*  printf("\n#Hessian matrix recomputed#\n");        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
   for (j=1;j<=npar;j++) {        linmin(p,xit,n,fret,func); 
     for (i=1;i<=npar;i++) x[i]=0;        if (fabs(fptt-(*fret)) > del) { 
     x[j]=1;          del=fabs(fptt-(*fret)); 
     lubksb(a,npar,indx,x);          ibig=i; 
     for (i=1;i<=npar;i++){        } 
       y[i][j]=x[i];  #ifdef DEBUG
       printf("%.3e ",y[i][j]);        printf("%d %.12e",i,(*fret));
       fprintf(ficlog,"%.3e ",y[i][j]);        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     printf("\n");          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     fprintf(ficlog,"\n");          printf(" x(%d)=%.12e",j,xit[j]);
   }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   */        }
         for(j=1;j<=n;j++) {
   free_matrix(a,1,npar,1,npar);          printf(" p=%.12e",p[j]);
   free_matrix(y,1,npar,1,npar);          fprintf(ficlog," p=%.12e",p[j]);
   free_vector(x,1,npar);        }
   free_ivector(indx,1,npar);        printf("\n");
   free_matrix(hess,1,npar,1,npar);        fprintf(ficlog,"\n");
   #endif
       } 
 }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
 /*************** hessian matrix ****************/        int k[2],l;
 double hessii( double x[], double delta, int theta, double delti[])        k[0]=1;
 {        k[1]=-1;
   int i;        printf("Max: %.12e",(*func)(p));
   int l=1, lmax=20;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   double k1,k2;        for (j=1;j<=n;j++) {
   double p2[NPARMAX+1];          printf(" %.12e",p[j]);
   double res;          fprintf(ficlog," %.12e",p[j]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        }
   double fx;        printf("\n");
   int k=0,kmax=10;        fprintf(ficlog,"\n");
   double l1;        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
   fx=func(x);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   for (i=1;i<=npar;i++) p2[i]=x[i];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for(l=0 ; l <=lmax; l++){            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     l1=pow(10,l);          }
     delts=delt;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(k=1 ; k <kmax; k=k+1){          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       delt = delta*(l1*k);        }
       p2[theta]=x[theta] +delt;  #endif
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;  
       k2=func(p2)-fx;        free_vector(xit,1,n); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */        free_vector(xits,1,n); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        free_vector(ptt,1,n); 
              free_vector(pt,1,n); 
 #ifdef DEBUG        return; 
       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);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 #endif      for (j=1;j<=n;j++) { 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        ptt[j]=2.0*p[j]-pt[j]; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        xit[j]=p[j]-pt[j]; 
         k=kmax;        pt[j]=p[j]; 
       }      } 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      fptt=(*func)(ptt); 
         k=kmax; l=lmax*10.;      if (fptt < fp) { 
       }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        if (t < 0.0) { 
         delts=delt;          linmin(p,xit,n,fret,func); 
       }          for (j=1;j<=n;j++) { 
     }            xi[j][ibig]=xi[j][n]; 
   }            xi[j][n]=xit[j]; 
   delti[theta]=delts;          }
   return res;  #ifdef DEBUG
            printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
 double hessij( double x[], double delti[], int thetai,int thetaj)            printf(" %.12e",xit[j]);
 {            fprintf(ficlog," %.12e",xit[j]);
   int i;          }
   int l=1, l1, lmax=20;          printf("\n");
   double k1,k2,k3,k4,res,fx;          fprintf(ficlog,"\n");
   double p2[NPARMAX+1];  #endif
   int k;        }
       } 
   fx=func(x);    } 
   for (k=1; k<=2; k++) {  } 
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;  /**** Prevalence limit (stable or period prevalence)  ****************/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
    {
     p2[thetai]=x[thetai]+delti[thetai]/k;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;       matrix by transitions matrix until convergence is reached */
     k2=func(p2)-fx;  
      int i, ii,j,k;
     p2[thetai]=x[thetai]-delti[thetai]/k;    double min, max, maxmin, maxmax,sumnew=0.;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    double **matprod2();
     k3=func(p2)-fx;    double **out, cov[NCOVMAX], **pmij();
      double **newm;
     p2[thetai]=x[thetai]-delti[thetai]/k;    double agefin, delaymax=50 ; /* Max number of years to converge */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;    for (ii=1;ii<=nlstate+ndeath;ii++)
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      for (j=1;j<=nlstate+ndeath;j++){
 #ifdef DEBUG        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      }
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif     cov[1]=1.;
   }   
   return res;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
 /************** Inverse of matrix **************/      /* Covariates have to be included here again */
 void ludcmp(double **a, int n, int *indx, double *d)       cov[2]=agefin;
 {    
   int i,imax,j,k;        for (k=1; k<=cptcovn;k++) {
   double big,dum,sum,temp;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double *vv;          /*      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]]);*/
          }
   vv=vector(1,n);        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   *d=1.0;        for (k=1; k<=cptcovprod;k++)
   for (i=1;i<=n;i++) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     big=0.0;  
     for (j=1;j<=n;j++)        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       if ((temp=fabs(a[i][j])) > big) big=temp;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     vv[i]=1.0/big;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   }  
   for (j=1;j<=n;j++) {      savm=oldm;
     for (i=1;i<j;i++) {      oldm=newm;
       sum=a[i][j];      maxmax=0.;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      for(j=1;j<=nlstate;j++){
       a[i][j]=sum;        min=1.;
     }        max=0.;
     big=0.0;        for(i=1; i<=nlstate; i++) {
     for (i=j;i<=n;i++) {          sumnew=0;
       sum=a[i][j];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       for (k=1;k<j;k++)          prlim[i][j]= newm[i][j]/(1-sumnew);
         sum -= a[i][k]*a[k][j];          max=FMAX(max,prlim[i][j]);
       a[i][j]=sum;          min=FMIN(min,prlim[i][j]);
       if ( (dum=vv[i]*fabs(sum)) >= big) {        }
         big=dum;        maxmin=max-min;
         imax=i;        maxmax=FMAX(maxmax,maxmin);
       }      }
     }      if(maxmax < ftolpl){
     if (j != imax) {        return prlim;
       for (k=1;k<=n;k++) {      }
         dum=a[imax][k];    }
         a[imax][k]=a[j][k];  }
         a[j][k]=dum;  
       }  /*************** transition probabilities ***************/ 
       *d = -(*d);  
       vv[imax]=vv[j];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     }  {
     indx[j]=imax;    double s1, s2;
     if (a[j][j] == 0.0) a[j][j]=TINY;    /*double t34;*/
     if (j != n) {    int i,j,j1, nc, ii, jj;
       dum=1.0/(a[j][j]);  
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      for(i=1; i<= nlstate; i++){
     }        for(j=1; j<i;j++){
   }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   free_vector(vv,1,n);  /* Doesn't work */            /*s2 += param[i][j][nc]*cov[nc];*/
 ;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 }  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
           }
 void lubksb(double **a, int n, int *indx, double b[])          ps[i][j]=s2;
 {  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   int i,ii=0,ip,j;        }
   double sum;        for(j=i+1; j<=nlstate+ndeath;j++){
            for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (i=1;i<=n;i++) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     ip=indx[i];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     sum=b[ip];          }
     b[ip]=b[i];          ps[i][j]=s2;
     if (ii)        }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      }
     else if (sum) ii=i;      /*ps[3][2]=1;*/
     b[i]=sum;      
   }      for(i=1; i<= nlstate; i++){
   for (i=n;i>=1;i--) {        s1=0;
     sum=b[i];        for(j=1; j<i; j++)
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          s1+=exp(ps[i][j]);
     b[i]=sum/a[i][i];        for(j=i+1; j<=nlstate+ndeath; j++)
   }          s1+=exp(ps[i][j]);
 }        ps[i][i]=1./(s1+1.);
         for(j=1; j<i; j++)
 /************ Frequencies ********************/          ps[i][j]= exp(ps[i][j])*ps[i][i];
 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)        for(j=i+1; j<=nlstate+ndeath; j++)
 {  /* Some frequencies */          ps[i][j]= exp(ps[i][j])*ps[i][i];
          /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      } /* end i */
   int first;      
   double ***freq; /* Frequencies */      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   double *pp;        for(jj=1; jj<= nlstate+ndeath; jj++){
   double pos, k2, dateintsum=0,k2cpt=0;          ps[ii][jj]=0;
   FILE *ficresp;          ps[ii][ii]=1;
   char fileresp[FILENAMELENGTH];        }
        }
   pp=vector(1,nlstate);      
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   strcat(fileresp,fileres);  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   if((ficresp=fopen(fileresp,"w"))==NULL) {  /*         printf("ddd %lf ",ps[ii][jj]); */
     printf("Problem with prevalence resultfile: %s\n", fileresp);  /*       } */
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);  /*       printf("\n "); */
     exit(0);  /*        } */
   }  /*        printf("\n ");printf("%lf ",cov[2]); */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);         /*
   j1=0;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
          goto end;*/
   j=cptcoveff;      return ps;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  }
   
   first=1;  /**************** Product of 2 matrices ******************/
   
   for(k1=1; k1<=j;k1++){  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     for(i1=1; i1<=ncodemax[k1];i1++){  {
       j1++;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         scanf("%d", i);*/    /* in, b, out are matrice of pointers which should have been initialized 
       for (i=-1; i<=nlstate+ndeath; i++)         before: only the contents of out is modified. The function returns
         for (jk=-1; jk<=nlstate+ndeath; jk++)         a pointer to pointers identical to out */
           for(m=agemin; m <= agemax+3; m++)    long i, j, k;
             freq[i][jk][m]=0;    for(i=nrl; i<= nrh; i++)
            for(k=ncolol; k<=ncoloh; k++)
       dateintsum=0;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       k2cpt=0;          out[i][k] +=in[i][j]*b[j][k];
       for (i=1; i<=imx; i++) {  
         bool=1;    return out;
         if  (cptcovn>0) {  }
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;  /************* Higher Matrix Product ***************/
         }  
         if (bool==1) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
           for(m=firstpass; m<=lastpass; m++){  {
             k2=anint[m][i]+(mint[m][i]/12.);    /* Computes the transition matrix starting at age 'age' over 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {       'nhstepm*hstepm*stepm' months (i.e. until
               if(agev[m][i]==0) agev[m][i]=agemax+1;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
               if(agev[m][i]==1) agev[m][i]=agemax+2;       nhstepm*hstepm matrices. 
               if (m<lastpass) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];       (typically every 2 years instead of every month which is too big 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];       for the memory).
               }       Model is determined by parameters x and covariates have to be 
                     included manually here. 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  
                 dateintsum=dateintsum+k2;       */
                 k2cpt++;  
               }    int i, j, d, h, k;
             }    double **out, cov[NCOVMAX];
           }    double **newm;
         }  
       }    /* Hstepm could be zero and should return the unit matrix */
            for (i=1;i<=nlstate+ndeath;i++)
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
       if  (cptcovn>0) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
         fprintf(ficresp, "\n#********** Variable ");      }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         fprintf(ficresp, "**********\n#");    for(h=1; h <=nhstepm; h++){
       }      for(d=1; d <=hstepm; d++){
       for(i=1; i<=nlstate;i++)        newm=savm;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        /* Covariates have to be included here again */
       fprintf(ficresp, "\n");        cov[1]=1.;
              cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for(i=(int)agemin; i <= (int)agemax+3; i++){        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         if(i==(int)agemax+3){        for (k=1; k<=cptcovage;k++)
           fprintf(ficlog,"Total");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         }else{        for (k=1; k<=cptcovprod;k++)
           if(first==1){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             first=0;  
             printf("See log file for details...\n");  
           }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
           fprintf(ficlog,"Age %d", i);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         for(jk=1; jk <=nlstate ; jk++){                     pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        savm=oldm;
             pp[jk] += freq[jk][m][i];        oldm=newm;
         }      }
         for(jk=1; jk <=nlstate ; jk++){      for(i=1; i<=nlstate+ndeath; i++)
           for(m=-1, pos=0; m <=0 ; m++)        for(j=1;j<=nlstate+ndeath;j++) {
             pos += freq[jk][m][i];          po[i][j][h]=newm[i][j];
           if(pp[jk]>=1.e-10){          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
             if(first==1){           */
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        }
             }    } /* end h */
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    return po;
           }else{  }
             if(first==1)  
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  /*************** log-likelihood *************/
           }  double func( double *x)
         }  {
     int i, ii, j, k, mi, d, kk;
         for(jk=1; jk <=nlstate ; jk++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double **out;
             pp[jk] += freq[jk][m][i];    double sw; /* Sum of weights */
         }    double lli; /* Individual log likelihood */
     int s1, s2;
         for(jk=1,pos=0; jk <=nlstate ; jk++)    double bbh, survp;
           pos += pp[jk];    long ipmx;
         for(jk=1; jk <=nlstate ; jk++){    /*extern weight */
           if(pos>=1.e-5){    /* We are differentiating ll according to initial status */
             if(first==1)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    /*for(i=1;i<imx;i++) 
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      printf(" %d\n",s[4][i]);
           }else{    */
             if(first==1)    cov[1]=1.;
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for(k=1; k<=nlstate; k++) ll[k]=0.;
           }  
           if( i <= (int) agemax){    if(mle==1){
             if(pos>=1.e-5){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               probs[i][jk][j1]= pp[jk]/pos;        for(mi=1; mi<= wav[i]-1; mi++){
               /*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 (ii=1;ii<=nlstate+ndeath;ii++)
             }            for (j=1;j<=nlstate+ndeath;j++){
             else              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            }
         }          for(d=0; d<dh[mi][i]; d++){
                    newm=savm;
         for(jk=-1; jk <=nlstate+ndeath; jk++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(m=-1; m <=nlstate+ndeath; m++)            for (kk=1; kk<=cptcovage;kk++) {
             if(freq[jk][m][i] !=0 ) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if(first==1)            }
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             }            savm=oldm;
         if(i <= (int) agemax)            oldm=newm;
           fprintf(ficresp,"\n");          } /* end mult */
         if(first==1)        
           printf("Others in log...\n");          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         fprintf(ficlog,"\n");          /* But now since version 0.9 we anticipate for bias at large stepm.
       }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     }           * (in months) between two waves is not a multiple of stepm, we rounded to 
   }           * the nearest (and in case of equal distance, to the lowest) interval but now
   dateintmean=dateintsum/k2cpt;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
             * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   fclose(ficresp);           * probability in order to take into account the bias as a fraction of the way
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   free_vector(pp,1,nlstate);           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
   /* End of Freq */           * For stepm > 1 the results are less biased than in previous versions. 
 }           */
           s1=s[mw[mi][i]][i];
 /************ Prevalence ********************/          s2=s[mw[mi+1][i]][i];
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)          bbh=(double)bh[mi][i]/(double)stepm; 
 {  /* Some frequencies */          /* bias bh is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;           */
   double ***freq; /* Frequencies */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double *pp;          if( s2 > nlstate){ 
   double pos, k2;            /* i.e. if s2 is a death state and if the date of death is known 
                then the contribution to the likelihood is the probability to 
   pp=vector(1,nlstate);               die between last step unit time and current  step unit time, 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);               which is also equal to probability to die before dh 
                 minus probability to die before dh-stepm . 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);               In version up to 0.92 likelihood was computed
   j1=0;          as if date of death was unknown. Death was treated as any other
            health state: the date of the interview describes the actual state
   j=cptcoveff;          and not the date of a change in health state. The former idea was
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          to consider that at each interview the state was recorded
            (healthy, disable or death) and IMaCh was corrected; but when we
   for(k1=1; k1<=j;k1++){          introduced the exact date of death then we should have modified
     for(i1=1; i1<=ncodemax[k1];i1++){          the contribution of an exact death to the likelihood. This new
       j1++;          contribution is smaller and very dependent of the step unit
                stepm. It is no more the probability to die between last interview
       for (i=-1; i<=nlstate+ndeath; i++)            and month of death but the probability to survive from last
         for (jk=-1; jk<=nlstate+ndeath; jk++)            interview up to one month before death multiplied by the
           for(m=agemin; m <= agemax+3; m++)          probability to die within a month. Thanks to Chris
             freq[i][jk][m]=0;          Jackson for correcting this bug.  Former versions increased
                mortality artificially. The bad side is that we add another loop
       for (i=1; i<=imx; i++) {          which slows down the processing. The difference can be up to 10%
         bool=1;          lower mortality.
         if  (cptcovn>0) {            */
           for (z1=1; z1<=cptcoveff; z1++)            lli=log(out[s1][s2] - savm[s1][s2]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;  
         }          } else if  (s2==-2) {
         if (bool==1) {            for (j=1,survp=0. ; j<=nlstate; j++) 
           for(m=firstpass; m<=lastpass; m++){              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             k2=anint[m][i]+(mint[m][i]/12.);            /*survp += out[s1][j]; */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            lli= log(survp);
               if(agev[m][i]==0) agev[m][i]=agemax+1;          }
               if(agev[m][i]==1) agev[m][i]=agemax+2;          
               if (m<lastpass) {          else if  (s2==-4) { 
                 if (calagedate>0)            for (j=3,survp=0. ; j<=nlstate; j++)  
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                 else            lli= log(survp); 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          } 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  
               }          else if  (s2==-5) { 
             }            for (j=1,survp=0. ; j<=2; j++)  
           }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         }            lli= log(survp); 
       }          } 
       for(i=(int)agemin; i <= (int)agemax+3; i++){          
         for(jk=1; jk <=nlstate ; jk++){          else{
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             pp[jk] += freq[jk][m][i];            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         }          } 
         for(jk=1; jk <=nlstate ; jk++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           for(m=-1, pos=0; m <=0 ; m++)          /*if(lli ==000.0)*/
             pos += freq[jk][m][i];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         }          ipmx +=1;
                  sw += weight[i];
         for(jk=1; jk <=nlstate ; jk++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        } /* end of wave */
             pp[jk] += freq[jk][m][i];      } /* end of individual */
         }    }  else if(mle==2){
              for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                for(mi=1; mi<= wav[i]-1; mi++){
         for(jk=1; jk <=nlstate ; jk++){              for (ii=1;ii<=nlstate+ndeath;ii++)
           if( i <= (int) agemax){            for (j=1;j<=nlstate+ndeath;j++){
             if(pos>=1.e-5){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               probs[i][jk][j1]= pp[jk]/pos;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }            }
           }          for(d=0; d<=dh[mi][i]; d++){
         }/* end jk */            newm=savm;
       }/* end i */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     } /* end i1 */            for (kk=1; kk<=cptcovage;kk++) {
   } /* end k1 */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_vector(pp,1,nlstate);            savm=oldm;
              oldm=newm;
 }  /* End of Freq */          } /* end mult */
         
 /************* Waves Concatenation ***************/          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          bbh=(double)bh[mi][i]/(double)stepm; 
 {          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 */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          ipmx +=1;
      Death is a valid wave (if date is known).          sw += weight[i];
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        } /* end of wave */
      and mw[mi+1][i]. dh depends on stepm.      } /* end of individual */
      */    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, mi, m;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for(mi=1; mi<= wav[i]-1; mi++){
      double sum=0., jmean=0.;*/          for (ii=1;ii<=nlstate+ndeath;ii++)
   int first;            for (j=1;j<=nlstate+ndeath;j++){
   int j, k=0,jk, ju, jl;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double sum=0.;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   first=0;            }
   jmin=1e+5;          for(d=0; d<dh[mi][i]; d++){
   jmax=-1;            newm=savm;
   jmean=0.;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(i=1; i<=imx; i++){            for (kk=1; kk<=cptcovage;kk++) {
     mi=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     m=firstpass;            }
     while(s[m][i] <= nlstate){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if(s[m][i]>=1)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         mw[++mi][i]=m;            savm=oldm;
       if(m >=lastpass)            oldm=newm;
         break;          } /* end mult */
       else        
         m++;          s1=s[mw[mi][i]][i];
     }/* end while */          s2=s[mw[mi+1][i]][i];
     if (s[m][i] > nlstate){          bbh=(double)bh[mi][i]/(double)stepm; 
       mi++;     /* Death is another wave */          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 */
       /* if(mi==0)  never been interviewed correctly before death */          ipmx +=1;
          /* Only death is a correct wave */          sw += weight[i];
       mw[mi][i]=m;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
       } /* end of individual */
     wav[i]=mi;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     if(mi==0){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if(first==0){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);        for(mi=1; mi<= wav[i]-1; mi++){
         first=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
       if(first==1){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
     } /* end mi==0 */          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(i=1; i<=imx; i++){            for (kk=1; kk<=cptcovage;kk++) {
     for(mi=1; mi<wav[i];mi++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if (stepm <=0)            }
         dh[mi][i]=1;          
       else{            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         if (s[mw[mi+1][i]][i] > nlstate) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           if (agedc[i] < 2*AGESUP) {            savm=oldm;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            oldm=newm;
           if(j==0) j=1;  /* Survives at least one month after exam */          } /* end mult */
           k=k+1;        
           if (j >= jmax) jmax=j;          s1=s[mw[mi][i]][i];
           if (j <= jmin) jmin=j;          s2=s[mw[mi+1][i]][i];
           sum=sum+j;          if( s2 > nlstate){ 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            lli=log(out[s1][s2] - savm[s1][s2]);
           }          }else{
         }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         else{          }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          ipmx +=1;
           k=k+1;          sw += weight[i];
           if (j >= jmax) jmax=j;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           else if (j <= jmin)jmin=j;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        } /* end of wave */
           sum=sum+j;      } /* end of individual */
         }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         jk= j/stepm;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         jl= j -jk*stepm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         ju= j -(jk+1)*stepm;        for(mi=1; mi<= wav[i]-1; mi++){
         if(jl <= -ju)          for (ii=1;ii<=nlstate+ndeath;ii++)
           dh[mi][i]=jk;            for (j=1;j<=nlstate+ndeath;j++){
         else              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           dh[mi][i]=jk+1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if(dh[mi][i]==0)            }
           dh[mi][i]=1; /* At least one step */          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
   jmean=sum/k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            }
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          
  }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /*********** Tricode ****************************/            savm=oldm;
 void tricode(int *Tvar, int **nbcode, int imx)            oldm=newm;
 {          } /* end mult */
   int Ndum[20],ij=1, k, j, i;        
   int cptcode=0;          s1=s[mw[mi][i]][i];
   cptcoveff=0;          s2=s[mw[mi+1][i]][i];
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   for (k=0; k<19; k++) Ndum[k]=0;          ipmx +=1;
   for (k=1; k<=7; k++) ncodemax[k]=0;          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (j=1; j<=(cptcovn+2*cptcovprod); 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]);*/
     for (i=1; i<=imx; i++) {        } /* end of wave */
       ij=(int)(covar[Tvar[j]][i]);      } /* end of individual */
       Ndum[ij]++;    } /* End of if */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       if (ij > cptcode) cptcode=ij;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
     for (i=0; i<=cptcode; i++) {  }
       if(Ndum[i]!=0) ncodemax[j]++;  
     }  /*************** log-likelihood *************/
     ij=1;  double funcone( double *x)
   {
     /* Same as likeli but slower because of a lot of printf and if */
     for (i=1; i<=ncodemax[j]; i++) {    int i, ii, j, k, mi, d, kk;
       for (k=0; k<=19; k++) {    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         if (Ndum[k] != 0) {    double **out;
           nbcode[Tvar[j]][ij]=k;    double lli; /* Individual log likelihood */
              double llt;
           ij++;    int s1, s2;
         }    double bbh, survp;
         if (ij > ncodemax[j]) break;    /*extern weight */
       }      /* We are differentiating ll according to initial status */
     }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   }      /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
  for (k=0; k<19; k++) Ndum[k]=0;    */
     cov[1]=1.;
  for (i=1; i<=ncovmodel-2; i++) {  
    ij=Tvar[i];    for(k=1; k<=nlstate; k++) ll[k]=0.;
    Ndum[ij]++;  
  }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  ij=1;      for(mi=1; mi<= wav[i]-1; mi++){
  for (i=1; i<=10; i++) {        for (ii=1;ii<=nlstate+ndeath;ii++)
    if((Ndum[i]!=0) && (i<=ncovcol)){          for (j=1;j<=nlstate+ndeath;j++){
      Tvaraff[ij]=i;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      ij++;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
    }          }
  }        for(d=0; d<dh[mi][i]; d++){
            newm=savm;
  cptcoveff=ij-1;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /*********** Health Expectancies ****************/          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 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 )                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
 {          oldm=newm;
   /* Health expectancies */        } /* end mult */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        
   double age, agelim, hf;        s1=s[mw[mi][i]][i];
   double ***p3mat,***varhe;        s2=s[mw[mi+1][i]][i];
   double **dnewm,**doldm;        bbh=(double)bh[mi][i]/(double)stepm; 
   double *xp;        /* bias is positive if real duration
   double **gp, **gm;         * is higher than the multiple of stepm and negative otherwise.
   double ***gradg, ***trgradg;         */
   int theta;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        } else if  (s2==-2) {
   xp=vector(1,npar);          for (j=1,survp=0. ; j<=nlstate; j++) 
   dnewm=matrix(1,nlstate*2,1,npar);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   doldm=matrix(1,nlstate*2,1,nlstate*2);          lli= log(survp);
          }else if (mle==1){
   fprintf(ficreseij,"# Health expectancies\n");          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   fprintf(ficreseij,"# Age");        } else if(mle==2){
   for(i=1; i<=nlstate;i++)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     for(j=1; j<=nlstate;j++)        } else if(mle==3){  /* exponential inter-extrapolation */
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          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 */
   fprintf(ficreseij,"\n");        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
   if(estepm < stepm){        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     printf ("Problem %d lower than %d\n",estepm, stepm);          lli=log(out[s1][s2]); /* Original formula */
   }        } /* End of if */
   else  hstepm=estepm;          ipmx +=1;
   /* We compute the life expectancy from trapezoids spaced every estepm months        sw += weight[i];
    * This is mainly to measure the difference between two models: for example        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    * if stepm=24 months pijx are given only every 2 years and by summing them  /*       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]); */
    * we are calculating an estimate of the Life Expectancy assuming a linear        if(globpr){
    * progression inbetween and thus overestimating or underestimating according          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    * to the curvature of the survival function. If, for the same date, we   %11.6f %11.6f %11.6f ", \
    * estimate the model with stepm=1 month, we can keep estepm to 24 months                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
    * to compare the new estimate of Life expectancy with the same linear                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
    * hypothesis. A more precise result, taking into account a more precise          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
    * curvature will be obtained if estepm is as small as stepm. */            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   /* 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.          fprintf(ficresilk," %10.6f\n", -llt);
      nhstepm is the number of hstepm from age to agelim        }
      nstepm is the number of stepm from age to agelin.      } /* end of wave */
      Look at hpijx to understand the reason of that which relies in memory size    } /* end of individual */
      and note for a fixed period like estepm months */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      survival function given by stepm (the optimization length). Unfortunately it    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      means that if the survival funtion is printed only each two years of age and if    if(globpr==0){ /* First time we count the contributions and weights */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      gipmx=ipmx;
      results. So we changed our mind and took the option of the best precision.      gsw=sw;
   */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    return -l;
   }
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     /* nhstepm age range expressed in number of stepm */  /*************** function likelione ***********/
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  {
     /* if (stepm >= YEARM) hstepm=1;*/    /* This routine should help understanding what is done with 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */       the selection of individuals/waves and
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       to check the exact contribution to the likelihood.
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);       Plotting could be done.
     gp=matrix(0,nhstepm,1,nlstate*2);     */
     gm=matrix(0,nhstepm,1,nlstate*2);    int k;
   
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    if(*globpri !=0){ /* Just counts and sums, no printings */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      strcpy(fileresilk,"ilk"); 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        strcat(fileresilk,fileres);
        if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
     /* Computing Variances of health expectancies */      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");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
      for(theta=1; theta <=npar; theta++){      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(i=1; i<=npar; i++){      for(k=1; k<=nlstate; k++) 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       }      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }
    
       cptj=0;    *fretone=(*funcone)(p);
       for(j=1; j<= nlstate; j++){    if(*globpri !=0){
         for(i=1; i<=nlstate; i++){      fclose(ficresilk);
           cptj=cptj+1;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      fflush(fichtm); 
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    } 
           }    return;
         }  }
       }  
        
        /*********** Maximum Likelihood Estimation ***************/
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    {
          int i,j, iter;
       cptj=0;    double **xi;
       for(j=1; j<= nlstate; j++){    double fret;
         for(i=1;i<=nlstate;i++){    double fretone; /* Only one call to likelihood */
           cptj=cptj+1;    /*  char filerespow[FILENAMELENGTH];*/
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    xi=matrix(1,npar,1,npar);
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    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");
       for(j=1; j<= nlstate*2; j++)    strcpy(filerespow,"pow"); 
         for(h=0; h<=nhstepm-1; h++){    strcat(filerespow,fileres);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
         }      printf("Problem with resultfile: %s\n", filerespow);
      }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
        }
 /* End theta */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      for(h=0; h<=nhstepm-1; h++)    fprintf(ficrespow,"\n");
       for(j=1; j<=nlstate*2;j++)  
         for(theta=1; theta <=npar; theta++)    powell(p,xi,npar,ftol,&iter,&fret,func);
           trgradg[h][j][theta]=gradg[h][theta][j];  
          free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
      for(i=1;i<=nlstate*2;i++)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       for(j=1;j<=nlstate*2;j++)    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         varhe[i][j][(int)age] =0.;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
      printf("%d|",(int)age);fflush(stdout);  }
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);  
      for(h=0;h<=nhstepm-1;h++){  /**** Computes Hessian and covariance matrix ***/
       for(k=0;k<=nhstepm-1;k++){  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  {
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    double  **a,**y,*x,pd;
         for(i=1;i<=nlstate*2;i++)    double **hess;
           for(j=1;j<=nlstate*2;j++)    int i, j,jk;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    int *indx;
       }  
     }    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     /* Computing expectancies */    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     for(i=1; i<=nlstate;i++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
       for(j=1; j<=nlstate;j++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    double gompertz(double p[]);
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    hess=matrix(1,npar,1,npar);
            
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         }    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
     fprintf(ficreseij,"%3.0f",age );      fprintf(ficlog,"%d",i);fflush(ficlog);
     cptj=0;     
     for(i=1; i<=nlstate;i++)       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       for(j=1; j<=nlstate;j++){      
         cptj++;      /*  printf(" %f ",p[i]);
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       }    }
     fprintf(ficreseij,"\n");    
        for (i=1;i<=npar;i++) {
     free_matrix(gm,0,nhstepm,1,nlstate*2);      for (j=1;j<=npar;j++)  {
     free_matrix(gp,0,nhstepm,1,nlstate*2);        if (j>i) { 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          printf(".%d%d",i,j);fflush(stdout);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          hess[i][j]=hessij(p,delti,i,j,func,npar);
   }          
   printf("\n");          hess[j][i]=hess[i][j];    
   fprintf(ficlog,"\n");          /*printf(" %lf ",hess[i][j]);*/
         }
   free_vector(xp,1,npar);      }
   free_matrix(dnewm,1,nlstate*2,1,npar);    }
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    printf("\n");
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    fprintf(ficlog,"\n");
 }  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 /************ Variance ******************/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 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)    
 {    a=matrix(1,npar,1,npar);
   /* Variance of health expectancies */    y=matrix(1,npar,1,npar);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    x=vector(1,npar);
   /* double **newm;*/    indx=ivector(1,npar);
   double **dnewm,**doldm;    for (i=1;i<=npar;i++)
   double **dnewmp,**doldmp;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   int i, j, nhstepm, hstepm, h, nstepm ;    ludcmp(a,npar,indx,&pd);
   int k, cptcode;  
   double *xp;    for (j=1;j<=npar;j++) {
   double **gp, **gm;  /* for var eij */      for (i=1;i<=npar;i++) x[i]=0;
   double ***gradg, ***trgradg; /*for var eij */      x[j]=1;
   double **gradgp, **trgradgp; /* for var p point j */      lubksb(a,npar,indx,x);
   double *gpp, *gmp; /* for var p point j */      for (i=1;i<=npar;i++){ 
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */        matcov[i][j]=x[i];
   double ***p3mat;      }
   double age,agelim, hf;    }
   int theta;  
   char digit[4];    printf("\n#Hessian matrix#\n");
   char digitp[16];    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
   char fileresprobmorprev[FILENAMELENGTH];      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
   if(popbased==1)        fprintf(ficlog,"%.3e ",hess[i][j]);
     strcpy(digitp,"-populbased-");      }
   else      printf("\n");
     strcpy(digitp,"-stablbased-");      fprintf(ficlog,"\n");
     }
   strcpy(fileresprobmorprev,"prmorprev");  
   sprintf(digit,"%-d",ij);    /* Recompute Inverse */
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    for (i=1;i<=npar;i++)
   strcat(fileresprobmorprev,digit); /* Tvar to be done */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   strcat(fileresprobmorprev,digitp); /* Popbased or not */    ludcmp(a,npar,indx,&pd);
   strcat(fileresprobmorprev,fileres);  
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {    /*  printf("\n#Hessian matrix recomputed#\n");
     printf("Problem with resultfile: %s\n", fileresprobmorprev);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      x[j]=1;
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      lubksb(a,npar,indx,x);
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");      for (i=1;i<=npar;i++){ 
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);        y[i][j]=x[i];
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){        printf("%.3e ",y[i][j]);
     fprintf(ficresprobmorprev," p.%-d SE",j);        fprintf(ficlog,"%.3e ",y[i][j]);
     for(i=1; i<=nlstate;i++)      }
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);      printf("\n");
   }        fprintf(ficlog,"\n");
   fprintf(ficresprobmorprev,"\n");    }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    */
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);  
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    free_matrix(a,1,npar,1,npar);
     exit(0);    free_matrix(y,1,npar,1,npar);
   }    free_vector(x,1,npar);
   else{    free_ivector(indx,1,npar);
     fprintf(ficgp,"\n# Routine varevsij");    free_matrix(hess,1,npar,1,npar);
   }  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  
     printf("Problem with html file: %s\n", optionfilehtm);  }
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);  
     exit(0);  /*************** hessian matrix ****************/
   }  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   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");    int i;
   }    int l=1, lmax=20;
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    double k1,k2;
     double p2[NPARMAX+1];
   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");    double res;
   fprintf(ficresvij,"# Age");    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   for(i=1; i<=nlstate;i++)    double fx;
     for(j=1; j<=nlstate;j++)    int k=0,kmax=10;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    double l1;
   fprintf(ficresvij,"\n");  
     fx=func(x);
   xp=vector(1,npar);    for (i=1;i<=npar;i++) p2[i]=x[i];
   dnewm=matrix(1,nlstate,1,npar);    for(l=0 ; l <=lmax; l++){
   doldm=matrix(1,nlstate,1,nlstate);      l1=pow(10,l);
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);      delts=delt;
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);        p2[theta]=x[theta] +delt;
   gpp=vector(nlstate+1,nlstate+ndeath);        k1=func(p2)-fx;
   gmp=vector(nlstate+1,nlstate+ndeath);        p2[theta]=x[theta]-delt;
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        k2=func(p2)-fx;
          /*res= (k1-2.0*fx+k2)/delt/delt; */
   if(estepm < stepm){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     printf ("Problem %d lower than %d\n",estepm, stepm);        
   }  #ifdef DEBUG
   else  hstepm=estepm;          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);
   /* For example we decided to compute the life expectancy with the smallest unit */        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);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  #endif
      nhstepm is the number of hstepm from age to agelim        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
      nstepm is the number of stepm from age to agelin.        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
      Look at hpijx to understand the reason of that which relies in memory size          k=kmax;
      and note for a fixed period like k years */        }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
      survival function given by stepm (the optimization length). Unfortunately it          k=kmax; l=lmax*10.;
      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        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
      results. So we changed our mind and took the option of the best precision.          delts=delt;
   */        }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      }
   agelim = AGESUP;    }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    delti[theta]=delts;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    return res; 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     gm=matrix(0,nhstepm,1,nlstate);  {
     int i;
     int l=1, l1, lmax=20;
     for(theta=1; theta <=npar; theta++){    double k1,k2,k3,k4,res,fx;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double p2[NPARMAX+1];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int k;
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      fx=func(x);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
       if (popbased==1) {      p2[thetai]=x[thetai]+delti[thetai]/k;
         for(i=1; i<=nlstate;i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           prlim[i][i]=probs[(int)age][i][ij];      k1=func(p2)-fx;
       }    
        p2[thetai]=x[thetai]+delti[thetai]/k;
       for(j=1; j<= nlstate; j++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         for(h=0; h<=nhstepm; h++){      k2=func(p2)-fx;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      p2[thetai]=x[thetai]-delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k3=func(p2)-fx;
       /* This for computing forces of mortality (h=1)as a weighted average */    
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){      p2[thetai]=x[thetai]-delti[thetai]/k;
         for(i=1; i<= nlstate; i++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           gpp[j] += prlim[i][i]*p3mat[i][j][1];      k4=func(p2)-fx;
       }          res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       /* end force of mortality */  #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);
       for(i=1; i<=npar; i++) /* Computes gradient */      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);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  #endif
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return res;
    }
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)  /************** Inverse of matrix **************/
           prlim[i][i]=probs[(int)age][i][ij];  void ludcmp(double **a, int n, int *indx, double *d) 
       }  { 
     int i,imax,j,k; 
       for(j=1; j<= nlstate; j++){    double big,dum,sum,temp; 
         for(h=0; h<=nhstepm; h++){    double *vv; 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)   
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    vv=vector(1,n); 
         }    *d=1.0; 
       }    for (i=1;i<=n;i++) { 
       /* This for computing force of mortality (h=1)as a weighted average */      big=0.0; 
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){      for (j=1;j<=n;j++) 
         for(i=1; i<= nlstate; i++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
           gmp[j] += prlim[i][i]*p3mat[i][j][1];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       }          vv[i]=1.0/big; 
       /* end force of mortality */    } 
     for (j=1;j<=n;j++) { 
       for(j=1; j<= nlstate; j++) /* vareij */      for (i=1;i<j;i++) { 
         for(h=0; h<=nhstepm; h++){        sum=a[i][j]; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         }        a[i][j]=sum; 
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */      } 
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];      big=0.0; 
       }      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
     } /* End theta */        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
     for(h=0; h<=nhstepm; h++) /* veij */          big=dum; 
       for(j=1; j<=nlstate;j++)          imax=i; 
         for(theta=1; theta <=npar; theta++)        } 
           trgradg[h][j][theta]=gradg[h][theta][j];      } 
       if (j != imax) { 
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */        for (k=1;k<=n;k++) { 
       for(theta=1; theta <=npar; theta++)          dum=a[imax][k]; 
         trgradgp[j][theta]=gradgp[theta][j];          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        } 
     for(i=1;i<=nlstate;i++)        *d = -(*d); 
       for(j=1;j<=nlstate;j++)        vv[imax]=vv[j]; 
         vareij[i][j][(int)age] =0.;      } 
       indx[j]=imax; 
     for(h=0;h<=nhstepm;h++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
       for(k=0;k<=nhstepm;k++){      if (j != n) { 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        dum=1.0/(a[j][j]); 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         for(i=1;i<=nlstate;i++)      } 
           for(j=1;j<=nlstate;j++)    } 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    free_vector(vv,1,n);  /* Doesn't work */
       }  ;
     }  } 
   
     /* pptj */  void lubksb(double **a, int n, int *indx, double b[]) 
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);  { 
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);    int i,ii=0,ip,j; 
     for(j=nlstate+1;j<=nlstate+ndeath;j++)    double sum; 
       for(i=nlstate+1;i<=nlstate+ndeath;i++)   
         varppt[j][i]=doldmp[j][i];    for (i=1;i<=n;i++) { 
     /* end ppptj */      ip=indx[i]; 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);        sum=b[ip]; 
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);      b[ip]=b[i]; 
        if (ii) 
     if (popbased==1) {        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       for(i=1; i<=nlstate;i++)      else if (sum) ii=i; 
         prlim[i][i]=probs[(int)age][i][ij];      b[i]=sum; 
     }    } 
        for (i=n;i>=1;i--) { 
     /* This for computing force of mortality (h=1)as a weighted average */      sum=b[i]; 
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       for(i=1; i<= nlstate; i++)      b[i]=sum/a[i][i]; 
         gmp[j] += prlim[i][i]*p3mat[i][j][1];    } 
     }      } 
     /* end force of mortality */  
   void pstamp(FILE *fichier)
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);  {
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));  }
       for(i=1; i<=nlstate;i++){  
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);  /************ Frequencies ********************/
       }  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
     }  {  /* Some frequencies */
     fprintf(ficresprobmorprev,"\n");    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     fprintf(ficresvij,"%.0f ",age );    int first;
     for(i=1; i<=nlstate;i++)    double ***freq; /* Frequencies */
       for(j=1; j<=nlstate;j++){    double *pp, **prop;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       }    char fileresp[FILENAMELENGTH];
     fprintf(ficresvij,"\n");    
     free_matrix(gp,0,nhstepm,1,nlstate);    pp=vector(1,nlstate);
     free_matrix(gm,0,nhstepm,1,nlstate);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    strcpy(fileresp,"p");
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    strcat(fileresp,fileres);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   } /* End age */      printf("Problem with prevalence resultfile: %s\n", fileresp);
   free_vector(gpp,nlstate+1,nlstate+ndeath);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   free_vector(gmp,nlstate+1,nlstate+ndeath);      exit(0);
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);    }
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");    j1=0;
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");    j=cptcoveff;
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);  
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);    first=1;
   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);    for(k1=1; k1<=j;k1++){
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
   free_vector(xp,1,npar);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   free_matrix(doldm,1,nlstate,1,nlstate);          scanf("%d", i);*/
   free_matrix(dnewm,1,nlstate,1,npar);        for (i=-5; i<=nlstate+ndeath; i++)  
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);            for(m=iagemin; m <= iagemax+3; m++)
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);              freq[i][jk][m]=0;
   fclose(ficresprobmorprev);  
   fclose(ficgp);      for (i=1; i<=nlstate; i++)  
   fclose(fichtm);        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
 }        
         dateintsum=0;
 /************ Variance of prevlim ******************/        k2cpt=0;
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        for (i=1; i<=imx; i++) {
 {          bool=1;
   /* Variance of prevalence limit */          if  (cptcovn>0) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            for (z1=1; z1<=cptcoveff; z1++) 
   double **newm;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double **dnewm,**doldm;                bool=0;
   int i, j, nhstepm, hstepm;          }
   int k, cptcode;          if (bool==1){
   double *xp;            for(m=firstpass; m<=lastpass; m++){
   double *gp, *gm;              k2=anint[m][i]+(mint[m][i]/12.);
   double **gradg, **trgradg;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   double age,agelim;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   int theta;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                    if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");                if (m<lastpass) {
   fprintf(ficresvpl,"# Age");                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   for(i=1; i<=nlstate;i++)                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       fprintf(ficresvpl," %1d-%1d",i,i);                }
   fprintf(ficresvpl,"\n");                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   xp=vector(1,npar);                  dateintsum=dateintsum+k2;
   dnewm=matrix(1,nlstate,1,npar);                  k2cpt++;
   doldm=matrix(1,nlstate,1,nlstate);                }
                  /*}*/
   hstepm=1*YEARM; /* Every year of age */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          }
   agelim = AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */         
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     if (stepm >= YEARM) hstepm=1;        pstamp(ficresp);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        if  (cptcovn>0) {
     gradg=matrix(1,npar,1,nlstate);          fprintf(ficresp, "\n#********** Variable "); 
     gp=vector(1,nlstate);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     gm=vector(1,nlstate);          fprintf(ficresp, "**********\n#");
         }
     for(theta=1; theta <=npar; theta++){        for(i=1; i<=nlstate;i++) 
       for(i=1; i<=npar; i++){ /* Computes gradient */          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        fprintf(ficresp, "\n");
       }        
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(i=iagemin; i <= iagemax+3; i++){
       for(i=1;i<=nlstate;i++)          if(i==iagemax+3){
         gp[i] = prlim[i][i];            fprintf(ficlog,"Total");
              }else{
       for(i=1; i<=npar; i++) /* Computes gradient */            if(first==1){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              first=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              printf("See log file for details...\n");
       for(i=1;i<=nlstate;i++)            }
         gm[i] = prlim[i][i];            fprintf(ficlog,"Age %d", i);
           }
       for(i=1;i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     } /* End theta */              pp[jk] += freq[jk][m][i]; 
           }
     trgradg =matrix(1,nlstate,1,npar);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
     for(j=1; j<=nlstate;j++)              pos += freq[jk][m][i];
       for(theta=1; theta <=npar; theta++)            if(pp[jk]>=1.e-10){
         trgradg[j][theta]=gradg[theta][j];              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     for(i=1;i<=nlstate;i++)              }
       varpl[i][(int)age] =0.;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            }else{
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);              if(first==1)
     for(i=1;i<=nlstate;i++)                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
     fprintf(ficresvpl,"%.0f ",age );          }
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficresvpl,"\n");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     free_vector(gp,1,nlstate);              pp[jk] += freq[jk][m][i];
     free_vector(gm,1,nlstate);          }       
     free_matrix(gradg,1,npar,1,nlstate);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     free_matrix(trgradg,1,nlstate,1,npar);            pos += pp[jk];
   } /* End age */            posprop += prop[jk][i];
           }
   free_vector(xp,1,npar);          for(jk=1; jk <=nlstate ; jk++){
   free_matrix(doldm,1,nlstate,1,npar);            if(pos>=1.e-5){
   free_matrix(dnewm,1,nlstate,1,nlstate);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
 /************ Variance of one-step probabilities  ******************/              if(first==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)                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   int i, j=0,  i1, k1, l1, t, tj;            }
   int k2, l2, j1,  z1;            if( i <= iagemax){
   int k=0,l, cptcode;              if(pos>=1.e-5){
   int first=1, first1;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;                /*probs[i][jk][j1]= pp[jk]/pos;*/
   double **dnewm,**doldm;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   double *xp;              }
   double *gp, *gm;              else
   double **gradg, **trgradg;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   double **mu;            }
   double age,agelim, cov[NCOVMAX];          }
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */          
   int theta;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   char fileresprob[FILENAMELENGTH];            for(m=-1; m <=nlstate+ndeath; m++)
   char fileresprobcov[FILENAMELENGTH];              if(freq[jk][m][i] !=0 ) {
   char fileresprobcor[FILENAMELENGTH];              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double ***varpij;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
   strcpy(fileresprob,"prob");          if(i <= iagemax)
   strcat(fileresprob,fileres);            fprintf(ficresp,"\n");
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          if(first==1)
     printf("Problem with resultfile: %s\n", fileresprob);            printf("Others in log...\n");
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);          fprintf(ficlog,"\n");
   }        }
   strcpy(fileresprobcov,"probcov");      }
   strcat(fileresprobcov,fileres);    }
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    dateintmean=dateintsum/k2cpt; 
     printf("Problem with resultfile: %s\n", fileresprobcov);   
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    fclose(ficresp);
   }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   strcpy(fileresprobcor,"probcor");    free_vector(pp,1,nlstate);
   strcat(fileresprobcor,fileres);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    /* End of Freq */
     printf("Problem with resultfile: %s\n", fileresprobcor);  }
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);  
   }  /************ Prevalence ********************/
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  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)
   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);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);       in each health status at the date of interview (if between dateprev1 and dateprev2).
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);       We still use firstpass and lastpass as another selection.
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    */
     
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   fprintf(ficresprob,"# Age");    double ***freq; /* Frequencies */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    double *pp, **prop;
   fprintf(ficresprobcov,"# Age");    double pos,posprop; 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    double  y2; /* in fractional years */
   fprintf(ficresprobcov,"# Age");    int iagemin, iagemax;
   
     iagemin= (int) agemin;
   for(i=1; i<=nlstate;i++)    iagemax= (int) agemax;
     for(j=1; j<=(nlstate+ndeath);j++){    /*pp=vector(1,nlstate);*/
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    j1=0;
     }      
   fprintf(ficresprob,"\n");    j=cptcoveff;
   fprintf(ficresprobcov,"\n");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   fprintf(ficresprobcor,"\n");    
   xp=vector(1,npar);    for(k1=1; k1<=j;k1++){
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      for(i1=1; i1<=ncodemax[k1];i1++){
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));        j1++;
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);        
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);        for (i=1; i<=nlstate; i++)  
   first=1;          for(m=iagemin; m <= iagemax+3; m++)
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            prop[i][m]=0.0;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);       
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);        for (i=1; i<=imx; i++) { /* Each individual */
     exit(0);          bool=1;
   }          if  (cptcovn>0) {
   else{            for (z1=1; z1<=cptcoveff; z1++) 
     fprintf(ficgp,"\n# Routine varprob");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   }                bool=0;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {          } 
     printf("Problem with html file: %s\n", optionfilehtm);          if (bool==1) { 
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     exit(0);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   else{                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fprintf(fichtm,"\n");                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     fprintf(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");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
   }              }
             } /* end selection of waves */
            }
   cov[1]=1;        }
   tj=cptcoveff;        for(i=iagemin; i <= iagemax+3; i++){  
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}          
   j1=0;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   for(t=1; t<=tj;t++){            posprop += prop[jk][i]; 
     for(i1=1; i1<=ncodemax[t];i1++){          } 
       j1++;  
                for(jk=1; jk <=nlstate ; jk++){     
       if  (cptcovn>0) {            if( i <=  iagemax){ 
         fprintf(ficresprob, "\n#********** Variable ");              if(posprop>=1.e-5){ 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                probs[i][jk][j1]= prop[jk][i]/posprop;
         fprintf(ficresprob, "**********\n#");              } 
         fprintf(ficresprobcov, "\n#********** Variable ");            } 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          }/* end jk */ 
         fprintf(ficresprobcov, "**********\n#");        }/* end i */ 
              } /* end i1 */
         fprintf(ficgp, "\n#********** Variable ");    } /* end k1 */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    
         fprintf(ficgp, "**********\n#");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
            /*free_vector(pp,1,nlstate);*/
            free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");  }  /* End of prevalence */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");  /************* Waves Concatenation ***************/
          
         fprintf(ficresprobcor, "\n#********** Variable ");      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 (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  {
         fprintf(ficgp, "**********\n#");        /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       }       Death is a valid wave (if date is known).
             mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       for (age=bage; age<=fage; age ++){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         cov[2]=age;       and mw[mi+1][i]. dh depends on stepm.
         for (k=1; k<=cptcovn;k++) {       */
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  
         }    int i, mi, m;
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         for (k=1; k<=cptcovprod;k++)       double sum=0., jmean=0.;*/
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    int first;
            int j, k=0,jk, ju, jl;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    double sum=0.;
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    first=0;
         gp=vector(1,(nlstate)*(nlstate+ndeath));    jmin=1e+5;
         gm=vector(1,(nlstate)*(nlstate+ndeath));    jmax=-1;
        jmean=0.;
         for(theta=1; theta <=npar; theta++){    for(i=1; i<=imx; i++){
           for(i=1; i<=npar; i++)      mi=0;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      m=firstpass;
                while(s[m][i] <= nlstate){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
                    mw[++mi][i]=m;
           k=0;        if(m >=lastpass)
           for(i=1; i<= (nlstate); i++){          break;
             for(j=1; j<=(nlstate+ndeath);j++){        else
               k=k+1;          m++;
               gp[k]=pmmij[i][j];      }/* end while */
             }      if (s[m][i] > nlstate){
           }        mi++;     /* Death is another wave */
                  /* if(mi==0)  never been interviewed correctly before death */
           for(i=1; i<=npar; i++)           /* Only death is a correct wave */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);        mw[mi][i]=m;
          }
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
           k=0;      wav[i]=mi;
           for(i=1; i<=(nlstate); i++){      if(mi==0){
             for(j=1; j<=(nlstate+ndeath);j++){        nbwarn++;
               k=k+1;        if(first==0){
               gm[k]=pmmij[i][j];          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
             }          first=1;
           }        }
              if(first==1){
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          }
         }      } /* end mi==0 */
     } /* End individuals */
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)  
           for(theta=1; theta <=npar; theta++)    for(i=1; i<=imx; i++){
             trgradg[j][theta]=gradg[theta][j];      for(mi=1; mi<wav[i];mi++){
                if (stepm <=0)
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);          dh[mi][i]=1;
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);        else{
                  if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         pmij(pmmij,cov,ncovmodel,x,nlstate);            if (agedc[i] < 2*AGESUP) {
                      j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         k=0;              if(j==0) j=1;  /* Survives at least one month after exam */
         for(i=1; i<=(nlstate); i++){              else if(j<0){
           for(j=1; j<=(nlstate+ndeath);j++){                nberr++;
             k=k+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]);
             mu[k][(int) age]=pmmij[i][j];                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);
         }                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]);
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)                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(j=1;j<=(nlstate)*(nlstate+ndeath);j++)              }
             varpij[i][j][(int)age] = doldm[i][j];              k=k+1;
               if (j >= jmax){
         /*printf("\n%d ",(int)age);                jmax=j;
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){                ijmax=i;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              }
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              if (j <= jmin){
      }*/                jmin=j;
                 ijmin=i;
         fprintf(ficresprob,"\n%d ",(int)age);              }
         fprintf(ficresprobcov,"\n%d ",(int)age);              sum=sum+j;
         fprintf(ficresprobcor,"\n%d ",(int)age);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)            }
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));          }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          else{
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);  /*        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]); */
         }  
         i=0;            k=k+1;
         for (k=1; k<=(nlstate);k++){            if (j >= jmax) {
           for (l=1; l<=(nlstate+ndeath);l++){              jmax=j;
             i=i++;              ijmax=i;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);            }
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);            else if (j <= jmin){
             for (j=1; j<=i;j++){              jmin=j;
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);              ijmin=i;
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));            }
             }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         }/* end of loop for state */            if(j<0){
       } /* end of loop for age */              nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       /* Confidence intervalle of pij  */              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]);
       /*            }
       fprintf(ficgp,"\nset noparametric;unset label");            sum=sum+j;
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");          }
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");          jk= j/stepm;
       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);          jl= j -jk*stepm;
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);          ju= j -(jk+1)*stepm;
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);            if(jl==0){
       */              dh[mi][i]=jk;
               bh[mi][i]=0;
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/            }else{ /* We want a negative bias in order to only have interpolation ie
       first1=1;                    * at the price of an extra matrix product in likelihood */
       for (k1=1; k1<=(nlstate);k1++){              dh[mi][i]=jk+1;
         for (l1=1; l1<=(nlstate+ndeath);l1++){              bh[mi][i]=ju;
           if(l1==k1) continue;            }
           i=(k1-1)*(nlstate+ndeath)+l1;          }else{
           for (k2=1; k2<=(nlstate);k2++){            if(jl <= -ju){
             for (l2=1; l2<=(nlstate+ndeath);l2++){              dh[mi][i]=jk;
               if(l2==k2) continue;              bh[mi][i]=jl;       /* bias is positive if real duration
               j=(k2-1)*(nlstate+ndeath)+l2;                                   * is higher than the multiple of stepm and negative otherwise.
               if(j<=i) continue;                                   */
               for (age=bage; age<=fage; age ++){            }
                 if ((int)age %5==0){            else{
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;              dh[mi][i]=jk+1;
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;              bh[mi][i]=ju;
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;            }
                   mu1=mu[i][(int) age]/stepm*YEARM ;            if(dh[mi][i]==0){
                   mu2=mu[j][(int) age]/stepm*YEARM;              dh[mi][i]=1; /* At least one step */
                   /* Computing eigen value of matrix of covariance */              bh[mi][i]=ju; /* At least one step */
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));              /*  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);*/
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));            }
                   if(first1==1){          } /* end if mle */
                     first1=0;        }
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);      } /* end wave */
                   }    }
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);    jmean=sum/k;
                   /* Eigen vectors */    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);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
                   v21=sqrt(1.-v11*v11);   }
                   v12=-v21;  
                   v22=v11;  /*********** Tricode ****************************/
                   /*printf(fignu*/  void tricode(int *Tvar, int **nbcode, int imx)
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */  {
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */    
                   if(first==1){    int Ndum[20],ij=1, k, j, i, maxncov=19;
                     first=0;    int cptcode=0;
                     fprintf(ficgp,"\nset parametric;set nolabel");    cptcoveff=0; 
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);   
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    for (k=0; k<maxncov; k++) Ndum[k]=0;
                     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);    for (k=1; k<=7; k++) ncodemax[k]=0;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);                                 modality*/ 
                     /*              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\"",\        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \        Ndum[ij]++; /*store the modality */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                     */        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                     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",\                                         Tvar[j]. If V=sex and male is 0 and 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \                                         female is 1, then  cptcode=1.*/
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));      }
                   }else{  
                     first=0;      for (i=0; i<=cptcode; i++) {
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);      }
                     /*  
                     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\"",\      ij=1; 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      for (i=1; i<=ncodemax[j]; i++) {
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);        for (k=0; k<= maxncov; k++) {
                     */          if (Ndum[k] != 0) {
                     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",\            nbcode[Tvar[j]][ij]=k; 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));            
                   }/* if first */            ij++;
                 } /* age mod 5 */          }
               } /* end loop age */          if (ij > ncodemax[j]) break; 
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);        }  
               first=1;      } 
             } /*l12 */    }  
           } /* k12 */  
         } /*l1 */   for (k=0; k< maxncov; k++) Ndum[k]=0;
       }/* k1 */  
     } /* loop covariates */   for (i=1; i<=ncovmodel-2; i++) { 
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));     ij=Tvar[i];
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));     Ndum[ij]++;
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);   }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);   ij=1;
   }   for (i=1; i<= maxncov; i++) {
   free_vector(xp,1,npar);     if((Ndum[i]!=0) && (i<=ncovcol)){
   fclose(ficresprob);       Tvaraff[ij]=i; /*For printing */
   fclose(ficresprobcov);       ij++;
   fclose(ficresprobcor);     }
   fclose(ficgp);   }
   fclose(fichtm);   
 }   cptcoveff=ij-1; /*Number of simple covariates*/
   }
   
 /******************* Printing html file ***********/  /*********** Health Expectancies ****************/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  
                   int lastpass, int stepm, int weightopt, char model[],\  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\  
                   int popforecast, int estepm ,\  {
                   double jprev1, double mprev1,double anprev1, \    /* Health expectancies, no variances */
                   double jprev2, double mprev2,double anprev2){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   int jj1, k1, i1, cpt;    int nhstepma, nstepma; /* Decreasing with age */
   /*char optionfilehtm[FILENAMELENGTH];*/    double age, agelim, hf;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    double ***p3mat;
     printf("Problem with %s \n",optionfilehtm), exit(0);    double eip;
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);  
   }    pstamp(ficreseij);
     fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n    fprintf(ficreseij,"# Age");
  - 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    for(i=1; i<=nlstate;i++){
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n      for(j=1; j<=nlstate;j++){
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n        fprintf(ficreseij," e%1d%1d ",i,j);
  - Life expectancies by age and initial health status (estepm=%2d months):      }
    <a href=\"e%s\">e%s</a> <br>\n</li>", \      fprintf(ficreseij," e%1d. ",i);
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    }
     fprintf(ficreseij,"\n");
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  
     
  m=cptcoveff;    if(estepm < stepm){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
  jj1=0;    else  hstepm=estepm;   
  for(k1=1; k1<=m;k1++){    /* We compute the life expectancy from trapezoids spaced every estepm months
    for(i1=1; i1<=ncodemax[k1];i1++){     * This is mainly to measure the difference between two models: for example
      jj1++;     * if stepm=24 months pijx are given only every 2 years and by summing them
      if (cptcovn > 0) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");     * progression in between and thus overestimating or underestimating according
        for (cpt=1; cpt<=cptcoveff;cpt++)     * to the curvature of the survival function. If, for the same date, we 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");     * to compare the new estimate of Life expectancy with the same linear 
      }     * hypothesis. A more precise result, taking into account a more precise
      /* Pij */     * curvature will be obtained if estepm is as small as stepm. */
      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 example we decided to compute the life expectancy with the smallest unit */
      /* Quasi-incidences */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      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>       nhstepm is the number of hstepm from age to agelim 
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);       nstepm is the number of stepm from age to agelin. 
        /* Stable prevalence in each health state */       Look at hpijx to understand the reason of that which relies in memory size
        for(cpt=1; cpt<nlstate;cpt++){       and note for a fixed period like estepm months */
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);       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
      for(cpt=1; cpt<=nlstate;cpt++) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>       results. So we changed our mind and took the option of the best precision.
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    */
      }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.png<br>    agelim=AGESUP;
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    /* If stepm=6 months */
    } /* end i1 */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
  }/* End k1 */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
  fprintf(fichtm,"</ul>");      
   /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    /* if (stepm >= YEARM) hstepm=1;*/
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n  
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    for (age=bage; age<=fage; age ++){ 
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
  - 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);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
  if(popforecast==1) fprintf(fichtm,"\n      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
  - 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      /* If stepm=6 months */
         <br>",fileres,fileres,fileres,fileres);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
  else         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);      
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
  m=cptcoveff;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      
       printf("%d|",(int)age);fflush(stdout);
  jj1=0;      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  for(k1=1; k1<=m;k1++){      
    for(i1=1; i1<=ncodemax[k1];i1++){      /* Computing expectancies */
      jj1++;      for(i=1; i<=nlstate;i++)
      if (cptcovn > 0) {        for(j=1; j<=nlstate;j++)
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
        for (cpt=1; cpt<=cptcoveff;cpt++)            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            /* 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(cpt=1; cpt<=nlstate;cpt++) {          }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.png <br>      fprintf(ficreseij,"%3.0f",age );
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for(i=1; i<=nlstate;i++){
      }        eip=0;
    } /* end i1 */        for(j=1; j<=nlstate;j++){
  }/* End k1 */          eip +=eij[i][j][(int)age];
  fprintf(fichtm,"</ul>");          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
 fclose(fichtm);        }
 }        fprintf(ficreseij,"%9.4f", eip );
       }
 /******************* Gnuplot file **************/      fprintf(ficreseij,"\n");
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      
     }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int ng;    printf("\n");
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    fprintf(ficlog,"\n");
     printf("Problem with file %s",optionfilegnuplot);    
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);  }
   }  
   void cvevsij(char fileres[], 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[] )
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);  {
 #endif    /* Covariances of health expectancies eij and of total life expectancies according
 m=pow(2,cptcoveff);     to initial status i, ei. .
      */
  /* 1eme*/    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    int nhstepma, nstepma; /* Decreasing with age */
    for (k1=1; k1<= m ; k1 ++) {    double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
 #ifdef windows    double **dnewm,**doldm;
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    double *xp, *xm;
      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);    double **gp, **gm;
 #endif    double ***gradg, ***trgradg;
 #ifdef unix    int theta;
 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);    double eip, vip;
 #endif  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 for (i=1; i<= nlstate ; i ++) {    xp=vector(1,npar);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    xm=vector(1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    dnewm=matrix(1,nlstate*nlstate,1,npar);
 }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    
     for (i=1; i<= nlstate ; i ++) {    pstamp(ficresstdeij);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficresstdeij,"# Age");
 }    for(i=1; i<=nlstate;i++){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      for(j=1; j<=nlstate;j++)
      for (i=1; i<= nlstate ; i ++) {        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficresstdeij," e%1d. ",i);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }      fprintf(ficresstdeij,"\n");
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix    pstamp(ficrescveij);
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
 #endif    fprintf(ficrescveij,"# Age");
    }    for(i=1; i<=nlstate;i++)
   }      for(j=1; j<=nlstate;j++){
   /*2 eme*/        cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
   for (k1=1; k1<= m ; k1 ++) {          for(j2=1; j2<=nlstate;j2++){
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);            cptj2= (j2-1)*nlstate+i2;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);            if(cptj2 <= cptj)
                  fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     for (i=1; i<= nlstate+1 ; i ++) {          }
       k=2*i;      }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficrescveij,"\n");
       for (j=1; j<= nlstate+1 ; j ++) {    
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    if(estepm < stepm){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      printf ("Problem %d lower than %d\n",estepm, stepm);
 }      }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    else  hstepm=estepm;   
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    /* We compute the life expectancy from trapezoids spaced every estepm months
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);     * This is mainly to measure the difference between two models: for example
       for (j=1; j<= nlstate+1 ; j ++) {     * if stepm=24 months pijx are given only every 2 years and by summing them
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");     * we are calculating an estimate of the Life Expectancy assuming a linear 
         else fprintf(ficgp," \%%*lf (\%%*lf)");     * progression in between and thus overestimating or underestimating according
 }       * to the curvature of the survival function. If, for the same date, we 
       fprintf(ficgp,"\" t\"\" w l 0,");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);     * to compare the new estimate of Life expectancy with the same linear 
       for (j=1; j<= nlstate+1 ; j ++) {     * hypothesis. A more precise result, taking into account a more precise
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");     * curvature will be obtained if estepm is as small as stepm. */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      /* For example we decided to compute the life expectancy with the smallest unit */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       else fprintf(ficgp,"\" t\"\" w l 0,");       nhstepm is the number of hstepm from age to agelim 
     }       nstepm is the number of stepm from age to agelin. 
   }       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like estepm months */
   /*3eme*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
   for (k1=1; k1<= m ; k1 ++) {       means that if the survival funtion is printed only each two years of age and if
     for (cpt=1; cpt<= nlstate ; cpt ++) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       k=2+nlstate*(2*cpt-2);       results. So we changed our mind and took the option of the best precision.
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    */
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    /* If stepm=6 months */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    /* nhstepm age range expressed in number of stepm */
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    agelim=AGESUP;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
 */    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       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);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   }    gp=matrix(0,nhstepm,1,nlstate*nlstate);
      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   /* CV preval stat */  
     for (k1=1; k1<= m ; k1 ++) {    for (age=bage; age<=fage; age ++){ 
     for (cpt=1; cpt<nlstate ; cpt ++) {      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       k=3;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      /* if (stepm >= YEARM) hstepm=1;*/
       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);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       for (i=1; i< nlstate ; i ++)      /* If stepm=6 months */
         fprintf(ficgp,"+$%d",k+i+1);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
            
       l=3+(nlstate+ndeath)*cpt;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {      /* Computing  Variances of health expectancies */
         l=3+(nlstate+ndeath)*cpt;      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
         fprintf(ficgp,"+$%d",l+i+1);         decrease memory allocation */
       }      for(theta=1; theta <=npar; theta++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          for(i=1; i<=npar; i++){ 
     }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }            xm[i] = x[i] - (i==theta ?delti[theta]:0);
          }
   /* proba elementaires */        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
    for(i=1,jk=1; i <=nlstate; i++){        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     for(k=1; k <=(nlstate+ndeath); k++){    
       if (k != i) {        for(j=1; j<= nlstate; j++){
         for(j=1; j <=ncovmodel; j++){          for(i=1; i<=nlstate; i++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            for(h=0; h<=nhstepm-1; h++){
           jk++;              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
           fprintf(ficgp,"\n");              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
         }            }
       }          }
     }        }
    }       
         for(ij=1; ij<= nlstate*nlstate; ij++)
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/          for(h=0; h<=nhstepm-1; h++){
      for(jk=1; jk <=m; jk++) {            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          }
        if (ng==2)      }/* End theta */
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");      
        else      
          fprintf(ficgp,"\nset title \"Probability\"\n");      for(h=0; h<=nhstepm-1; h++)
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        for(j=1; j<=nlstate*nlstate;j++)
        i=1;          for(theta=1; theta <=npar; theta++)
        for(k2=1; k2<=nlstate; k2++) {            trgradg[h][j][theta]=gradg[h][theta][j];
          k3=i;      
          for(k=1; k<=(nlstate+ndeath); k++) {  
            if (k != k2){       for(ij=1;ij<=nlstate*nlstate;ij++)
              if(ng==2)        for(ji=1;ji<=nlstate*nlstate;ji++)
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          varhe[ij][ji][(int)age] =0.;
              else  
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);       printf("%d|",(int)age);fflush(stdout);
              ij=1;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
              for(j=3; j <=ncovmodel; j++) {       for(h=0;h<=nhstepm-1;h++){
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for(k=0;k<=nhstepm-1;k++){
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                  ij++;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                }          for(ij=1;ij<=nlstate*nlstate;ij++)
                else            for(ji=1;ji<=nlstate*nlstate;ji++)
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
              }        }
              fprintf(ficgp,")/(1");      }
                
              for(k1=1; k1 <=nlstate; k1++){        /* Computing expectancies */
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
                ij=1;      for(i=1; i<=nlstate;i++)
                for(j=3; j <=ncovmodel; j++){        for(j=1; j<=nlstate;j++)
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                    ij++;            
                  }            /* 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]);*/
                  else  
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }
                }  
                fprintf(ficgp,")");      fprintf(ficresstdeij,"%3.0f",age );
              }      for(i=1; i<=nlstate;i++){
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);        eip=0.;
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        vip=0.;
              i=i+ncovmodel;        for(j=1; j<=nlstate;j++){
            }          eip += eij[i][j][(int)age];
          } /* end k */          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
        } /* end k2 */            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
      } /* end jk */          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
    } /* end ng */        }
    fclose(ficgp);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
 }  /* end gnuplot */      }
       fprintf(ficresstdeij,"\n");
   
 /*************** Moving average **************/      fprintf(ficrescveij,"%3.0f",age );
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   int i, cpt, cptcod;          cptj= (j-1)*nlstate+i;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          for(i2=1; i2<=nlstate;i2++)
       for (i=1; i<=nlstate;i++)            for(j2=1; j2<=nlstate;j2++){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)              cptj2= (j2-1)*nlstate+i2;
           mobaverage[(int)agedeb][i][cptcod]=0.;              if(cptj2 <= cptj)
                    fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){            }
       for (i=1; i<=nlstate;i++){        }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fprintf(ficrescveij,"\n");
           for (cpt=0;cpt<=4;cpt++){     
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    }
           }    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    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);
     }    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 }    printf("\n");
     fprintf(ficlog,"\n");
   
 /************** Forecasting ******************/    free_vector(xm,1,npar);
 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){    free_vector(xp,1,npar);
      free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   int *popage;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  }
   double *popeffectif,*popcount;  
   double ***p3mat;  /************ Variance ******************/
   char fileresf[FILENAMELENGTH];  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[])
   {
  agelim=AGESUP;    /* Variance of health expectancies */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double **dnewm,**doldm;
      double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
   strcpy(fileresf,"f");    int k, cptcode;
   strcat(fileresf,fileres);    double *xp;
   if((ficresf=fopen(fileresf,"w"))==NULL) {    double **gp, **gm;  /* for var eij */
     printf("Problem with forecast resultfile: %s\n", fileresf);    double ***gradg, ***trgradg; /*for var eij */
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    double **gradgp, **trgradgp; /* for var p point j */
   }    double *gpp, *gmp; /* for var p point j */
   printf("Computing forecasting: result on file '%s' \n", fileresf);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    double ***p3mat;
     double age,agelim, hf;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    double ***mobaverage;
     int theta;
   if (mobilav==1) {    char digit[4];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    char digitp[25];
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }    char fileresprobmorprev[FILENAMELENGTH];
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    if(popbased==1){
   if (stepm<=12) stepsize=1;      if(mobilav!=0)
          strcpy(digitp,"-populbased-mobilav-");
   agelim=AGESUP;      else strcpy(digitp,"-populbased-nomobil-");
      }
   hstepm=1;    else 
   hstepm=hstepm/stepm;      strcpy(digitp,"-stablbased-");
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;    if (mobilav!=0) {
   yp2=modf((yp1*12),&yp);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   mprojmean=yp;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   yp1=modf((yp2*30.5),&yp);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   jprojmean=yp;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if(jprojmean==0) jprojmean=1;      }
   if(mprojmean==0) jprojmean=1;    }
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    strcpy(fileresprobmorprev,"prmorprev"); 
      sprintf(digit,"%-d",ij);
   for(cptcov=1;cptcov<=i2;cptcov++){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       k=k+1;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       fprintf(ficresf,"\n#******");    strcat(fileresprobmorprev,fileres);
       for(j=1;j<=cptcoveff;j++) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficresf,"******\n");    }
       fprintf(ficresf,"# StartingAge FinalAge");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);   
          fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
          pstamp(ficresprobmorprev);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    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);
         fprintf(ficresf,"\n");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      for(i=1; i<=nlstate;i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           nhstepm = nhstepm/hstepm;    }  
              fprintf(ficresprobmorprev,"\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\n# Routine varevsij");
           oldm=oldms;savm=savms;    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      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");
            fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           for (h=0; h<=nhstepm; h++){  /*   } */
             if (h==(int) (calagedate+YEARM*cpt)) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    pstamp(ficresvij);
             }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
             for(j=1; j<=nlstate+ndeath;j++) {    if(popbased==1)
               kk1=0.;kk2=0;      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
               for(i=1; i<=nlstate;i++) {                  else
                 if (mobilav==1)      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    fprintf(ficresvij,"# Age");
                 else {    for(i=1; i<=nlstate;i++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for(j=1; j<=nlstate;j++)
                 }        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
                    fprintf(ficresvij,"\n");
               }  
               if (h==(int)(calagedate+12*cpt)){    xp=vector(1,npar);
                 fprintf(ficresf," %.3f", kk1);    dnewm=matrix(1,nlstate,1,npar);
                            doldm=matrix(1,nlstate,1,nlstate);
               }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
             }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         }    gpp=vector(nlstate+1,nlstate+ndeath);
       }    gmp=vector(nlstate+1,nlstate+ndeath);
     }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   }    
            if(estepm < stepm){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   fclose(ficresf);    else  hstepm=estepm;   
 }    /* For example we decided to compute the life expectancy with the smallest unit */
 /************** Forecasting ******************/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 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){       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       Look at hpijx to understand the reason of that which relies in memory size
   int *popage;       and note for a fixed period like k years */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double *popeffectif,*popcount;       survival function given by stepm (the optimization length). Unfortunately it
   double ***p3mat,***tabpop,***tabpopprev;       means that if the survival funtion is printed every two years of age and if
   char filerespop[FILENAMELENGTH];       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.
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   agelim=AGESUP;    agelim = AGESUP;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   strcpy(filerespop,"pop");      gp=matrix(0,nhstepm,1,nlstate);
   strcat(filerespop,fileres);      gm=matrix(0,nhstepm,1,nlstate);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", filerespop);  
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   printf("Computing forecasting: result on file '%s' \n", filerespop);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
   if (mobilav==1) {        if (popbased==1) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          if(mobilav ==0){
     movingaverage(agedeb, fage, ageminpar, mobaverage);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   stepsize=(int) (stepm+YEARM-1)/YEARM;            for(i=1; i<=nlstate;i++)
   if (stepm<=12) stepsize=1;              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
   agelim=AGESUP;        }
      
   hstepm=1;        for(j=1; j<= nlstate; j++){
   hstepm=hstepm/stepm;          for(h=0; h<=nhstepm; h++){
              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   if (popforecast==1) {              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     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);        /* This for computing probability of death (h=1 means
     }           computed over hstepm matrices product = hstepm*stepm months) 
     popage=ivector(0,AGESUP);           as a weighted average of prlim.
     popeffectif=vector(0,AGESUP);        */
     popcount=vector(0,AGESUP);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              for(i=1,gpp[j]=0.; i<= nlstate; i++)
     i=1;              gpp[j] += prlim[i][i]*p3mat[i][j][1];
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        }    
            /* end probability of death */
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   for(cptcov=1;cptcov<=i2;cptcov++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   
       k=k+1;        if (popbased==1) {
       fprintf(ficrespop,"\n#******");          if(mobilav ==0){
       for(j=1;j<=cptcoveff;j++) {            for(i=1; i<=nlstate;i++)
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              prlim[i][i]=probs[(int)age][i][ij];
       }          }else{ /* mobilav */ 
       fprintf(ficrespop,"******\n");            for(i=1; i<=nlstate;i++)
       fprintf(ficrespop,"# Age");              prlim[i][i]=mobaverage[(int)age][i][ij];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          }
       if (popforecast==1)  fprintf(ficrespop," [Population]");        }
        
       for (cpt=0; cpt<=0;cpt++) {        for(j=1; j<= nlstate; j++){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            for(h=0; h<=nhstepm; h++){
                    for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          }
           nhstepm = nhstepm/hstepm;        }
                  /* This for computing probability of death (h=1 means
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           computed over hstepm matrices product = hstepm*stepm months) 
           oldm=oldms;savm=savms;           as a weighted average of prlim.
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          */
                for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for (h=0; h<=nhstepm; h++){          for(i=1,gmp[j]=0.; i<= nlstate; i++)
             if (h==(int) (calagedate+YEARM*cpt)) {           gmp[j] += prlim[i][i]*p3mat[i][j][1];
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        }    
             }        /* end probability of death */
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;        for(j=1; j<= nlstate; j++) /* vareij */
               for(i=1; i<=nlstate;i++) {                        for(h=0; h<=nhstepm; h++){
                 if (mobilav==1)            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   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];        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                 }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
               }        }
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      } /* End theta */
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
               }  
             }      for(h=0; h<=nhstepm; h++) /* veij */
             for(i=1; i<=nlstate;i++){        for(j=1; j<=nlstate;j++)
               kk1=0.;          for(theta=1; theta <=npar; theta++)
                 for(j=1; j<=nlstate;j++){            trgradg[h][j][theta]=gradg[h][theta][j];
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  
                 }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        for(theta=1; theta <=npar; theta++)
             }          trgradgp[j][theta]=gradgp[theta][j];
     
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           }      for(i=1;i<=nlstate;i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(j=1;j<=nlstate;j++)
         }          vareij[i][j][(int)age] =0.;
       }  
        for(h=0;h<=nhstepm;h++){
   /******/        for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            for(i=1;i<=nlstate;i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            for(j=1;j<=nlstate;j++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           nhstepm = nhstepm/hstepm;        }
                }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           oldm=oldms;savm=savms;      /* pptj */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           for (h=0; h<=nhstepm; h++){      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
             if (h==(int) (calagedate+YEARM*cpt)) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
             }          varppt[j][i]=doldmp[j][i];
             for(j=1; j<=nlstate+ndeath;j++) {      /* end ppptj */
               kk1=0.;kk2=0;      /*  x centered again */
               for(i=1; i<=nlstate;i++) {                    hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
               }   
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      if (popbased==1) {
             }        if(mobilav ==0){
           }          for(i=1; i<=nlstate;i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            prlim[i][i]=probs[(int)age][i][ij];
         }        }else{ /* mobilav */ 
       }          for(i=1; i<=nlstate;i++)
    }            prlim[i][i]=mobaverage[(int)age][i][ij];
   }        }
        }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);               
       /* This for computing probability of death (h=1 means
   if (popforecast==1) {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     free_ivector(popage,0,AGESUP);         as a weighted average of prlim.
     free_vector(popeffectif,0,AGESUP);      */
     free_vector(popcount,0,AGESUP);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      }    
   fclose(ficrespop);      /* end probability of death */
 }  
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
 /***********************************************/      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 /**************** Main Program *****************/        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
 /***********************************************/        for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
 int main(int argc, char *argv[])        }
 {      } 
       fprintf(ficresprobmorprev,"\n");
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  
   double agedeb, agefin,hf;      fprintf(ficresvij,"%.0f ",age );
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   double fret;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   double **xi,tmp,delta;        }
       fprintf(ficresvij,"\n");
   double dum; /* Dummy variable */      free_matrix(gp,0,nhstepm,1,nlstate);
   double ***p3mat;      free_matrix(gm,0,nhstepm,1,nlstate);
   int *indx;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   char line[MAXLINE], linepar[MAXLINE];      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int firstobs=1, lastobs=10;    } /* End age */
   int sdeb, sfin; /* Status at beginning and end */    free_vector(gpp,nlstate+1,nlstate+ndeath);
   int c,  h , cpt,l;    free_vector(gmp,nlstate+1,nlstate+ndeath);
   int ju,jl, mi;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   int mobilav=0,popforecast=0;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   int hstepm, nhstepm;    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  /*   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); */
   double bage, fage, age, agelim, agebase;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   double ftolpl=FTOL;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   double **prlim;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   double *severity;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   double ***param; /* Matrix of parameters */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   double  *p;    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);
   double **matcov; /* Matrix of covariance */    /*  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);
   double ***delti3; /* Scale */  */
   double *delti; /* Scale */  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   double ***eij, ***vareij;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;    free_vector(xp,1,npar);
   double kk1, kk2;    free_matrix(doldm,1,nlstate,1,nlstate);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    free_matrix(dnewm,1,nlstate,1,npar);
      free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   char *alph[]={"a","a","b","c","d","e"}, str[4];    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
   char z[1]="c", occ;    fflush(ficgp);
 #include <sys/time.h>    fflush(fichtm); 
 #include <time.h>  }  /* end varevsij */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
    /************ Variance of prevlim ******************/
   /* long total_usecs;  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[])
   struct timeval start_time, end_time;  {
      /* Variance of prevalence limit */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   getcwd(pathcd, size);    double **newm;
     double **dnewm,**doldm;
   printf("\n%s",version);    int i, j, nhstepm, hstepm;
   if(argc <=1){    int k, cptcode;
     printf("\nEnter the parameter file name: ");    double *xp;
     scanf("%s",pathtot);    double *gp, *gm;
   }    double **gradg, **trgradg;
   else{    double age,agelim;
     strcpy(pathtot,argv[1]);    int theta;
   }    
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    pstamp(ficresvpl);
   /*cygwin_split_path(pathtot,path,optionfile);    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    fprintf(ficresvpl,"# Age");
   /* cutv(path,optionfile,pathtot,'\\');*/    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    fprintf(ficresvpl,"\n");
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);    xp=vector(1,npar);
   replace(pathc,path);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
 /*-------- arguments in the command line --------*/    
     hstepm=1*YEARM; /* Every year of age */
   /* Log file */    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   strcat(filelog, optionfilefiname);    agelim = AGESUP;
   strcat(filelog,".log");    /* */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   if((ficlog=fopen(filelog,"w"))==NULL)    {      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     printf("Problem with logfile %s\n",filelog);      if (stepm >= YEARM) hstepm=1;
     goto end;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   }      gradg=matrix(1,npar,1,nlstate);
   fprintf(ficlog,"Log filename:%s\n",filelog);      gp=vector(1,nlstate);
   fprintf(ficlog,"\n%s",version);      gm=vector(1,nlstate);
   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);      for(theta=1; theta <=npar; theta++){
   fflush(ficlog);        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /* */        }
   strcpy(fileres,"r");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcat(fileres, optionfilefiname);        for(i=1;i<=nlstate;i++)
   strcat(fileres,".txt");    /* Other files have txt extension */          gp[i] = prlim[i][i];
       
   /*---------arguments file --------*/        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("Problem with optionfile %s\n",optionfile);        for(i=1;i<=nlstate;i++)
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);          gm[i] = prlim[i][i];
     goto end;  
   }        for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   strcpy(filereso,"o");      } /* End theta */
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {      trgradg =matrix(1,nlstate,1,npar);
     printf("Problem with Output resultfile: %s\n", filereso);  
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);      for(j=1; j<=nlstate;j++)
     goto end;        for(theta=1; theta <=npar; theta++)
   }          trgradg[j][theta]=gradg[theta][j];
   
   /* Reads comments: lines beginning with '#' */      for(i=1;i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){        varpl[i][(int)age] =0.;
     ungetc(c,ficpar);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     fgets(line, MAXLINE, ficpar);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     puts(line);      for(i=1;i<=nlstate;i++)
     fputs(line,ficparo);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   }  
   ungetc(c,ficpar);      fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   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(ficresvpl,"\n");
   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);      free_vector(gp,1,nlstate);
 while((c=getc(ficpar))=='#' && c!= EOF){      free_vector(gm,1,nlstate);
     ungetc(c,ficpar);      free_matrix(gradg,1,npar,1,nlstate);
     fgets(line, MAXLINE, ficpar);      free_matrix(trgradg,1,nlstate,1,npar);
     puts(line);    } /* End age */
     fputs(line,ficparo);  
   }    free_vector(xp,1,npar);
   ungetc(c,ficpar);    free_matrix(doldm,1,nlstate,1,npar);
      free_matrix(dnewm,1,nlstate,1,nlstate);
      
   covar=matrix(0,NCOVMAX,1,n);  }
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   ncovmodel=2+cptcovn;  {
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    int i, j=0,  i1, k1, l1, t, tj;
      int k2, l2, j1,  z1;
   /* Read guess parameters */    int k=0,l, cptcode;
   /* Reads comments: lines beginning with '#' */    int first=1, first1;
   while((c=getc(ficpar))=='#' && c!= EOF){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     ungetc(c,ficpar);    double **dnewm,**doldm;
     fgets(line, MAXLINE, ficpar);    double *xp;
     puts(line);    double *gp, *gm;
     fputs(line,ficparo);    double **gradg, **trgradg;
   }    double **mu;
   ungetc(c,ficpar);    double age,agelim, cov[NCOVMAX];
      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    int theta;
     for(i=1; i <=nlstate; i++)    char fileresprob[FILENAMELENGTH];
     for(j=1; j <=nlstate+ndeath-1; j++){    char fileresprobcov[FILENAMELENGTH];
       fscanf(ficpar,"%1d%1d",&i1,&j1);    char fileresprobcor[FILENAMELENGTH];
       fprintf(ficparo,"%1d%1d",i1,j1);  
       if(mle==1)    double ***varpij;
         printf("%1d%1d",i,j);  
       fprintf(ficlog,"%1d%1d",i,j);    strcpy(fileresprob,"prob"); 
       for(k=1; k<=ncovmodel;k++){    strcat(fileresprob,fileres);
         fscanf(ficpar," %lf",&param[i][j][k]);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
         if(mle==1){      printf("Problem with resultfile: %s\n", fileresprob);
           printf(" %lf",param[i][j][k]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
           fprintf(ficlog," %lf",param[i][j][k]);    }
         }    strcpy(fileresprobcov,"probcov"); 
         else    strcat(fileresprobcov,fileres);
           fprintf(ficlog," %lf",param[i][j][k]);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
         fprintf(ficparo," %lf",param[i][j][k]);      printf("Problem with resultfile: %s\n", fileresprobcov);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       fscanf(ficpar,"\n");    }
       if(mle==1)    strcpy(fileresprobcor,"probcor"); 
         printf("\n");    strcat(fileresprobcor,fileres);
       fprintf(ficlog,"\n");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       fprintf(ficparo,"\n");      printf("Problem with resultfile: %s\n", fileresprobcor);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    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);
   p=param[1][1];    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   /* Reads comments: lines beginning with '#' */    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     ungetc(c,ficpar);    pstamp(ficresprob);
     fgets(line, MAXLINE, ficpar);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     puts(line);    fprintf(ficresprob,"# Age");
     fputs(line,ficparo);    pstamp(ficresprobcov);
   }    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   ungetc(c,ficpar);    fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    fprintf(ficresprobcor,"# Age");
   for(i=1; i <=nlstate; i++){  
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    for(i=1; i<=nlstate;i++)
       printf("%1d%1d",i,j);      for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficparo,"%1d%1d",i1,j1);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       for(k=1; k<=ncovmodel;k++){        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fscanf(ficpar,"%le",&delti3[i][j][k]);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
         printf(" %le",delti3[i][j][k]);      }  
         fprintf(ficparo," %le",delti3[i][j][k]);   /* fprintf(ficresprob,"\n");
       }    fprintf(ficresprobcov,"\n");
       fscanf(ficpar,"\n");    fprintf(ficresprobcor,"\n");
       printf("\n");   */
       fprintf(ficparo,"\n");   xp=vector(1,npar);
     }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   delti=delti3[1][1];    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
      varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   /* Reads comments: lines beginning with '#' */    first=1;
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficgp,"\n# Routine varprob");
     ungetc(c,ficpar);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fgets(line, MAXLINE, ficpar);    fprintf(fichtm,"\n");
     puts(line);  
     fputs(line,ficparo);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   }    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   ungetc(c,ficpar);    file %s<br>\n",optionfilehtmcov);
      fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   matcov=matrix(1,npar,1,npar);  and drawn. It helps understanding how is the covariance between two incidences.\
   for(i=1; i <=npar; i++){   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fscanf(ficpar,"%s",&str);    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. \
     if(mle==1)  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
       printf("%s",str);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     fprintf(ficlog,"%s",str);  standard deviations wide on each axis. <br>\
     fprintf(ficparo,"%s",str);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     for(j=1; j <=i; j++){   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
       fscanf(ficpar," %le",&matcov[i][j]);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
       if(mle==1){  
         printf(" %.5le",matcov[i][j]);    cov[1]=1;
         fprintf(ficlog," %.5le",matcov[i][j]);    tj=cptcoveff;
       }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       else    j1=0;
         fprintf(ficlog," %.5le",matcov[i][j]);    for(t=1; t<=tj;t++){
       fprintf(ficparo," %.5le",matcov[i][j]);      for(i1=1; i1<=ncodemax[t];i1++){ 
     }        j1++;
     fscanf(ficpar,"\n");        if  (cptcovn>0) {
     if(mle==1)          fprintf(ficresprob, "\n#********** Variable "); 
       printf("\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficlog,"\n");          fprintf(ficresprob, "**********\n#\n");
     fprintf(ficparo,"\n");          fprintf(ficresprobcov, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for(i=1; i <=npar; i++)          fprintf(ficresprobcov, "**********\n#\n");
     for(j=i+1;j<=npar;j++)          
       matcov[i][j]=matcov[j][i];          fprintf(ficgp, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if(mle==1)          fprintf(ficgp, "**********\n#\n");
     printf("\n");          
   fprintf(ficlog,"\n");          
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     /*-------- Rewriting paramater file ----------*/          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
      strcpy(rfileres,"r");    /* "Rparameterfile */          
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          fprintf(ficresprobcor, "\n#********** Variable ");    
      strcat(rfileres,".");    /* */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          fprintf(ficresprobcor, "**********\n#");    
     if((ficres =fopen(rfileres,"w"))==NULL) {        }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;        for (age=bage; age<=fage; age ++){ 
     }          cov[2]=age;
     fprintf(ficres,"#%s\n",version);          for (k=1; k<=cptcovn;k++) {
                cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     /*-------- data file ----------*/          }
     if((fic=fopen(datafile,"r"))==NULL)    {          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       printf("Problem with datafile: %s\n", datafile);goto end;          for (k=1; k<=cptcovprod;k++)
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     }          
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     n= lastobs;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     severity = vector(1,maxwav);          gp=vector(1,(nlstate)*(nlstate+ndeath));
     outcome=imatrix(1,maxwav+1,1,n);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     num=ivector(1,n);      
     moisnais=vector(1,n);          for(theta=1; theta <=npar; theta++){
     annais=vector(1,n);            for(i=1; i<=npar; i++)
     moisdc=vector(1,n);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     andc=vector(1,n);            
     agedc=vector(1,n);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     cod=ivector(1,n);            
     weight=vector(1,n);            k=0;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            for(i=1; i<= (nlstate); i++){
     mint=matrix(1,maxwav,1,n);              for(j=1; j<=(nlstate+ndeath);j++){
     anint=matrix(1,maxwav,1,n);                k=k+1;
     s=imatrix(1,maxwav+1,1,n);                gp[k]=pmmij[i][j];
     adl=imatrix(1,maxwav+1,1,n);                  }
     tab=ivector(1,NCOVMAX);            }
     ncodemax=ivector(1,8);            
             for(i=1; i<=npar; i++)
     i=1;              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     while (fgets(line, MAXLINE, fic) != NULL)    {      
       if ((i >= firstobs) && (i <=lastobs)) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                    k=0;
         for (j=maxwav;j>=1;j--){            for(i=1; i<=(nlstate); i++){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              for(j=1; j<=(nlstate+ndeath);j++){
           strcpy(line,stra);                k=k+1;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                gm[k]=pmmij[i][j];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              }
         }            }
               
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              trgradg[j][theta]=gradg[theta][j];
         for (j=ncovcol;j>=1;j--){          
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          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);
         num[i]=atol(stra);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
                  free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           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;}*/          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
         i=i+1;          pmij(pmmij,cov,ncovmodel,x,nlstate);
       }          
     }          k=0;
     /* printf("ii=%d", ij);          for(i=1; i<=(nlstate); i++){
        scanf("%d",i);*/            for(j=1; j<=(nlstate+ndeath);j++){
   imx=i-1; /* Number of individuals */              k=k+1;
               mu[k][(int) age]=pmmij[i][j];
   /* for (i=1; i<=imx; i++){            }
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          }
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     }*/              varpij[i][j][(int)age] = doldm[i][j];
    /*  for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;          /*printf("\n%d ",(int)age);
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
              printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   /* Calculation of the number of parameter from char model*/            }*/
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */  
   Tprod=ivector(1,15);          fprintf(ficresprob,"\n%d ",(int)age);
   Tvaraff=ivector(1,15);          fprintf(ficresprobcov,"\n%d ",(int)age);
   Tvard=imatrix(1,15,1,2);          fprintf(ficresprobcor,"\n%d ",(int)age);
   Tage=ivector(1,15);        
              for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   if (strlen(model) >1){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     j=0, j1=0, k1=1, k2=1;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     j=nbocc(model,'+');            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     j1=nbocc(model,'*');            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     cptcovn=j+1;          }
     cptcovprod=j1;          i=0;
              for (k=1; k<=(nlstate);k++){
     strcpy(modelsav,model);            for (l=1; l<=(nlstate+ndeath);l++){ 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){              i=i++;
       printf("Error. Non available option model=%s ",model);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
       fprintf(ficlog,"Error. Non available option model=%s ",model);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       goto end;              for (j=1; j<=i;j++){
     }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                    fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     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 */          }/* end of loop for state */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        } /* end of loop for age */
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {  /* Model includes a product */        /* Confidence intervalle of pij  */
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/        /*
         if (strcmp(strc,"age")==0) { /* Vn*age */          fprintf(ficgp,"\nset noparametric;unset label");
           cptcovprod--;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           cutv(strb,stre,strd,'V');          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/          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);
           cptcovage++;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
             Tage[cptcovage]=i;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
             /*printf("stre=%s ", stre);*/          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         }        */
         else if (strcmp(strd,"age")==0) { /* or age*Vn */  
           cptcovprod--;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           cutv(strb,stre,strc,'V');        first1=1;
           Tvar[i]=atoi(stre);        for (k2=1; k2<=(nlstate);k2++){
           cptcovage++;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
           Tage[cptcovage]=i;            if(l2==k2) continue;
         }            j=(k2-1)*(nlstate+ndeath)+l2;
         else {  /* Age is not in the model */            for (k1=1; k1<=(nlstate);k1++){
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
           Tvar[i]=ncovcol+k1;                if(l1==k1) continue;
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */                i=(k1-1)*(nlstate+ndeath)+l1;
           Tprod[k1]=i;                if(i<=j) continue;
           Tvard[k1][1]=atoi(strc); /* m*/                for (age=bage; age<=fage; age ++){ 
           Tvard[k1][2]=atoi(stre); /* n */                  if ((int)age %5==0){
           Tvar[cptcovn+k2]=Tvard[k1][1];                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
           for (k=1; k<=lastobs;k++)                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                    mu1=mu[i][(int) age]/stepm*YEARM ;
           k1++;                    mu2=mu[j][(int) age]/stepm*YEARM;
           k2=k2+2;                    c12=cv12/sqrt(v1*v2);
         }                    /* Computing eigen value of matrix of covariance */
       }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       else { /* no more sum */                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                    /* Eigen vectors */
        /*  scanf("%d",i);*/                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       cutv(strd,strc,strb,'V');                    /*v21=sqrt(1.-v11*v11); *//* error */
       Tvar[i]=atoi(strc);                    v21=(lc1-v1)/cv12*v11;
       }                    v12=-v21;
       strcpy(modelsav,stra);                      v22=v11;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                    tnalp=v21/v11;
         scanf("%d",i);*/                    if(first1==1){
     } /* end of loop + */                      first1=0;
   } /* end model */                      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);
                      }
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   printf("cptcovprod=%d ", cptcovprod);                    /*printf(fignu*/
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   scanf("%d ",i);*/                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     fclose(fic);                    if(first==1){
                       first=0;
     /*  if(mle==1){*/                      fprintf(ficgp,"\nset parametric;unset label");
     if (weightopt != 1) { /* Maximisation without weights*/                      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(i=1;i<=n;i++) weight[i]=1.0;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     }                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     /*-calculation of age at interview from date of interview and age at death -*/   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
     agev=matrix(1,maxwav,1,imx);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     for (i=1; i<=imx; i++) {                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       for(m=2; (m<= maxwav); m++) {                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
          anint[m][i]=9999;                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
          s[m][i]=-1;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
        }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
       }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
     for (i=1; i<=imx; i++)  {                      first=0;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
       for(m=1; (m<= maxwav); m++){                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         if(s[m][i] >0){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           if (s[m][i] >= nlstate+1) {                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
             if(agedc[i]>0)                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
               if(moisdc[i]!=99 && andc[i]!=9999)                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                 agev[m][i]=agedc[i];                    }/* if first */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/                  } /* age mod 5 */
            else {                } /* end loop age */
               if (andc[i]!=9999){                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                first=1;
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);              } /*l12 */
               agev[m][i]=-1;            } /* k12 */
               }          } /*l1 */
             }        }/* k1 */
           }      } /* loop covariates */
           else if(s[m][i] !=9){ /* Should no more exist */    }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
             if(mint[m][i]==99 || anint[m][i]==9999)    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
               agev[m][i]=1;    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
             else if(agev[m][i] <agemin){    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
               agemin=agev[m][i];    free_vector(xp,1,npar);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    fclose(ficresprob);
             }    fclose(ficresprobcov);
             else if(agev[m][i] >agemax){    fclose(ficresprobcor);
               agemax=agev[m][i];    fflush(ficgp);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    fflush(fichtmcov);
             }  }
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/  
           }  /******************* Printing html file ***********/
           else { /* =9 */  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
             agev[m][i]=1;                    int lastpass, int stepm, int weightopt, char model[],\
             s[m][i]=-1;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
           }                    int popforecast, int estepm ,\
         }                    double jprev1, double mprev1,double anprev1, \
         else /*= 0 Unknown */                    double jprev2, double mprev2,double anprev2){
           agev[m][i]=1;    int jj1, k1, i1, cpt;
       }  
         fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     }     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
     for (i=1; i<=imx; i++)  {  </ul>");
       for(m=1; (m<= maxwav); m++){     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
         if (s[m][i] > (nlstate+ndeath)) {   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
           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);               jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
           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(fichtm,"\
           goto end;   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
         }             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
       }     fprintf(fichtm,"\
     }   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);     fprintf(fichtm,"\
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);   - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
     free_vector(severity,1,maxwav);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     free_imatrix(outcome,1,maxwav+1,1,n);     fprintf(fichtm,"\
     free_vector(moisnais,1,n);   - Population projections by age and states: \
     free_vector(annais,1,n);     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
      
     wav=ivector(1,imx);   jj1=0;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);   for(k1=1; k1<=m;k1++){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);     for(i1=1; i1<=ncodemax[k1];i1++){
           jj1++;
     /* Concatenates waves */       if (cptcovn > 0) {
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       Tcode=ivector(1,100);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);       }
       ncodemax[1]=1;       /* Pij */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
        <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
    codtab=imatrix(1,100,1,10);       /* Quasi-incidences */
    h=0;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    m=pow(2,cptcoveff);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
    <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
    for(k=1;k<=cptcoveff; k++){         /* Period (stable) prevalence in each health state */
      for(i=1; i <=(m/pow(2,k));i++){         for(cpt=1; cpt<nlstate;cpt++){
        for(j=1; j <= ncodemax[k]; j++){           fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
            h++;         }
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;       for(cpt=1; cpt<=nlstate;cpt++) {
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
          }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }       }
      }     } /* end i1 */
    }   }/* End k1 */
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);   fprintf(fichtm,"</ul>");
       codtab[1][2]=1;codtab[2][2]=2; */  
    /* for(i=1; i <=m ;i++){  
       for(k=1; k <=cptcovn; k++){   fprintf(fichtm,"\
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
       }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
       printf("\n");  
       }   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       scanf("%d",i);*/           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
       fprintf(fichtm,"\
    /* Calculates basic frequencies. Computes observed prevalence at single age   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
        and prints on file fileres'p'. */           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
       fprintf(fichtm,"\
       - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   fprintf(fichtm,"\
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   - 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): \
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     <a href=\"%s\">%s</a> <br>\n</li>",
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
         fprintf(fichtm,"\
     /* For Powell, parameters are in a vector p[] starting at p[1]   - (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): \
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */     <a href=\"%s\">%s</a> <br>\n</li>",
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
     if(mle==1){   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij 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",
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
     }   fprintf(fichtm,"\
       - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
     /*--------- results files --------------*/           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
     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(fichtm,"\
     - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
    jk=1;  
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  /*  if(popforecast==1) fprintf(fichtm,"\n */
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
    for(i=1,jk=1; i <=nlstate; i++){  /*      <br>",fileres,fileres,fileres,fileres); */
      for(k=1; k <=(nlstate+ndeath); k++){  /*  else  */
        if (k != i)  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
          {   fflush(fichtm);
            printf("%d%d ",i,k);   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
            fprintf(ficlog,"%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);   m=cptcoveff;
            for(j=1; j <=ncovmodel; j++){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
              printf("%f ",p[jk]);  
              fprintf(ficlog,"%f ",p[jk]);   jj1=0;
              fprintf(ficres,"%f ",p[jk]);   for(k1=1; k1<=m;k1++){
              jk++;     for(i1=1; i1<=ncodemax[k1];i1++){
            }       jj1++;
            printf("\n");       if (cptcovn > 0) {
            fprintf(ficlog,"\n");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
            fprintf(ficres,"\n");         for (cpt=1; cpt<=cptcoveff;cpt++) 
          }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
      }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
    }       }
    if(mle==1){       for(cpt=1; cpt<=nlstate;cpt++) {
      /* Computing hessian and covariance matrix */         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
      ftolhess=ftol; /* Usually correct */  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
      hesscov(matcov, p, npar, delti, ftolhess, func);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
    }       }
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
    printf("# Scales (for hessian or gradient estimation)\n");  health expectancies in states (1) and (2): %s%d.png<br>\
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    for(i=1,jk=1; i <=nlstate; i++){     } /* end i1 */
      for(j=1; j <=nlstate+ndeath; j++){   }/* End k1 */
        if (j!=i) {   fprintf(fichtm,"</ul>");
          fprintf(ficres,"%1d%1d",i,j);   fflush(fichtm);
          printf("%1d%1d",i,j);  }
          fprintf(ficlog,"%1d%1d",i,j);  
          for(k=1; k<=ncovmodel;k++){  /******************* Gnuplot file **************/
            printf(" %.5e",delti[jk]);  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
            fprintf(ficlog," %.5e",delti[jk]);  
            fprintf(ficres," %.5e",delti[jk]);    char dirfileres[132],optfileres[132];
            jk++;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
          }    int ng;
          printf("\n");  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
          fprintf(ficlog,"\n");  /*     printf("Problem with file %s",optionfilegnuplot); */
          fprintf(ficres,"\n");  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
        }  /*   } */
      }  
    }    /*#ifdef windows */
        fprintf(ficgp,"cd \"%s\" \n",pathc);
    k=1;      /*#endif */
    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");    m=pow(2,cptcoveff);
    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");    strcpy(dirfileres,optionfilefiname);
    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");    strcpy(optfileres,"vpl");
    for(i=1;i<=npar;i++){   /* 1eme*/
      /*  if (k>nlstate) k=1;    for (cpt=1; cpt<= nlstate ; cpt ++) {
          i1=(i-1)/(ncovmodel*nlstate)+1;     for (k1=1; k1<= m ; k1 ++) {
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
          printf("%s%d%d",alph[k],i1,tab[i]);*/       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
      fprintf(ficres,"%3d",i);       fprintf(ficgp,"set xlabel \"Age\" \n\
      if(mle==1)  set ylabel \"Probability\" \n\
        printf("%3d",i);  set ter png small\n\
      fprintf(ficlog,"%3d",i);  set size 0.65,0.65\n\
      for(j=1; j<=i;j++){  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
        fprintf(ficres," %.5e",matcov[i][j]);  
        if(mle==1)       for (i=1; i<= nlstate ; i ++) {
          printf(" %.5e",matcov[i][j]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        fprintf(ficlog," %.5e",matcov[i][j]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
      }       }
      fprintf(ficres,"\n");       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
      if(mle==1)       for (i=1; i<= nlstate ; i ++) {
        printf("\n");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
      fprintf(ficlog,"\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
      k++;       } 
    }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
           for (i=1; i<= nlstate ; i ++) {
    while((c=getc(ficpar))=='#' && c!= EOF){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
      ungetc(c,ficpar);         else fprintf(ficgp," \%%*lf (\%%*lf)");
      fgets(line, MAXLINE, ficpar);       }  
      puts(line);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      fputs(line,ficparo);     }
    }    }
    ungetc(c,ficpar);    /*2 eme*/
    estepm=0;    
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    for (k1=1; k1<= m ; k1 ++) { 
    if (estepm==0 || estepm < stepm) estepm=stepm;      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
    if (fage <= 2) {      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
      bage = ageminpar;      
      fage = agemaxpar;      for (i=1; i<= nlstate+1 ; i ++) {
    }        k=2*i;
            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        for (j=1; j<= nlstate+1 ; j ++) {
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);          else fprintf(ficgp," \%%*lf (\%%*lf)");
            }   
    while((c=getc(ficpar))=='#' && c!= EOF){        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
      ungetc(c,ficpar);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
      fgets(line, MAXLINE, ficpar);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
      puts(line);        for (j=1; j<= nlstate+1 ; j ++) {
      fputs(line,ficparo);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
    }          else fprintf(ficgp," \%%*lf (\%%*lf)");
    ungetc(c,ficpar);        }   
          fprintf(ficgp,"\" t\"\" w l 0,");
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for (j=1; j<= nlstate+1 ; j ++) {
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
              else fprintf(ficgp," \%%*lf (\%%*lf)");
    while((c=getc(ficpar))=='#' && c!= EOF){        }   
      ungetc(c,ficpar);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
      fgets(line, MAXLINE, ficpar);        else fprintf(ficgp,"\" t\"\" w l 0,");
      puts(line);      }
      fputs(line,ficparo);    }
    }    
    ungetc(c,ficpar);    /*3eme*/
      
     for (k1=1; k1<= m ; k1 ++) { 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      for (cpt=1; cpt<= nlstate ; cpt ++) {
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
   fscanf(ficpar,"pop_based=%d\n",&popbased);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
   fprintf(ficparo,"pop_based=%d\n",popbased);          fprintf(ficgp,"set ter png small\n\
   fprintf(ficres,"pop_based=%d\n",popbased);    set size 0.65,0.65\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);
   while((c=getc(ficpar))=='#' && c!= EOF){        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     ungetc(c,ficpar);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     puts(line);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     fputs(line,ficparo);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   ungetc(c,ficpar);          
         */
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);        for (i=1; i< nlstate ; i ++) {
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          fprintf(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(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          /*      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);*/
           
         } 
 while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    
     fputs(line,ficparo);    /* CV preval stable (period) */
   }    for (k1=1; k1<= m ; k1 ++) { 
   ungetc(c,ficpar);      for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
 /*------------ gnuplot -------------*/        for (i=1; i< nlstate ; i ++)
   strcpy(optionfilegnuplot,optionfilefiname);          fprintf(ficgp,"+$%d",k+i+1);
   strcat(optionfilegnuplot,".gp");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        
     printf("Problem with file %s",optionfilegnuplot);        l=3+(nlstate+ndeath)*cpt;
   }        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   fclose(ficgp);        for (i=1; i< nlstate ; i ++) {
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);          l=3+(nlstate+ndeath)*cpt;
 /*--------- index.htm --------*/          fprintf(ficgp,"+$%d",l+i+1);
         }
   strcpy(optionfilehtm,optionfile);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   strcat(optionfilehtm,".htm");      } 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    }  
     printf("Problem with %s \n",optionfilehtm), exit(0);    
   }    /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n      for(k=1; k <=(nlstate+ndeath); k++){
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        if (k != i) {
 \n          for(j=1; j <=ncovmodel; j++){
 Total number of observations=%d <br>\n            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n            jk++; 
 <hr  size=\"2\" color=\"#EC5E5E\">            fprintf(ficgp,"\n");
  <ul><li><h4>Parameter files</h4>\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></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);     }
   fclose(fichtm);  
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);       for(jk=1; jk <=m; jk++) {
           fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
 /*------------ free_vector  -------------*/         if (ng==2)
  chdir(path);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           else
  free_ivector(wav,1,imx);           fprintf(ficgp,"\nset title \"Probability\"\n");
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);           i=1;
  free_ivector(num,1,n);         for(k2=1; k2<=nlstate; k2++) {
  free_vector(agedc,1,n);           k3=i;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/           for(k=1; k<=(nlstate+ndeath); k++) {
  fclose(ficparo);             if (k != k2){
  fclose(ficres);               if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
   /*--------------- Prevalence limit --------------*/                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 ij=1;
   strcpy(filerespl,"pl");               for(j=3; j <=ncovmodel; j++) {
   strcat(filerespl,fileres);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                   ij++;
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;                 }
   }                 else
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);               }
   fprintf(ficrespl,"#Prevalence limit\n");               fprintf(ficgp,")/(1");
   fprintf(ficrespl,"#Age ");               
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);               for(k1=1; k1 <=nlstate; k1++){   
   fprintf(ficrespl,"\n");                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                   ij=1;
   prlim=matrix(1,nlstate,1,nlstate);                 for(j=3; j <=ncovmodel; j++){
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                     ij++;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                   }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                   else
   k=0;                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   agebase=ageminpar;                 }
   agelim=agemaxpar;                 fprintf(ficgp,")");
   ftolpl=1.e-10;               }
   i1=cptcoveff;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   if (cptcovn < 1){i1=1;}               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
   for(cptcov=1;cptcov<=i1;cptcov++){             }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           } /* end k */
         k=k+1;         } /* end k2 */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/       } /* end jk */
         fprintf(ficrespl,"\n#******");     } /* end ng */
         printf("\n#******");     fflush(ficgp); 
         fprintf(ficlog,"\n#******");  }  /* end gnuplot */
         for(j=1;j<=cptcoveff;j++) {  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*************** Moving average **************/
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
         }  
         fprintf(ficrespl,"******\n");    int i, cpt, cptcod;
         printf("******\n");    int modcovmax =1;
         fprintf(ficlog,"******\n");    int mobilavrange, mob;
            double age;
         for (age=agebase; age<=agelim; age++){  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
           fprintf(ficrespl,"%.0f",age );                             a covariate has 2 modalities */
           for(i=1; i<=nlstate;i++)    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
         }      if(mobilav==1) mobilavrange=5; /* default */
       }      else mobilavrange=mobilav;
     }      for (age=bage; age<=fage; age++)
   fclose(ficrespl);        for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
   /*------------- h Pij x at various ages ------------*/            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        /* We keep the original values on the extreme ages bage, fage and for 
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   if((ficrespij=fopen(filerespij,"w"))==NULL) {         we use a 5 terms etc. until the borders are no more concerned. 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      */ 
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;      for (mob=3;mob <=mobilavrange;mob=mob+2){
   }        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   printf("Computing pij: result on file '%s' \n", filerespij);          for (i=1; i<=nlstate;i++){
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
                mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   stepsize=(int) (stepm+YEARM-1)/YEARM;                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   /*if (stepm<=24) stepsize=2;*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   agelim=AGESUP;                }
   hstepm=stepsize*YEARM; /* Every year of age */              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            }
           }
   /* hstepm=1;   aff par mois*/        }/* end age */
       }/* end mob */
   k=0;    }else return -1;
   for(cptcov=1;cptcov<=i1;cptcov++){    return 0;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  }/* End movingaverage */
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)  /************** Forecasting ******************/
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  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){
         fprintf(ficrespij,"******\n");    /* proj1, year, month, day of starting projection 
               agemin, agemax range of age
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */       dateprev1 dateprev2 range of dates during which prevalence is computed
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       anproj2 year of en of projection (same day and month as proj1).
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
           /*      nhstepm=nhstepm*YEARM; aff par mois*/    int *popage;
     double agec; /* generic age */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
           oldm=oldms;savm=savms;    double *popeffectif,*popcount;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double ***p3mat;
           fprintf(ficrespij,"# Age");    double ***mobaverage;
           for(i=1; i<=nlstate;i++)    char fileresf[FILENAMELENGTH];
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);    agelim=AGESUP;
           fprintf(ficrespij,"\n");    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
            for (h=0; h<=nhstepm; h++){   
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    strcpy(fileresf,"f"); 
             for(i=1; i<=nlstate;i++)    strcat(fileresf,fileres);
               for(j=1; j<=nlstate+ndeath;j++)    if((ficresf=fopen(fileresf,"w"))==NULL) {
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      printf("Problem with forecast resultfile: %s\n", fileresf);
             fprintf(ficrespij,"\n");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
              }    }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("Computing forecasting: result on file '%s' \n", fileresf);
           fprintf(ficrespij,"\n");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
         }  
     }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   }  
     if (mobilav!=0) {
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   fclose(ficrespij);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
   /*---------- Forecasting ------------------*/    }
   if((stepm == 1) && (strcmp(model,".")==0)){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    if (stepm<=12) stepsize=1;
   }    if(estepm < stepm){
   else{      printf ("Problem %d lower than %d\n",estepm, stepm);
     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);    else  hstepm=estepm;   
     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);  
   }    hstepm=hstepm/stepm; 
      yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
   /*---------- Health expectancies and variances ------------*/    anprojmean=yp;
     yp2=modf((yp1*12),&yp);
   strcpy(filerest,"t");    mprojmean=yp;
   strcat(filerest,fileres);    yp1=modf((yp2*30.5),&yp);
   if((ficrest=fopen(filerest,"w"))==NULL) {    jprojmean=yp;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    if(jprojmean==0) jprojmean=1;
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;    if(mprojmean==0) jprojmean=1;
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    i1=cptcoveff;
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);    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); 
   strcpy(filerese,"e");    
   strcat(filerese,fileres);    fprintf(ficresf,"#****** Routine prevforecast **\n");
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  /*            if (h==(int)(YEARM*yearp)){ */
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   }      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        k=k+1;
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);        fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
   strcpy(fileresv,"v");          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]]);
   strcat(fileresv,fileres);        }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        fprintf(ficresf,"******\n");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);        for(j=1; j<=nlstate+ndeath;j++){ 
   }          for(i=1; i<=nlstate;i++)              
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);            fprintf(ficresf," p%d%d",i,j);
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          fprintf(ficresf," p.%d",j);
   calagedate=-1;        }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
   k=0;          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (agec=fage; agec>=(ageminpar-1); agec--){ 
       k=k+1;            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
       fprintf(ficrest,"\n#****** ");            nhstepm = nhstepm/hstepm; 
       for(j=1;j<=cptcoveff;j++)            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            oldm=oldms;savm=savms;
       fprintf(ficrest,"******\n");            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
       fprintf(ficreseij,"\n#****** ");            for (h=0; h<=nhstepm; h++){
       for(j=1;j<=cptcoveff;j++)              if (h*hstepm/YEARM*stepm ==yearp) {
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                fprintf(ficresf,"\n");
       fprintf(ficreseij,"******\n");                for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficresvij,"\n#****** ");                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
       for(j=1;j<=cptcoveff;j++)              } 
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              for(j=1; j<=nlstate+ndeath;j++) {
       fprintf(ficresvij,"******\n");                ppij=0.;
                 for(i=1; i<=nlstate;i++) {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                  if (mobilav==1) 
       oldm=oldms;savm=savms;                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);                    else {
                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                  }
       oldm=oldms;savm=savms;                  if (h*hstepm/YEARM*stepm== yearp) {
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
       if(popbased==1){                  }
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);                } /* end i */
        }                if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                  }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");              }/* end j */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            } /* end h */
       fprintf(ficrest,"\n");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
       epj=vector(1,nlstate+1);        } /* end yearp */
       for(age=bage; age <=fage ;age++){      } /* end cptcod */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    } /* end  cptcov */
         if (popbased==1) {         
           for(i=1; i<=nlstate;i++)    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             prlim[i][i]=probs[(int)age][i][k];  
         }    fclose(ficresf);
          }
         fprintf(ficrest," %4.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  /************** Forecasting *****not tested NB*************/
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
           }    int *popage;
           epj[nlstate+1] +=epj[j];    double calagedatem, agelim, kk1, kk2;
         }    double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
         for(i=1, vepp=0.;i <=nlstate;i++)    double ***mobaverage;
           for(j=1;j <=nlstate;j++)    char filerespop[FILENAMELENGTH];
             vepp += vareij[i][j][(int)age];  
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for(j=1;j <=nlstate;j++){    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    agelim=AGESUP;
         }    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
         fprintf(ficrest,"\n");    
       }    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     }    
   }    
 free_matrix(mint,1,maxwav,1,n);    strcpy(filerespop,"pop"); 
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    strcat(filerespop,fileres);
     free_vector(weight,1,n);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   fclose(ficreseij);      printf("Problem with forecast resultfile: %s\n", filerespop);
   fclose(ficresvij);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   fclose(ficrest);    }
   fclose(ficpar);    printf("Computing forecasting: result on file '%s' \n", filerespop);
   free_vector(epj,1,nlstate+1);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
    
   /*------- Variance limit prevalence------*/      if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   strcpy(fileresvpl,"vpl");    if (mobilav!=0) {
   strcat(fileresvpl,fileres);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     exit(0);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   }      }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    }
   
   k=0;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   for(cptcov=1;cptcov<=i1;cptcov++){    if (stepm<=12) stepsize=1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    agelim=AGESUP;
       fprintf(ficresvpl,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    hstepm=1;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    hstepm=hstepm/stepm; 
       fprintf(ficresvpl,"******\n");    
          if (popforecast==1) {
       varpl=matrix(1,nlstate,(int) bage, (int) fage);      if((ficpop=fopen(popfile,"r"))==NULL) {
       oldm=oldms;savm=savms;        printf("Problem with population file : %s\n",popfile);exit(0);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
     }      } 
  }      popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
   fclose(ficresvpl);      popcount=vector(0,AGESUP);
       
   /*---------- End : free ----------------*/      i=1;   
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
       
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      imx=i;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
      }
    
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        k=k+1;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficrespop,"\n#******");
          for(j=1;j<=cptcoveff;j++) {
   free_matrix(matcov,1,npar,1,npar);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   free_vector(delti,1,npar);        }
   free_matrix(agev,1,maxwav,1,imx);        fprintf(ficrespop,"******\n");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   fprintf(fichtm,"\n</body>");        if (popforecast==1)  fprintf(ficrespop," [Population]");
   fclose(fichtm);        
   fclose(ficgp);        for (cpt=0; cpt<=0;cpt++) { 
            fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
   if(erreur >0){          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     printf("End of Imach with error or warning %d\n",erreur);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);            nhstepm = nhstepm/hstepm; 
   }else{            
    printf("End of Imach\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    fprintf(ficlog,"End of Imach\n");            oldm=oldms;savm=savms;
   }            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   printf("See log file on %s\n",filelog);          
   fclose(ficlog);            for (h=0; h<=nhstepm; h++){
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */              if (h==(int) (calagedatem+YEARM*cpt)) {
                  fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   /* 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);*/              } 
   /*printf("Total time was %d uSec.\n", total_usecs);*/              for(j=1; j<=nlstate+ndeath;j++) {
   /*------ End -----------*/                kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
  end:                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
 #ifdef windows                  else {
   /* chdir(pathcd);*/                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
 #endif                  }
  /*system("wgnuplot graph.plt");*/                }
  /*system("../gp37mgw/wgnuplot graph.plt");*/                if (h==(int)(calagedatem+12*cpt)){
  /*system("cd ../gp37mgw");*/                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                    /*fprintf(ficrespop," %.3f", kk1);
  strcpy(plotcmd,GNUPLOTPROGRAM);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
  strcat(plotcmd," ");                }
  strcat(plotcmd,optionfilegnuplot);              }
  system(plotcmd);              for(i=1; i<=nlstate;i++){
                 kk1=0.;
 #ifdef windows                  for(j=1; j<=nlstate;j++){
   while (z[0] != 'q') {                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     /* chdir(path); */                  }
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
     scanf("%s",z);              }
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
     else if (z[0] == 'g') system(plotcmd);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
     else if (z[0] == 'q') exit(0);            }
   }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #endif          }
 }        }
    
     /******/
   
         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;
   }
   
   /******************* 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\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);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     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;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  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, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*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 *severity;
     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];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     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 */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_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.tv_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';
      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.tv_sec-start_time.tv_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\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     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++;
       puts(line);
       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++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     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 guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         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);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         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);
   
       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++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       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 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     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);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     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;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         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 '%d' at line number %d %s 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);
           exit(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.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(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 %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(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.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(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 %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         exit(1);
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld 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);
           exit(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 */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        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]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       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 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 */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*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);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       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(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     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);     
           goto end;
         }
       }
     }
   
     /*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); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     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 */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* 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);*/
       
     /*------------ 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");
     }
     /*  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);
       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]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       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);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  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");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       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);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       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);
         puts(line);
         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);
         puts(line);
         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);
         puts(line);
         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);
         puts(line);
         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) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       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;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       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); */
         /*      } */
       }
     
   
       /*---------- 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(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);
   
       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);
   
       /* 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);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           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(ficreseij,"\n#****** ");
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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(ficreseij,"******\n");
           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;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
           cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# 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 (popbased==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,1,15,1,2);
       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(ficreseij);
       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++){
           k=k+1;
           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 */
     free_matrix(prlim,1,nlstate,1,nlstate);
       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,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       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);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     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(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  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");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error 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("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       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.1.126


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