Diff for /imach/src/imach.c between versions 1.51 and 1.127

version 1.51, 2002/07/19 12:22:25 version 1.127, 2006/04/28 18:11:50
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.127  2006/04/28 18:11:50  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    (Module): In order to speed up (in case of numerous covariates) we
   interviewed on their health status or degree of disability (in the    compute health expectancies (without variances) in a first step
   case of a health survey which is our main interest) -2- at least a    and then all the health expectancies with variances or standard
   second wave of interviews ("longitudinal") which measure each change    deviation (needs data from the Hessian matrices) which slows the
   (if any) in individual health status.  Health expectancies are    computation.
   computed from the time spent in each health state according to a    In the future we should be able to stop the program is only health
   model. More health states you consider, more time is necessary to reach the    expectancies and graph are needed without standard deviations.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.126  2006/04/28 17:23:28  brouard
   probability to be observed in state j at the second wave    (Module): Yes the sum of survivors was wrong since
   conditional to be observed in state i at the first wave. Therefore    imach-114 because nhstepm was no more computed in the age
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    loop. Now we define nhstepma in the age loop.
   'age' is age and 'sex' is a covariate. If you want to have a more    Version 0.98h
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.125  2006/04/04 15:20:31  lievre
   you to do it.  More covariates you add, slower the    Errors in calculation of health expectancies. Age was not initialized.
   convergence.    Forecasting file added.
   
   The advantage of this computer programme, compared to a simple    Revision 1.124  2006/03/22 17:13:53  lievre
   multinomial logistic model, is clear when the delay between waves is not    Parameters are printed with %lf instead of %f (more numbers after the comma).
   identical for each individual. Also, if a individual missed an    The log-likelihood is printed in the log file
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
   hPijx is the probability to be observed in state i at age x+h    name. <head> headers where missing.
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    * imach.c (Module): Weights can have a decimal point as for
   states. This elementary transition (by month or quarter trimester,    English (a comma might work with a correct LC_NUMERIC environment,
   semester or year) is model as a multinomial logistic.  The hPx    otherwise the weight is truncated).
   matrix is simply the matrix product of nh*stepm elementary matrices    Modification of warning when the covariates values are not 0 or
   and the contribution of each individual to the likelihood is simply    1.
   hPijx.    Version 0.98g
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.122  2006/03/20 09:45:41  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Weights can have a decimal point as for
      English (a comma might work with a correct LC_NUMERIC environment,
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    otherwise the weight is truncated).
            Institut national d'études démographiques, Paris.    Modification of warning when the covariates values are not 0 or
   This software have been partly granted by Euro-REVES, a concerted action    1.
   from the European Union.    Version 0.98g
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.121  2006/03/16 17:45:01  lievre
   can be accessed at http://euroreves.ined.fr/imach .    * imach.c (Module): Comments concerning covariates added
   **********************************************************************/  
      * imach.c (Module): refinements in the computation of lli if
 #include <math.h>    status=-2 in order to have more reliable computation if stepm is
 #include <stdio.h>    not 1 month. Version 0.98f
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
 #define MAXLINE 256    status=-2 in order to have more reliable computation if stepm is
 #define GNUPLOTPROGRAM "gnuplot"    not 1 month. Version 0.98f
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.119  2006/03/15 17:42:26  brouard
 /*#define DEBUG*/    (Module): Bug if status = -2, the loglikelihood was
 #define windows    computed as likelihood omitting the logarithm. Version O.98e
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.118  2006/03/14 18:20:07  brouard
     (Module): varevsij Comments added explaining the second
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    table of variances if popbased=1 .
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 #define NINTERVMAX 8    (Module): Version 0.98d
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.117  2006/03/14 17:16:22  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    (Module): varevsij Comments added explaining the second
 #define MAXN 20000    table of variances if popbased=1 .
 #define YEARM 12. /* Number of months per year */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define AGESUP 130    (Module): Function pstamp added
 #define AGEBASE 40    (Module): Version 0.98d
 #ifdef windows  
 #define DIRSEPARATOR '\\'    Revision 1.116  2006/03/06 10:29:27  brouard
 #define ODIRSEPARATOR '/'    (Module): Variance-covariance wrong links and
 #else    varian-covariance of ej. is needed (Saito).
 #define DIRSEPARATOR '/'  
 #define ODIRSEPARATOR '\\'    Revision 1.115  2006/02/27 12:17:45  brouard
 #endif    (Module): One freematrix added in mlikeli! 0.98c
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Revision 1.114  2006/02/26 12:57:58  brouard
 int erreur; /* Error number */    (Module): Some improvements in processing parameter
 int nvar;    filename with strsep.
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.113  2006/02/24 14:20:24  brouard
 int nlstate=2; /* Number of live states */    (Module): Memory leaks checks with valgrind and:
 int ndeath=1; /* Number of dead states */    datafile was not closed, some imatrix were not freed and on matrix
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    allocation too.
 int popbased=0;  
     Revision 1.112  2006/01/30 09:55:26  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.111  2006/01/25 20:38:18  brouard
 int mle, weightopt;    (Module): Lots of cleaning and bugs added (Gompertz)
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Comments can be added in data file. Missing date values
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    can be a simple dot '.'.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.110  2006/01/25 00:51:50  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Lots of cleaning and bugs added (Gompertz)
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficlog;    Revision 1.109  2006/01/24 19:37:15  brouard
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    (Module): Comments (lines starting with a #) are allowed in data.
 FILE *ficresprobmorprev;  
 FILE *fichtm; /* Html File */    Revision 1.108  2006/01/19 18:05:42  lievre
 FILE *ficreseij;    Gnuplot problem appeared...
 char filerese[FILENAMELENGTH];    To be fixed
 FILE  *ficresvij;  
 char fileresv[FILENAMELENGTH];    Revision 1.107  2006/01/19 16:20:37  brouard
 FILE  *ficresvpl;    Test existence of gnuplot in imach path
 char fileresvpl[FILENAMELENGTH];  
 char title[MAXLINE];    Revision 1.106  2006/01/19 13:24:36  brouard
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    Some cleaning and links added in html output
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  
     Revision 1.105  2006/01/05 20:23:19  lievre
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    *** empty log message ***
 char filelog[FILENAMELENGTH]; /* Log file */  
 char filerest[FILENAMELENGTH];    Revision 1.104  2005/09/30 16:11:43  lievre
 char fileregp[FILENAMELENGTH];    (Module): sump fixed, loop imx fixed, and simplifications.
 char popfile[FILENAMELENGTH];    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 #define NR_END 1    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #define FREE_ARG char*    the healthy state at last known wave). Version is 0.98
 #define FTOL 1.0e-10  
     Revision 1.103  2005/09/30 15:54:49  lievre
 #define NRANSI    (Module): sump fixed, loop imx fixed, and simplifications.
 #define ITMAX 200  
     Revision 1.102  2004/09/15 17:31:30  brouard
 #define TOL 2.0e-4    Add the possibility to read data file including tab characters.
   
 #define CGOLD 0.3819660    Revision 1.101  2004/09/15 10:38:38  brouard
 #define ZEPS 1.0e-10    Fix on curr_time
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.100  2004/07/12 18:29:06  brouard
 #define GOLD 1.618034    Add version for Mac OS X. Just define UNIX in Makefile
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.98  2004/05/16 15:05:56  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    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 SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    state at each age, but using a Gompertz model: log u =a + b*age .
 #define rint(a) floor(a+0.5)    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 static double sqrarg;    cross-longitudinal survey is different from the mortality estimated
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    from other sources like vital statistic data.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     The same imach parameter file can be used but the option for mle should be -3.
 int imx;  
 int stepm;    Agnès, who wrote this part of the code, tried to keep most of the
 /* Stepm, step in month: minimum step interpolation*/    former routines in order to include the new code within the former code.
   
 int estepm;    The output is very simple: only an estimate of the intercept and of
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    the slope with 95% confident intervals.
   
 int m,nb;    Current limitations:
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    A) Even if you enter covariates, i.e. with the
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 double **pmmij, ***probs, ***mobaverage;    B) There is no computation of Life Expectancy nor Life Table.
 double dateintmean=0;  
     Revision 1.97  2004/02/20 13:25:42  lievre
 double *weight;    Version 0.96d. Population forecasting command line is (temporarily)
 int **s; /* Status */    suppressed.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    rewritten within the same printf. Workaround: many printfs.
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.95  2003/07/08 07:54:34  brouard
 /**************** split *************************/    * imach.c (Repository):
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    (Repository): Using imachwizard code to output a more meaningful covariance
 {    matrix (cov(a12,c31) instead of numbers.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.93  2003/06/25 16:33:55  brouard
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    (Module): On windows (cygwin) function asctime_r doesn't
    if ( s == NULL ) {                   /* no directory, so use current */    exist so I changed back to asctime which exists.
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    (Module): Version 0.96b
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.92  2003/06/25 16:30:45  brouard
       extern char       *getwd( );    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.91  2003/06/25 15:30:29  brouard
       extern char       *getcwd( );    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    helps to forecast when convergence will be reached. Elapsed time
 #endif    is stamped in powell.  We created a new html file for the graphs
          return( GLOCK_ERROR_GETCWD );    concerning matrix of covariance. It has extension -cov.htm.
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.90  2003/06/24 12:34:15  brouard
    } else {                             /* strip direcotry from path */    (Module): Some bugs corrected for windows. Also, when
       s++;                              /* after this, the filename */    mle=-1 a template is output in file "or"mypar.txt with the design
       l2 = strlen( s );                 /* length of filename */    of the covariance matrix to be input.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.89  2003/06/24 12:30:52  brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    (Module): Some bugs corrected for windows. Also, when
       dirc[l1-l2] = 0;                  /* add zero */    mle=-1 a template is output in file "or"mypar.txt with the design
    }    of the covariance matrix to be input.
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.88  2003/06/23 17:54:56  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    * 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.
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.87  2003/06/18 12:26:01  brouard
 #endif    Version 0.96
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.86  2003/06/17 20:04:08  brouard
    strcpy(ext,s);                       /* save extension */    (Module): Change position of html and gnuplot routines and added
    l1= strlen( name);    routine fileappend.
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.85  2003/06/17 13:12:43  brouard
    finame[l1-l2]= 0;    * imach.c (Repository): Check when date of death was earlier that
    return( 0 );                         /* we're done */    current date of interview. It may happen when the death was just
 }    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 /******************************************/    interview.
     (Repository): Because some people have very long ID (first column)
 void replace(char *s, char*t)    we changed int to long in num[] and we added a new lvector for
 {    memory allocation. But we also truncated to 8 characters (left
   int i;    truncation)
   int lg=20;    (Repository): No more line truncation errors.
   i=0;  
   lg=strlen(t);    Revision 1.84  2003/06/13 21:44:43  brouard
   for(i=0; i<= lg; i++) {    * imach.c (Repository): Replace "freqsummary" at a correct
     (s[i] = t[i]);    place. It differs from routine "prevalence" which may be called
     if (t[i]== '\\') s[i]='/';    many times. Probs is memory consuming and must be used with
   }    parcimony.
 }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 int nbocc(char *s, char occ)    Revision 1.83  2003/06/10 13:39:11  lievre
 {    *** empty log message ***
   int i,j=0;  
   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(s);  
   for(i=0; i<= lg; i++) {  */
   if  (s[i] == occ ) j++;  /*
   }     Interpolated Markov Chain
   return j;  
 }    Short summary of the programme:
     
 void cutv(char *u,char *v, char*t, char occ)    This program computes Healthy Life Expectancies from
 {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   /* cuts string t into u and v where u is ended by char occ excluding it    first survey ("cross") where individuals from different ages are
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    interviewed on their health status or degree of disability (in the
      gives u="abcedf" and v="ghi2j" */    case of a health survey which is our main interest) -2- at least a
   int i,lg,j,p=0;    second wave of interviews ("longitudinal") which measure each change
   i=0;    (if any) in individual health status.  Health expectancies are
   for(j=0; j<=strlen(t)-1; j++) {    computed from the time spent in each health state according to a
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    model. More health states you consider, more time is necessary to reach the
   }    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
   lg=strlen(t);    probability to be observed in state j at the second wave
   for(j=0; j<p; j++) {    conditional to be observed in state i at the first wave. Therefore
     (u[j] = t[j]);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   }    'age' is age and 'sex' is a covariate. If you want to have a more
      u[p]='\0';    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
    for(j=0; j<= lg; j++) {    you to do it.  More covariates you add, slower the
     if (j>=(p+1))(v[j-p-1] = t[j]);    convergence.
   }  
 }    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 /********************** nrerror ********************/    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 void nrerror(char error_text[])    account using an interpolation or extrapolation.  
 {  
   fprintf(stderr,"ERREUR ...\n");    hPijx is the probability to be observed in state i at age x+h
   fprintf(stderr,"%s\n",error_text);    conditional to the observed state i at age x. The delay 'h' can be
   exit(1);    split into an exact number (nh*stepm) of unobserved intermediate
 }    states. This elementary transition (by month, quarter,
 /*********************** vector *******************/    semester or year) is modelled as a multinomial logistic.  The hPx
 double *vector(int nl, int nh)    matrix is simply the matrix product of nh*stepm elementary matrices
 {    and the contribution of each individual to the likelihood is simply
   double *v;    hPijx.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Also this programme outputs the covariance matrix of the parameters but also
   return v-nl+NR_END;    of the life expectancies. It also computes the period (stable) prevalence. 
 }    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 /************************ free vector ******************/             Institut national d'études démographiques, Paris.
 void free_vector(double*v, int nl, int nh)    This software have been partly granted by Euro-REVES, a concerted action
 {    from the European Union.
   free((FREE_ARG)(v+nl-NR_END));    It is copyrighted identically to a GNU software product, ie programme and
 }    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 {    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   int *v;    
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    **********************************************************************/
   if (!v) nrerror("allocation failure in ivector");  /*
   return v-nl+NR_END;    main
 }    read parameterfile
     read datafile
 /******************free ivector **************************/    concatwav
 void free_ivector(int *v, long nl, long nh)    freqsummary
 {    if (mle >= 1)
   free((FREE_ARG)(v+nl-NR_END));      mlikeli
 }    print results files
     if mle==1 
 /******************* imatrix *******************************/       computes hessian
 int **imatrix(long nrl, long nrh, long ncl, long nch)    read end of parameter file: agemin, agemax, bage, fage, estepm
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */        begin-prev-date,...
 {    open gnuplot file
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    open html file
   int **m;    period (stable) prevalence
       for age prevalim()
   /* allocate pointers to rows */    h Pij x
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    variance of p varprob
   if (!m) nrerror("allocation failure 1 in matrix()");    forecasting if prevfcast==1 prevforecast call prevalence()
   m += NR_END;    health expectancies
   m -= nrl;    Variance-covariance of DFLE
      prevalence()
       movingaverage()
   /* allocate rows and set pointers to them */    varevsij() 
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    if popbased==1 varevsij(,popbased)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    total life expectancies
   m[nrl] += NR_END;    Variance of period (stable) prevalence
   m[nrl] -= ncl;   end
    */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    
   /* return pointer to array of pointers to rows */  
   return m;   
 }  #include <math.h>
   #include <stdio.h>
 /****************** free_imatrix *************************/  #include <stdlib.h>
 void free_imatrix(m,nrl,nrh,ncl,nch)  #include <string.h>
       int **m;  #include <unistd.h>
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  #include <limits.h>
 {  #include <sys/types.h>
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #include <sys/stat.h>
   free((FREE_ARG) (m+nrl-NR_END));  #include <errno.h>
 }  extern int errno;
   
 /******************* matrix *******************************/  /* #include <sys/time.h> */
 double **matrix(long nrl, long nrh, long ncl, long nch)  #include <time.h>
 {  #include "timeval.h"
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  #define MAXLINE 256
   m += NR_END;  
   m -= nrl;  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define FILENAMELENGTH 132
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   m[nrl] -= ncl;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   return m;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 }  
   #define NINTERVMAX 8
 /*************************free matrix ************************/  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 {  #define NCOVMAX 8 /* Maximum number of covariates */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define MAXN 20000
   free((FREE_ARG)(m+nrl-NR_END));  #define YEARM 12. /* Number of months per year */
 }  #define AGESUP 130
   #define AGEBASE 40
 /******************* ma3x *******************************/  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #ifdef UNIX
 {  #define DIRSEPARATOR '/'
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #define CHARSEPARATOR "/"
   double ***m;  #define ODIRSEPARATOR '\\'
   #else
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define DIRSEPARATOR '\\'
   if (!m) nrerror("allocation failure 1 in matrix()");  #define CHARSEPARATOR "\\"
   m += NR_END;  #define ODIRSEPARATOR '/'
   m -= nrl;  #endif
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /* $Id$ */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /* $State$ */
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  char version[]="Imach version 0.98h, April 2006, INED-EUROREVES-Institut de longevite ";
   char fullversion[]="$Revision$ $Date$"; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char strstart[80];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  int nvar;
   m[nrl][ncl] += NR_END;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m[nrl][ncl] -= nll;  int npar=NPARMAX;
   for (j=ncl+1; j<=nch; j++)  int nlstate=2; /* Number of live states */
     m[nrl][j]=m[nrl][j-1]+nlay;  int ndeath=1; /* Number of dead states */
    int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   for (i=nrl+1; i<=nrh; i++) {  int popbased=0;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  int *wav; /* Number of waves for this individuual 0 is possible */
       m[i][j]=m[i][j-1]+nlay;  int maxwav; /* Maxim number of waves */
   }  int jmin, jmax; /* min, max spacing between 2 waves */
   return m;  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 }  int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 /*************************free ma3x ************************/  int mle, weightopt;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  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 */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   free((FREE_ARG)(m[nrl]+ncl-NR_END));             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   free((FREE_ARG)(m+nrl-NR_END));  double jmean; /* Mean space between 2 waves */
 }  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 /***************** f1dim *************************/  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 extern int ncom;  FILE *ficlog, *ficrespow;
 extern double *pcom,*xicom;  int globpr; /* Global variable for printing or not */
 extern double (*nrfunc)(double []);  double fretone; /* Only one call to likelihood */
    long ipmx; /* Number of contributions */
 double f1dim(double x)  double sw; /* Sum of weights */
 {  char filerespow[FILENAMELENGTH];
   int j;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   double f;  FILE *ficresilk;
   double *xt;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    FILE *ficresprobmorprev;
   xt=vector(1,ncom);  FILE *fichtm, *fichtmcov; /* Html File */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  FILE *ficreseij;
   f=(*nrfunc)(xt);  char filerese[FILENAMELENGTH];
   free_vector(xt,1,ncom);  FILE *ficresstdeij;
   return f;  char fileresstde[FILENAMELENGTH];
 }  FILE *ficrescveij;
   char filerescve[FILENAMELENGTH];
 /*****************brent *************************/  FILE  *ficresvij;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  char fileresv[FILENAMELENGTH];
 {  FILE  *ficresvpl;
   int iter;  char fileresvpl[FILENAMELENGTH];
   double a,b,d,etemp;  char title[MAXLINE];
   double fu,fv,fw,fx;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   double ftemp;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   double p,q,r,tol1,tol2,u,v,w,x,xm;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   double e=0.0;  char command[FILENAMELENGTH];
    int  outcmd=0;
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  char filelog[FILENAMELENGTH]; /* Log file */
   for (iter=1;iter<=ITMAX;iter++) {  char filerest[FILENAMELENGTH];
     xm=0.5*(a+b);  char fileregp[FILENAMELENGTH];
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  char popfile[FILENAMELENGTH];
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     fprintf(ficlog,".");fflush(ficlog);  
 #ifdef DEBUG  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
     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);  struct timezone tzp;
     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);  extern int gettimeofday();
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  struct tm tmg, tm, tmf, *gmtime(), *localtime();
 #endif  long time_value;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  extern long time();
       *xmin=x;  char strcurr[80], strfor[80];
       return fx;  
     }  char *endptr;
     ftemp=fu;  long lval;
     if (fabs(e) > tol1) {  double dval;
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  #define NR_END 1
       p=(x-v)*q-(x-w)*r;  #define FREE_ARG char*
       q=2.0*(q-r);  #define FTOL 1.0e-10
       if (q > 0.0) p = -p;  
       q=fabs(q);  #define NRANSI 
       etemp=e;  #define ITMAX 200 
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #define TOL 2.0e-4 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  #define CGOLD 0.3819660 
         d=p/q;  #define ZEPS 1.0e-10 
         u=x+d;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  #define GOLD 1.618034 
       }  #define GLIMIT 100.0 
     } else {  #define TINY 1.0e-20 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  static double maxarg1,maxarg2;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     fu=(*f)(u);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     if (fu <= fx) {    
       if (u >= x) a=x; else b=x;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       SHFT(v,w,x,u)  #define rint(a) floor(a+0.5)
         SHFT(fv,fw,fx,fu)  
         } else {  static double sqrarg;
           if (u < x) a=u; else b=u;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
           if (fu <= fw || w == x) {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
             v=w;  int agegomp= AGEGOMP;
             w=u;  
             fv=fw;  int imx; 
             fw=fu;  int stepm=1;
           } else if (fu <= fv || v == x || v == w) {  /* Stepm, step in month: minimum step interpolation*/
             v=u;  
             fv=fu;  int estepm;
           }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
         }  
   }  int m,nb;
   nrerror("Too many iterations in brent");  long *num;
   *xmin=x;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   return fx;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 }  double **pmmij, ***probs;
   double *ageexmed,*agecens;
 /****************** mnbrak ***********************/  double dateintmean=0;
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  double *weight;
             double (*func)(double))  int **s; /* Status */
 {  double *agedc, **covar, idx;
   double ulim,u,r,q, dum;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double fu;  double *lsurv, *lpop, *tpop;
    
   *fa=(*func)(*ax);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   *fb=(*func)(*bx);  double ftolhess; /* Tolerance for computing hessian */
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)  /**************** split *************************/
       SHFT(dum,*fb,*fa,dum)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       }  {
   *cx=(*bx)+GOLD*(*bx-*ax);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   *fc=(*func)(*cx);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   while (*fb > *fc) {    */ 
     r=(*bx-*ax)*(*fb-*fc);    char  *ss;                            /* pointer */
     q=(*bx-*cx)*(*fb-*fa);    int   l1, l2;                         /* length counters */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    l1 = strlen(path );                   /* length of path */
     ulim=(*bx)+GLIMIT*(*cx-*bx);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     if ((*bx-u)*(u-*cx) > 0.0) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       fu=(*func)(u);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     } else if ((*cx-u)*(u-ulim) > 0.0) {      strcpy( name, path );               /* we got the fullname name because no directory */
       fu=(*func)(u);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       if (fu < *fc) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      /* get current working directory */
           SHFT(*fb,*fc,fu,(*func)(u))      /*    extern  char* getcwd ( char *buf , int len);*/
           }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {        return( GLOCK_ERROR_GETCWD );
       u=ulim;      }
       fu=(*func)(u);      /* got dirc from getcwd*/
     } else {      printf(" DIRC = %s \n",dirc);
       u=(*cx)+GOLD*(*cx-*bx);    } else {                              /* strip direcotry from path */
       fu=(*func)(u);      ss++;                               /* after this, the filename */
     }      l2 = strlen( ss );                  /* length of filename */
     SHFT(*ax,*bx,*cx,u)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       SHFT(*fa,*fb,*fc,fu)      strcpy( name, ss );         /* save file name */
       }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 }      dirc[l1-l2] = 0;                    /* add zero */
       printf(" DIRC2 = %s \n",dirc);
 /*************** linmin ************************/    }
     /* We add a separator at the end of dirc if not exists */
 int ncom;    l1 = strlen( dirc );                  /* length of directory */
 double *pcom,*xicom;    if( dirc[l1-1] != DIRSEPARATOR ){
 double (*nrfunc)(double []);      dirc[l1] =  DIRSEPARATOR;
        dirc[l1+1] = 0; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      printf(" DIRC3 = %s \n",dirc);
 {    }
   double brent(double ax, double bx, double cx,    ss = strrchr( name, '.' );            /* find last / */
                double (*f)(double), double tol, double *xmin);    if (ss >0){
   double f1dim(double x);      ss++;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      strcpy(ext,ss);                     /* save extension */
               double *fc, double (*func)(double));      l1= strlen( name);
   int j;      l2= strlen(ss)+1;
   double xx,xmin,bx,ax;      strncpy( finame, name, l1-l2);
   double fx,fb,fa;      finame[l1-l2]= 0;
      }
   ncom=n;  
   pcom=vector(1,n);    return( 0 );                          /* we're done */
   xicom=vector(1,n);  }
   nrfunc=func;  
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  /******************************************/
     xicom[j]=xi[j];  
   }  void replace_back_to_slash(char *s, char*t)
   ax=0.0;  {
   xx=1.0;    int i;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    int lg=0;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    i=0;
 #ifdef DEBUG    lg=strlen(t);
   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);      (s[i] = t[i]);
 #endif      if (t[i]== '\\') s[i]='/';
   for (j=1;j<=n;j++) {    }
     xi[j] *= xmin;  }
     p[j] += xi[j];  
   }  int nbocc(char *s, char occ)
   free_vector(xicom,1,n);  {
   free_vector(pcom,1,n);    int i,j=0;
 }    int lg=20;
     i=0;
 /*************** powell ************************/    lg=strlen(s);
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    for(i=0; i<= lg; i++) {
             double (*func)(double []))    if  (s[i] == occ ) j++;
 {    }
   void linmin(double p[], double xi[], int n, double *fret,    return j;
               double (*func)(double []));  }
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  void cutv(char *u,char *v, char*t, char occ)
   double fp,fptt;  {
   double *xits;    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   pt=vector(1,n);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   ptt=vector(1,n);       gives u="abcedf" and v="ghi2j" */
   xit=vector(1,n);    int i,lg,j,p=0;
   xits=vector(1,n);    i=0;
   *fret=(*func)(p);    for(j=0; j<=strlen(t)-1; j++) {
   for (j=1;j<=n;j++) pt[j]=p[j];      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   for (*iter=1;;++(*iter)) {    }
     fp=(*fret);  
     ibig=0;    lg=strlen(t);
     del=0.0;    for(j=0; j<p; j++) {
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      (u[j] = t[j]);
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    }
     for (i=1;i<=n;i++)       u[p]='\0';
       printf(" %d %.12f",i, p[i]);  
     fprintf(ficlog," %d %.12f",i, p[i]);     for(j=0; j<= lg; j++) {
     printf("\n");      if (j>=(p+1))(v[j-p-1] = t[j]);
     fprintf(ficlog,"\n");    }
     for (i=1;i<=n;i++) {  }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  /********************** nrerror ********************/
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  void nrerror(char error_text[])
       fprintf(ficlog,"fret=%lf \n",*fret);  {
 #endif    fprintf(stderr,"ERREUR ...\n");
       printf("%d",i);fflush(stdout);    fprintf(stderr,"%s\n",error_text);
       fprintf(ficlog,"%d",i);fflush(ficlog);    exit(EXIT_FAILURE);
       linmin(p,xit,n,fret,func);  }
       if (fabs(fptt-(*fret)) > del) {  /*********************** vector *******************/
         del=fabs(fptt-(*fret));  double *vector(int nl, int nh)
         ibig=i;  {
       }    double *v;
 #ifdef DEBUG    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       printf("%d %.12e",i,(*fret));    if (!v) nrerror("allocation failure in vector");
       fprintf(ficlog,"%d %.12e",i,(*fret));    return v-nl+NR_END;
       for (j=1;j<=n;j++) {  }
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  /************************ free vector ******************/
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  void free_vector(double*v, int nl, int nh)
       }  {
       for(j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
         printf(" p=%.12e",p[j]);  }
         fprintf(ficlog," p=%.12e",p[j]);  
       }  /************************ivector *******************************/
       printf("\n");  int *ivector(long nl,long nh)
       fprintf(ficlog,"\n");  {
 #endif    int *v;
     }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    if (!v) nrerror("allocation failure in ivector");
 #ifdef DEBUG    return v-nl+NR_END;
       int k[2],l;  }
       k[0]=1;  
       k[1]=-1;  /******************free ivector **************************/
       printf("Max: %.12e",(*func)(p));  void free_ivector(int *v, long nl, long nh)
       fprintf(ficlog,"Max: %.12e",(*func)(p));  {
       for (j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
         printf(" %.12e",p[j]);  }
         fprintf(ficlog," %.12e",p[j]);  
       }  /************************lvector *******************************/
       printf("\n");  long *lvector(long nl,long nh)
       fprintf(ficlog,"\n");  {
       for(l=0;l<=1;l++) {    long *v;
         for (j=1;j<=n;j++) {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    if (!v) nrerror("allocation failure in ivector");
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    return v-nl+NR_END;
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  }
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /******************free lvector **************************/
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  void free_lvector(long *v, long nl, long nh)
       }  {
 #endif    free((FREE_ARG)(v+nl-NR_END));
   }
   
       free_vector(xit,1,n);  /******************* imatrix *******************************/
       free_vector(xits,1,n);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       free_vector(ptt,1,n);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       free_vector(pt,1,n);  { 
       return;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     }    int **m; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    
     for (j=1;j<=n;j++) {    /* allocate pointers to rows */ 
       ptt[j]=2.0*p[j]-pt[j];    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       xit[j]=p[j]-pt[j];    if (!m) nrerror("allocation failure 1 in matrix()"); 
       pt[j]=p[j];    m += NR_END; 
     }    m -= nrl; 
     fptt=(*func)(ptt);    
     if (fptt < fp) {    
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    /* allocate rows and set pointers to them */ 
       if (t < 0.0) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         linmin(p,xit,n,fret,func);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         for (j=1;j<=n;j++) {    m[nrl] += NR_END; 
           xi[j][ibig]=xi[j][n];    m[nrl] -= ncl; 
           xi[j][n]=xit[j];    
         }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 #ifdef DEBUG    
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    /* return pointer to array of pointers to rows */ 
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    return m; 
         for(j=1;j<=n;j++){  } 
           printf(" %.12e",xit[j]);  
           fprintf(ficlog," %.12e",xit[j]);  /****************** free_imatrix *************************/
         }  void free_imatrix(m,nrl,nrh,ncl,nch)
         printf("\n");        int **m;
         fprintf(ficlog,"\n");        long nch,ncl,nrh,nrl; 
 #endif       /* free an int matrix allocated by imatrix() */ 
       }  { 
     }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   }    free((FREE_ARG) (m+nrl-NR_END)); 
 }  } 
   
 /**** Prevalence limit ****************/  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  {
 {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    double **m;
      matrix by transitions matrix until convergence is reached */  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   int i, ii,j,k;    if (!m) nrerror("allocation failure 1 in matrix()");
   double min, max, maxmin, maxmax,sumnew=0.;    m += NR_END;
   double **matprod2();    m -= nrl;
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double agefin, delaymax=50 ; /* Max number of years to converge */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   for (ii=1;ii<=nlstate+ndeath;ii++)    m[nrl] -= ncl;
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
    cov[1]=1.;     */
    }
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  /*************************free matrix ************************/
     newm=savm;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     /* Covariates have to be included here again */  {
      cov[2]=agefin;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
       for (k=1; k<=cptcovn;k++) {  }
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*      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]]);*/  /******************* ma3x *******************************/
       }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  {
       for (k=1; k<=cptcovprod;k++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double ***m;
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    if (!m) nrerror("allocation failure 1 in matrix()");
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    m += NR_END;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    m -= nrl;
   
     savm=oldm;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     oldm=newm;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     maxmax=0.;    m[nrl] += NR_END;
     for(j=1;j<=nlstate;j++){    m[nrl] -= ncl;
       min=1.;  
       max=0.;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         prlim[i][j]= newm[i][j]/(1-sumnew);    m[nrl][ncl] += NR_END;
         max=FMAX(max,prlim[i][j]);    m[nrl][ncl] -= nll;
         min=FMIN(min,prlim[i][j]);    for (j=ncl+1; j<=nch; j++) 
       }      m[nrl][j]=m[nrl][j-1]+nlay;
       maxmin=max-min;    
       maxmax=FMAX(maxmax,maxmin);    for (i=nrl+1; i<=nrh; i++) {
     }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     if(maxmax < ftolpl){      for (j=ncl+1; j<=nch; j++) 
       return prlim;        m[i][j]=m[i][j-1]+nlay;
     }    }
   }    return m; 
 }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
              &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 /*************** transition probabilities ***************/    */
   }
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  /*************************free ma3x ************************/
   double s1, s2;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   /*double t34;*/  {
   int i,j,j1, nc, ii, jj;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for(i=1; i<= nlstate; i++){    free((FREE_ARG)(m+nrl-NR_END));
     for(j=1; j<i;j++){  }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/  /*************** function subdirf ***********/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  char *subdirf(char fileres[])
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  {
       }    /* Caution optionfilefiname is hidden */
       ps[i][j]=s2;    strcpy(tmpout,optionfilefiname);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    strcat(tmpout,"/"); /* Add to the right */
     }    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 subdirf2 ***********/
       }  char *subdirf2(char fileres[], char *preop)
       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,fileres);
     for(j=1; j<i; j++)    return tmpout;
       s1+=exp(ps[i][j]);  }
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  /*************** function subdirf3 ***********/
     ps[i][i]=1./(s1+1.);  char *subdirf3(char fileres[], char *preop, char *preop2)
     for(j=1; j<i; j++)  {
       ps[i][j]= exp(ps[i][j])*ps[i][i];    
     for(j=i+1; j<=nlstate+ndeath; j++)    /* Caution optionfilefiname is hidden */
       ps[i][j]= exp(ps[i][j])*ps[i][i];    strcpy(tmpout,optionfilefiname);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    strcat(tmpout,"/");
   } /* end i */    strcat(tmpout,preop);
     strcat(tmpout,preop2);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    strcat(tmpout,fileres);
     for(jj=1; jj<= nlstate+ndeath; jj++){    return tmpout;
       ps[ii][jj]=0;  }
       ps[ii][ii]=1;  
     }  /***************** f1dim *************************/
   }  extern int ncom; 
   extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){   
     for(jj=1; jj<= nlstate+ndeath; jj++){  double f1dim(double x) 
      printf("%lf ",ps[ii][jj]);  { 
    }    int j; 
     printf("\n ");    double f;
     }    double *xt; 
     printf("\n ");printf("%lf ",cov[2]);*/   
 /*    xt=vector(1,ncom); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   goto end;*/    f=(*nrfunc)(xt); 
     return ps;    free_vector(xt,1,ncom); 
 }    return f; 
   } 
 /**************** Product of 2 matrices ******************/  
   /*****************brent *************************/
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 {  { 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    int iter; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    double a,b,d,etemp;
   /* in, b, out are matrice of pointers which should have been initialized    double fu,fv,fw,fx;
      before: only the contents of out is modified. The function returns    double ftemp;
      a pointer to pointers identical to out */    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   long i, j, k;    double e=0.0; 
   for(i=nrl; i<= nrh; i++)   
     for(k=ncolol; k<=ncoloh; k++)    a=(ax < cx ? ax : cx); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    b=(ax > cx ? ax : cx); 
         out[i][k] +=in[i][j]*b[j][k];    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
   return out;    for (iter=1;iter<=ITMAX;iter++) { 
 }      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 /************* Higher Matrix Product ***************/      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  #ifdef DEBUG
 {      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);
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      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);
      duration (i.e. until      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  #endif
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
      (typically every 2 years instead of every month which is too big).        *xmin=x; 
      Model is determined by parameters x and covariates have to be        return fx; 
      included manually here.      } 
       ftemp=fu;
      */      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
   int i, j, d, h, k;        q=(x-v)*(fx-fw); 
   double **out, cov[NCOVMAX];        p=(x-v)*q-(x-w)*r; 
   double **newm;        q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
   /* Hstepm could be zero and should return the unit matrix */        q=fabs(q); 
   for (i=1;i<=nlstate+ndeath;i++)        etemp=e; 
     for (j=1;j<=nlstate+ndeath;j++){        e=d; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       po[i][j][0]=(i==j ? 1.0 : 0.0);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }        else { 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          d=p/q; 
   for(h=1; h <=nhstepm; h++){          u=x+d; 
     for(d=1; d <=hstepm; d++){          if (u-a < tol2 || b-u < tol2) 
       newm=savm;            d=SIGN(tol1,xm-x); 
       /* Covariates have to be included here again */        } 
       cov[1]=1.;      } else { 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      } 
       for (k=1; k<=cptcovage;k++)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      fu=(*f)(u); 
       for (k=1; k<=cptcovprod;k++)      if (fu <= fx) { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          } else { 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/            if (u < x) a=u; else b=u; 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,            if (fu <= fw || w == x) { 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));              v=w; 
       savm=oldm;              w=u; 
       oldm=newm;              fv=fw; 
     }              fw=fu; 
     for(i=1; i<=nlstate+ndeath; i++)            } else if (fu <= fv || v == x || v == w) { 
       for(j=1;j<=nlstate+ndeath;j++) {              v=u; 
         po[i][j][h]=newm[i][j];              fv=fu; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);            } 
          */          } 
       }    } 
   } /* end h */    nrerror("Too many iterations in brent"); 
   return po;    *xmin=x; 
 }    return fx; 
   } 
   
 /*************** log-likelihood *************/  /****************** mnbrak ***********************/
 double func( double *x)  
 {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   int i, ii, j, k, mi, d, kk;              double (*func)(double)) 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  { 
   double **out;    double ulim,u,r,q, dum;
   double sw; /* Sum of weights */    double fu; 
   double lli; /* Individual log likelihood */   
   long ipmx;    *fa=(*func)(*ax); 
   /*extern weight */    *fb=(*func)(*bx); 
   /* We are differentiating ll according to initial status */    if (*fb > *fa) { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      SHFT(dum,*ax,*bx,dum) 
   /*for(i=1;i<imx;i++)        SHFT(dum,*fb,*fa,dum) 
     printf(" %d\n",s[4][i]);        } 
   */    *cx=(*bx)+GOLD*(*bx-*ax); 
   cov[1]=1.;    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      r=(*bx-*ax)*(*fb-*fc); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      q=(*bx-*cx)*(*fb-*fa); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     for(mi=1; mi<= wav[i]-1; mi++){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       for (ii=1;ii<=nlstate+ndeath;ii++)      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      if ((*bx-u)*(u-*cx) > 0.0) { 
       for(d=0; d<dh[mi][i]; d++){        fu=(*func)(u); 
         newm=savm;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        fu=(*func)(u); 
         for (kk=1; kk<=cptcovage;kk++) {        if (fu < *fc) { 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         }            SHFT(*fb,*fc,fu,(*func)(u)) 
                    } 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        u=ulim; 
         savm=oldm;        fu=(*func)(u); 
         oldm=newm;      } else { 
                u=(*cx)+GOLD*(*cx-*bx); 
                fu=(*func)(u); 
       } /* end mult */      } 
            SHFT(*ax,*bx,*cx,u) 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        SHFT(*fa,*fb,*fc,fu) 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        } 
       ipmx +=1;  } 
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  /*************** linmin ************************/
     } /* end of wave */  
   } /* end of individual */  int ncom; 
   double *pcom,*xicom;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  double (*nrfunc)(double []); 
   /* 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 */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   return -l;  { 
 }    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
 /*********** Maximum Likelihood Estimation ***************/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    int j; 
 {    double xx,xmin,bx,ax; 
   int i,j, iter;    double fx,fb,fa;
   double **xi,*delti;   
   double fret;    ncom=n; 
   xi=matrix(1,npar,1,npar);    pcom=vector(1,n); 
   for (i=1;i<=npar;i++)    xicom=vector(1,n); 
     for (j=1;j<=npar;j++)    nrfunc=func; 
       xi[i][j]=(i==j ? 1.0 : 0.0);    for (j=1;j<=n;j++) { 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");      pcom[j]=p[j]; 
   powell(p,xi,npar,ftol,&iter,&fret,func);      xicom[j]=xi[j]; 
     } 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    ax=0.0; 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    xx=1.0; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 }  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 /**** Computes Hessian and covariance matrix ***/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  #endif
 {    for (j=1;j<=n;j++) { 
   double  **a,**y,*x,pd;      xi[j] *= xmin; 
   double **hess;      p[j] += xi[j]; 
   int i, j,jk;    } 
   int *indx;    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
   double hessii(double p[], double delta, int theta, double delti[]);  } 
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;  char *asc_diff_time(long time_sec, char ascdiff[])
   void ludcmp(double **a, int npar, int *indx, double *d) ;  {
     long sec_left, days, hours, minutes;
   hess=matrix(1,npar,1,npar);    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
   printf("\nCalculation of the hessian matrix. Wait...\n");    hours = (sec_left) / (60*60) ;
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    sec_left = (sec_left) %(60*60);
   for (i=1;i<=npar;i++){    minutes = (sec_left) /60;
     printf("%d",i);fflush(stdout);    sec_left = (sec_left) % (60);
     fprintf(ficlog,"%d",i);fflush(ficlog);    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     hess[i][i]=hessii(p,ftolhess,i,delti);    return ascdiff;
     /*printf(" %f ",p[i]);*/  }
     /*printf(" %lf ",hess[i][i]);*/  
   }  /*************** powell ************************/
    void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   for (i=1;i<=npar;i++) {              double (*func)(double [])) 
     for (j=1;j<=npar;j++)  {  { 
       if (j>i) {    void linmin(double p[], double xi[], int n, double *fret, 
         printf(".%d%d",i,j);fflush(stdout);                double (*func)(double [])); 
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    int i,ibig,j; 
         hess[i][j]=hessij(p,delti,i,j);    double del,t,*pt,*ptt,*xit;
         hess[j][i]=hess[i][j];        double fp,fptt;
         /*printf(" %lf ",hess[i][j]);*/    double *xits;
       }    int niterf, itmp;
     }  
   }    pt=vector(1,n); 
   printf("\n");    ptt=vector(1,n); 
   fprintf(ficlog,"\n");    xit=vector(1,n); 
     xits=vector(1,n); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    *fret=(*func)(p); 
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    for (j=1;j<=n;j++) pt[j]=p[j]; 
      for (*iter=1;;++(*iter)) { 
   a=matrix(1,npar,1,npar);      fp=(*fret); 
   y=matrix(1,npar,1,npar);      ibig=0; 
   x=vector(1,npar);      del=0.0; 
   indx=ivector(1,npar);      last_time=curr_time;
   for (i=1;i<=npar;i++)      (void) gettimeofday(&curr_time,&tzp);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      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);
   ludcmp(a,npar,indx,&pd);      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(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
   for (j=1;j<=npar;j++) {     for (i=1;i<=n;i++) {
     for (i=1;i<=npar;i++) x[i]=0;        printf(" %d %.12f",i, p[i]);
     x[j]=1;        fprintf(ficlog," %d %.12lf",i, p[i]);
     lubksb(a,npar,indx,x);        fprintf(ficrespow," %.12lf", p[i]);
     for (i=1;i<=npar;i++){      }
       matcov[i][j]=x[i];      printf("\n");
     }      fprintf(ficlog,"\n");
   }      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
   printf("\n#Hessian matrix#\n");        tm = *localtime(&curr_time.tv_sec);
   fprintf(ficlog,"\n#Hessian matrix#\n");        strcpy(strcurr,asctime(&tm));
   for (i=1;i<=npar;i++) {  /*       asctime_r(&tm,strcurr); */
     for (j=1;j<=npar;j++) {        forecast_time=curr_time; 
       printf("%.3e ",hess[i][j]);        itmp = strlen(strcurr);
       fprintf(ficlog,"%.3e ",hess[i][j]);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     }          strcurr[itmp-1]='\0';
     printf("\n");        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     fprintf(ficlog,"\n");        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);
   /* Recompute Inverse */          tmf = *localtime(&forecast_time.tv_sec);
   for (i=1;i<=npar;i++)  /*      asctime_r(&tmf,strfor); */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          strcpy(strfor,asctime(&tmf));
   ludcmp(a,npar,indx,&pd);          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
   /*  printf("\n#Hessian matrix recomputed#\n");          strfor[itmp-1]='\0';
           printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   for (j=1;j<=npar;j++) {          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);
     for (i=1;i<=npar;i++) x[i]=0;        }
     x[j]=1;      }
     lubksb(a,npar,indx,x);      for (i=1;i<=n;i++) { 
     for (i=1;i<=npar;i++){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       y[i][j]=x[i];        fptt=(*fret); 
       printf("%.3e ",y[i][j]);  #ifdef DEBUG
       fprintf(ficlog,"%.3e ",y[i][j]);        printf("fret=%lf \n",*fret);
     }        fprintf(ficlog,"fret=%lf \n",*fret);
     printf("\n");  #endif
     fprintf(ficlog,"\n");        printf("%d",i);fflush(stdout);
   }        fprintf(ficlog,"%d",i);fflush(ficlog);
   */        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
   free_matrix(a,1,npar,1,npar);          del=fabs(fptt-(*fret)); 
   free_matrix(y,1,npar,1,npar);          ibig=i; 
   free_vector(x,1,npar);        } 
   free_ivector(indx,1,npar);  #ifdef DEBUG
   free_matrix(hess,1,npar,1,npar);        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
 }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
 /*************** hessian matrix ****************/          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
 double hessii( double x[], double delta, int theta, double delti[])        }
 {        for(j=1;j<=n;j++) {
   int i;          printf(" p=%.12e",p[j]);
   int l=1, lmax=20;          fprintf(ficlog," p=%.12e",p[j]);
   double k1,k2;        }
   double p2[NPARMAX+1];        printf("\n");
   double res;        fprintf(ficlog,"\n");
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  #endif
   double fx;      } 
   int k=0,kmax=10;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double l1;  #ifdef DEBUG
         int k[2],l;
   fx=func(x);        k[0]=1;
   for (i=1;i<=npar;i++) p2[i]=x[i];        k[1]=-1;
   for(l=0 ; l <=lmax; l++){        printf("Max: %.12e",(*func)(p));
     l1=pow(10,l);        fprintf(ficlog,"Max: %.12e",(*func)(p));
     delts=delt;        for (j=1;j<=n;j++) {
     for(k=1 ; k <kmax; k=k+1){          printf(" %.12e",p[j]);
       delt = delta*(l1*k);          fprintf(ficlog," %.12e",p[j]);
       p2[theta]=x[theta] +delt;        }
       k1=func(p2)-fx;        printf("\n");
       p2[theta]=x[theta]-delt;        fprintf(ficlog,"\n");
       k2=func(p2)-fx;        for(l=0;l<=1;l++) {
       /*res= (k1-2.0*fx+k2)/delt/delt; */          for (j=1;j<=n;j++) {
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
                  printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 #ifdef DEBUG            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       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);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 #endif          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  #endif
         k=kmax;  
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        free_vector(xit,1,n); 
         k=kmax; l=lmax*10.;        free_vector(xits,1,n); 
       }        free_vector(ptt,1,n); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        free_vector(pt,1,n); 
         delts=delt;        return; 
       }      } 
     }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   }      for (j=1;j<=n;j++) { 
   delti[theta]=delts;        ptt[j]=2.0*p[j]-pt[j]; 
   return res;        xit[j]=p[j]-pt[j]; 
          pt[j]=p[j]; 
 }      } 
       fptt=(*func)(ptt); 
 double hessij( double x[], double delti[], int thetai,int thetaj)      if (fptt < fp) { 
 {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   int i;        if (t < 0.0) { 
   int l=1, l1, lmax=20;          linmin(p,xit,n,fret,func); 
   double k1,k2,k3,k4,res,fx;          for (j=1;j<=n;j++) { 
   double p2[NPARMAX+1];            xi[j][ibig]=xi[j][n]; 
   int k;            xi[j][n]=xit[j]; 
           }
   fx=func(x);  #ifdef DEBUG
   for (k=1; k<=2; k++) {          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for (i=1;i<=npar;i++) p2[i]=x[i];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     p2[thetai]=x[thetai]+delti[thetai]/k;          for(j=1;j<=n;j++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            printf(" %.12e",xit[j]);
     k1=func(p2)-fx;            fprintf(ficlog," %.12e",xit[j]);
            }
     p2[thetai]=x[thetai]+delti[thetai]/k;          printf("\n");
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          fprintf(ficlog,"\n");
     k2=func(p2)-fx;  #endif
          }
     p2[thetai]=x[thetai]-delti[thetai]/k;      } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    } 
     k3=func(p2)-fx;  } 
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /**** Prevalence limit (stable or period prevalence)  ****************/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  {
 #ifdef DEBUG    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     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);       matrix by transitions matrix until convergence is reached */
     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    int i, ii,j,k;
   }    double min, max, maxmin, maxmax,sumnew=0.;
   return res;    double **matprod2();
 }    double **out, cov[NCOVMAX], **pmij();
     double **newm;
 /************** Inverse of matrix **************/    double agefin, delaymax=50 ; /* Max number of years to converge */
 void ludcmp(double **a, int n, int *indx, double *d)  
 {    for (ii=1;ii<=nlstate+ndeath;ii++)
   int i,imax,j,k;      for (j=1;j<=nlstate+ndeath;j++){
   double big,dum,sum,temp;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *vv;      }
    
   vv=vector(1,n);     cov[1]=1.;
   *d=1.0;   
   for (i=1;i<=n;i++) {   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     big=0.0;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for (j=1;j<=n;j++)      newm=savm;
       if ((temp=fabs(a[i][j])) > big) big=temp;      /* Covariates have to be included here again */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");       cov[2]=agefin;
     vv[i]=1.0/big;    
   }        for (k=1; k<=cptcovn;k++) {
   for (j=1;j<=n;j++) {          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for (i=1;i<j;i++) {          /*      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]]);*/
       sum=a[i][j];        }
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       a[i][j]=sum;        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]]];
     big=0.0;  
     for (i=j;i<=n;i++) {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       sum=a[i][j];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       for (k=1;k<j;k++)        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         sum -= a[i][k]*a[k][j];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {      savm=oldm;
         big=dum;      oldm=newm;
         imax=i;      maxmax=0.;
       }      for(j=1;j<=nlstate;j++){
     }        min=1.;
     if (j != imax) {        max=0.;
       for (k=1;k<=n;k++) {        for(i=1; i<=nlstate; i++) {
         dum=a[imax][k];          sumnew=0;
         a[imax][k]=a[j][k];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         a[j][k]=dum;          prlim[i][j]= newm[i][j]/(1-sumnew);
       }          max=FMAX(max,prlim[i][j]);
       *d = -(*d);          min=FMIN(min,prlim[i][j]);
       vv[imax]=vv[j];        }
     }        maxmin=max-min;
     indx[j]=imax;        maxmax=FMAX(maxmax,maxmin);
     if (a[j][j] == 0.0) a[j][j]=TINY;      }
     if (j != n) {      if(maxmax < ftolpl){
       dum=1.0/(a[j][j]);        return prlim;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      }
     }    }
   }  }
   free_vector(vv,1,n);  /* Doesn't work */  
 ;  /*************** transition probabilities ***************/ 
 }  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 void lubksb(double **a, int n, int *indx, double b[])  {
 {    double s1, s2;
   int i,ii=0,ip,j;    /*double t34;*/
   double sum;    int i,j,j1, nc, ii, jj;
    
   for (i=1;i<=n;i++) {      for(i=1; i<= nlstate; i++){
     ip=indx[i];        for(j=1; j<i;j++){
     sum=b[ip];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     b[ip]=b[i];            /*s2 += param[i][j][nc]*cov[nc];*/
     if (ii)            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     else if (sum) ii=i;          }
     b[i]=sum;          ps[i][j]=s2;
   }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   for (i=n;i>=1;i--) {        }
     sum=b[i];        for(j=i+1; j<=nlstate+ndeath;j++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     b[i]=sum/a[i][i];            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); */
 }          }
           ps[i][j]=s2;
 /************ Frequencies ********************/        }
 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)      }
 {  /* Some frequencies */      /*ps[3][2]=1;*/
        
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      for(i=1; i<= nlstate; i++){
   int first;        s1=0;
   double ***freq; /* Frequencies */        for(j=1; j<i; j++)
   double *pp;          s1+=exp(ps[i][j]);
   double pos, k2, dateintsum=0,k2cpt=0;        for(j=i+1; j<=nlstate+ndeath; j++)
   FILE *ficresp;          s1+=exp(ps[i][j]);
   char fileresp[FILENAMELENGTH];        ps[i][i]=1./(s1+1.);
          for(j=1; j<i; j++)
   pp=vector(1,nlstate);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=i+1; j<=nlstate+ndeath; j++)
   strcpy(fileresp,"p");          ps[i][j]= exp(ps[i][j])*ps[i][i];
   strcat(fileresp,fileres);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   if((ficresp=fopen(fileresp,"w"))==NULL) {      } /* end i */
     printf("Problem with prevalence resultfile: %s\n", fileresp);      
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     exit(0);        for(jj=1; jj<= nlstate+ndeath; jj++){
   }          ps[ii][jj]=0;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          ps[ii][ii]=1;
   j1=0;        }
        }
   j=cptcoveff;      
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   first=1;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*         printf("ddd %lf ",ps[ii][jj]); */
   for(k1=1; k1<=j;k1++){  /*       } */
     for(i1=1; i1<=ncodemax[k1];i1++){  /*       printf("\n "); */
       j1++;  /*        } */
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  /*        printf("\n ");printf("%lf ",cov[2]); */
         scanf("%d", i);*/         /*
       for (i=-1; i<=nlstate+ndeath; i++)          for(i=1; i<= npar; i++) printf("%f ",x[i]);
         for (jk=-1; jk<=nlstate+ndeath; jk++)          goto end;*/
           for(m=agemin; m <= agemax+3; m++)      return ps;
             freq[i][jk][m]=0;  }
        
       dateintsum=0;  /**************** Product of 2 matrices ******************/
       k2cpt=0;  
       for (i=1; i<=imx; i++) {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         bool=1;  {
         if  (cptcovn>0) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
           for (z1=1; z1<=cptcoveff; z1++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    /* in, b, out are matrice of pointers which should have been initialized 
               bool=0;       before: only the contents of out is modified. The function returns
         }       a pointer to pointers identical to out */
         if (bool==1) {    long i, j, k;
           for(m=firstpass; m<=lastpass; m++){    for(i=nrl; i<= nrh; i++)
             k2=anint[m][i]+(mint[m][i]/12.);      for(k=ncolol; k<=ncoloh; k++)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
               if(agev[m][i]==0) agev[m][i]=agemax+1;          out[i][k] +=in[i][j]*b[j][k];
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {    return out;
                 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];  
               }  
                /************* Higher Matrix Product ***************/
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  
                 dateintsum=dateintsum+k2;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
                 k2cpt++;  {
               }    /* Computes the transition matrix starting at age 'age' over 
             }       'nhstepm*hstepm*stepm' months (i.e. until
           }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         }       nhstepm*hstepm matrices. 
       }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
               (typically every 2 years instead of every month which is too big 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       for the memory).
        Model is determined by parameters x and covariates have to be 
       if  (cptcovn>0) {       included manually here. 
         fprintf(ficresp, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       */
         fprintf(ficresp, "**********\n#");  
       }    int i, j, d, h, k;
       for(i=1; i<=nlstate;i++)    double **out, cov[NCOVMAX];
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double **newm;
       fprintf(ficresp, "\n");  
          /* Hstepm could be zero and should return the unit matrix */
       for(i=(int)agemin; i <= (int)agemax+3; i++){    for (i=1;i<=nlstate+ndeath;i++)
         if(i==(int)agemax+3){      for (j=1;j<=nlstate+ndeath;j++){
           fprintf(ficlog,"Total");        oldm[i][j]=(i==j ? 1.0 : 0.0);
         }else{        po[i][j][0]=(i==j ? 1.0 : 0.0);
           if(first==1){      }
             first=0;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
             printf("See log file for details...\n");    for(h=1; h <=nhstepm; h++){
           }      for(d=1; d <=hstepm; d++){
           fprintf(ficlog,"Age %d", i);        newm=savm;
         }        /* Covariates have to be included here again */
         for(jk=1; jk <=nlstate ; jk++){        cov[1]=1.;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
             pp[jk] += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         }        for (k=1; k<=cptcovage;k++)
         for(jk=1; jk <=nlstate ; jk++){          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for(m=-1, pos=0; m <=0 ; m++)        for (k=1; k<=cptcovprod;k++)
             pos += freq[jk][m][i];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           if(pp[jk]>=1.e-10){  
             if(first==1){  
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
             }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
           }else{                     pmij(pmmij,cov,ncovmodel,x,nlstate));
             if(first==1)        savm=oldm;
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        oldm=newm;
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      }
           }      for(i=1; i<=nlstate+ndeath; i++)
         }        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
         for(jk=1; jk <=nlstate ; jk++){          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)           */
             pp[jk] += freq[jk][m][i];        }
         }    } /* end h */
     return po;
         for(jk=1,pos=0; jk <=nlstate ; jk++)  }
           pos += pp[jk];  
         for(jk=1; jk <=nlstate ; jk++){  
           if(pos>=1.e-5){  /*************** log-likelihood *************/
             if(first==1)  double func( double *x)
               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);    int i, ii, j, k, mi, d, kk;
           }else{    double l, ll[NLSTATEMAX], cov[NCOVMAX];
             if(first==1)    double **out;
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    double sw; /* Sum of weights */
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    double lli; /* Individual log likelihood */
           }    int s1, s2;
           if( i <= (int) agemax){    double bbh, survp;
             if(pos>=1.e-5){    long ipmx;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    /*extern weight */
               probs[i][jk][j1]= pp[jk]/pos;    /* We are differentiating ll according to initial status */
               /*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 (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             }    /*for(i=1;i<imx;i++) 
             else      printf(" %d\n",s[4][i]);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    */
           }    cov[1]=1.;
         }  
            for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(jk=-1; jk <=nlstate+ndeath; jk++)  
           for(m=-1; m <=nlstate+ndeath; m++)    if(mle==1){
             if(freq[jk][m][i] !=0 ) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             if(first==1)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        for(mi=1; mi<= wav[i]-1; mi++){
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);          for (ii=1;ii<=nlstate+ndeath;ii++)
             }            for (j=1;j<=nlstate+ndeath;j++){
         if(i <= (int) agemax)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           fprintf(ficresp,"\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if(first==1)            }
           printf("Others in log...\n");          for(d=0; d<dh[mi][i]; d++){
         fprintf(ficlog,"\n");            newm=savm;
       }            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];
   dateintmean=dateintsum/k2cpt;            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fclose(ficresp);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            savm=oldm;
   free_vector(pp,1,nlstate);            oldm=newm;
            } /* end mult */
   /* End of Freq */        
 }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
 /************ Prevalence ********************/           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 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)           * (in months) between two waves is not a multiple of stepm, we rounded to 
 {  /* Some frequencies */           * the nearest (and in case of equal distance, to the lowest) interval but now
             * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   double ***freq; /* Frequencies */           * probability in order to take into account the bias as a fraction of the way
   double *pp;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   double pos, k2;           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
   pp=vector(1,nlstate);           * For stepm > 1 the results are less biased than in previous versions. 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           */
            s1=s[mw[mi][i]][i];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          s2=s[mw[mi+1][i]][i];
   j1=0;          bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias bh is positive if real duration
   j=cptcoveff;           * is higher than the multiple of stepm and negative otherwise.
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           */
            /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   for(k1=1; k1<=j;k1++){          if( s2 > nlstate){ 
     for(i1=1; i1<=ncodemax[k1];i1++){            /* i.e. if s2 is a death state and if the date of death is known 
       j1++;               then the contribution to the likelihood is the probability to 
                     die between last step unit time and current  step unit time, 
       for (i=-1; i<=nlstate+ndeath; i++)                 which is also equal to probability to die before dh 
         for (jk=-1; jk<=nlstate+ndeath; jk++)                 minus probability to die before dh-stepm . 
           for(m=agemin; m <= agemax+3; m++)               In version up to 0.92 likelihood was computed
             freq[i][jk][m]=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
       for (i=1; i<=imx; i++) {          and not the date of a change in health state. The former idea was
         bool=1;          to consider that at each interview the state was recorded
         if  (cptcovn>0) {          (healthy, disable or death) and IMaCh was corrected; but when we
           for (z1=1; z1<=cptcoveff; z1++)          introduced the exact date of death then we should have modified
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          the contribution of an exact death to the likelihood. This new
               bool=0;          contribution is smaller and very dependent of the step unit
         }          stepm. It is no more the probability to die between last interview
         if (bool==1) {          and month of death but the probability to survive from last
           for(m=firstpass; m<=lastpass; m++){          interview up to one month before death multiplied by the
             k2=anint[m][i]+(mint[m][i]/12.);          probability to die within a month. Thanks to Chris
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          Jackson for correcting this bug.  Former versions increased
               if(agev[m][i]==0) agev[m][i]=agemax+1;          mortality artificially. The bad side is that we add another loop
               if(agev[m][i]==1) agev[m][i]=agemax+2;          which slows down the processing. The difference can be up to 10%
               if (m<lastpass) {          lower mortality.
                 if (calagedate>0)            */
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            lli=log(out[s1][s2] - savm[s1][s2]);
                 else  
                   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==-2) {
               }            for (j=1,survp=0. ; j<=nlstate; j++) 
             }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           }            /*survp += out[s1][j]; */
         }            lli= log(survp);
       }          }
       for(i=(int)agemin; i <= (int)agemax+3; i++){          
         for(jk=1; jk <=nlstate ; jk++){          else if  (s2==-4) { 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            for (j=3,survp=0. ; j<=nlstate; j++)  
             pp[jk] += freq[jk][m][i];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         }            lli= log(survp); 
         for(jk=1; jk <=nlstate ; jk++){          } 
           for(m=-1, pos=0; m <=0 ; m++)  
             pos += freq[jk][m][i];          else if  (s2==-5) { 
         }            for (j=1,survp=0. ; j<=2; j++)  
                      survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         for(jk=1; jk <=nlstate ; jk++){            lli= log(survp); 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          } 
             pp[jk] += freq[jk][m][i];          
         }          else{
                    lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            /*  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]);*/
           if( i <= (int) agemax){          /*if(lli ==000.0)*/
             if(pos>=1.e-5){          /*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); */
               probs[i][jk][j1]= pp[jk]/pos;          ipmx +=1;
             }          sw += weight[i];
           }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }/* end jk */        } /* end of wave */
       }/* end i */      } /* end of individual */
     } /* end i1 */    }  else if(mle==2){
   } /* end k1 */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_vector(pp,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }  /* End of Freq */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
 /************* Waves Concatenation ***************/          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      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            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      and mw[mi+1][i]. dh depends on stepm.            savm=oldm;
      */            oldm=newm;
           } /* end mult */
   int i, mi, m;        
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          s1=s[mw[mi][i]][i];
      double sum=0., jmean=0.;*/          s2=s[mw[mi+1][i]][i];
   int first;          bbh=(double)bh[mi][i]/(double)stepm; 
   int j, k=0,jk, ju, jl;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   double sum=0.;          ipmx +=1;
   first=0;          sw += weight[i];
   jmin=1e+5;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   jmax=-1;        } /* end of wave */
   jmean=0.;      } /* end of individual */
   for(i=1; i<=imx; i++){    }  else if(mle==3){  /* exponential inter-extrapolation */
     mi=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     m=firstpass;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     while(s[m][i] <= nlstate){        for(mi=1; mi<= wav[i]-1; mi++){
       if(s[m][i]>=1)          for (ii=1;ii<=nlstate+ndeath;ii++)
         mw[++mi][i]=m;            for (j=1;j<=nlstate+ndeath;j++){
       if(m >=lastpass)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         break;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       else            }
         m++;          for(d=0; d<dh[mi][i]; d++){
     }/* end while */            newm=savm;
     if (s[m][i] > nlstate){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       mi++;     /* Death is another wave */            for (kk=1; kk<=cptcovage;kk++) {
       /* if(mi==0)  never been interviewed correctly before death */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          /* Only death is a correct wave */            }
       mw[mi][i]=m;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     wav[i]=mi;            oldm=newm;
     if(mi==0){          } /* end mult */
       if(first==0){        
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);          s1=s[mw[mi][i]][i];
         first=1;          s2=s[mw[mi+1][i]][i];
       }          bbh=(double)bh[mi][i]/(double)stepm; 
       if(first==1){          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);          ipmx +=1;
       }          sw += weight[i];
     } /* end mi==0 */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
       } /* end of individual */
   for(i=1; i<=imx; i++){    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     for(mi=1; mi<wav[i];mi++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if (stepm <=0)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         dh[mi][i]=1;        for(mi=1; mi<= wav[i]-1; mi++){
       else{          for (ii=1;ii<=nlstate+ndeath;ii++)
         if (s[mw[mi+1][i]][i] > nlstate) {            for (j=1;j<=nlstate+ndeath;j++){
           if (agedc[i] < 2*AGESUP) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           if(j==0) j=1;  /* Survives at least one month after exam */            }
           k=k+1;          for(d=0; d<dh[mi][i]; d++){
           if (j >= jmax) jmax=j;            newm=savm;
           if (j <= jmin) jmin=j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           sum=sum+j;            for (kk=1; kk<=cptcovage;kk++) {
           /*if (j<0) printf("j=%d num=%d \n",j,i); */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }            }
         }          
         else{            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           k=k+1;            savm=oldm;
           if (j >= jmax) jmax=j;            oldm=newm;
           else if (j <= jmin)jmin=j;          } /* end mult */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        
           sum=sum+j;          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
         jk= j/stepm;          if( s2 > nlstate){ 
         jl= j -jk*stepm;            lli=log(out[s1][s2] - savm[s1][s2]);
         ju= j -(jk+1)*stepm;          }else{
         if(jl <= -ju)            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           dh[mi][i]=jk;          }
         else          ipmx +=1;
           dh[mi][i]=jk+1;          sw += weight[i];
         if(dh[mi][i]==0)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           dh[mi][i]=1; /* At least one step */  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       }        } /* end of wave */
     }      } /* end of individual */
   }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   jmean=sum/k;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        for(mi=1; mi<= wav[i]-1; mi++){
  }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 /*********** Tricode ****************************/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 void tricode(int *Tvar, int **nbcode, int imx)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {            }
   int Ndum[20],ij=1, k, j, i;          for(d=0; d<dh[mi][i]; d++){
   int cptcode=0;            newm=savm;
   cptcoveff=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
   for (k=0; k<19; k++) Ndum[k]=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (k=1; k<=7; k++) ncodemax[k]=0;            }
           
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=1; i<=imx; i++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       ij=(int)(covar[Tvar[j]][i]);            savm=oldm;
       Ndum[ij]++;            oldm=newm;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          } /* end mult */
       if (ij > cptcode) cptcode=ij;        
     }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     for (i=0; i<=cptcode; i++) {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       if(Ndum[i]!=0) ncodemax[j]++;          ipmx +=1;
     }          sw += weight[i];
     ij=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
     for (i=1; i<=ncodemax[j]; i++) {      } /* end of individual */
       for (k=0; k<=19; k++) {    } /* End of if */
         if (Ndum[k] != 0) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           nbcode[Tvar[j]][ij]=k;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
              l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           ij++;    return -l;
         }  }
         if (ij > ncodemax[j]) break;  
       }    /*************** log-likelihood *************/
     }  double funcone( double *x)
   }    {
     /* Same as likeli but slower because of a lot of printf and if */
  for (k=0; k<19; k++) Ndum[k]=0;    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
  for (i=1; i<=ncovmodel-2; i++) {    double **out;
    ij=Tvar[i];    double lli; /* Individual log likelihood */
    Ndum[ij]++;    double llt;
  }    int s1, s2;
     double bbh, survp;
  ij=1;    /*extern weight */
  for (i=1; i<=10; i++) {    /* We are differentiating ll according to initial status */
    if((Ndum[i]!=0) && (i<=ncovcol)){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      Tvaraff[ij]=i;    /*for(i=1;i<imx;i++) 
      ij++;      printf(" %d\n",s[4][i]);
    }    */
  }    cov[1]=1.;
    
  cptcoveff=ij-1;    for(k=1; k<=nlstate; k++) ll[k]=0.;
 }  
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 /*********** Health Expectancies ****************/      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
 {            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* Health expectancies */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          }
   double age, agelim, hf;        for(d=0; d<dh[mi][i]; d++){
   double ***p3mat,***varhe;          newm=savm;
   double **dnewm,**doldm;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double *xp;          for (kk=1; kk<=cptcovage;kk++) {
   double **gp, **gm;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double ***gradg, ***trgradg;          }
   int theta;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          savm=oldm;
   xp=vector(1,npar);          oldm=newm;
   dnewm=matrix(1,nlstate*2,1,npar);        } /* end mult */
   doldm=matrix(1,nlstate*2,1,nlstate*2);        
          s1=s[mw[mi][i]][i];
   fprintf(ficreseij,"# Health expectancies\n");        s2=s[mw[mi+1][i]][i];
   fprintf(ficreseij,"# Age");        bbh=(double)bh[mi][i]/(double)stepm; 
   for(i=1; i<=nlstate;i++)        /* bias is positive if real duration
     for(j=1; j<=nlstate;j++)         * is higher than the multiple of stepm and negative otherwise.
       fprintf(ficreseij," %1d-%1d (SE)",i,j);         */
   fprintf(ficreseij,"\n");        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
   if(estepm < stepm){        } else if  (s2==-2) {
     printf ("Problem %d lower than %d\n",estepm, stepm);          for (j=1,survp=0. ; j<=nlstate; j++) 
   }            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   else  hstepm=estepm;            lli= log(survp);
   /* We compute the life expectancy from trapezoids spaced every estepm months        }else if (mle==1){
    * This is mainly to measure the difference between two models: for example          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
    * if stepm=24 months pijx are given only every 2 years and by summing them        } else if(mle==2){
    * we are calculating an estimate of the Life Expectancy assuming a linear          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 */
    * progression inbetween and thus overestimating or underestimating according        } else if(mle==3){  /* exponential inter-extrapolation */
    * to the curvature of the survival function. If, for the same date, we          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 */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        } else if (mle==4){  /* mle=4 no inter-extrapolation */
    * to compare the new estimate of Life expectancy with the same linear          lli=log(out[s1][s2]); /* Original formula */
    * hypothesis. A more precise result, taking into account a more precise        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
    * curvature will be obtained if estepm is as small as stepm. */          lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
   /* For example we decided to compute the life expectancy with the smallest unit */        ipmx +=1;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        sw += weight[i];
      nhstepm is the number of hstepm from age to agelim        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      nstepm is the number of stepm from age to agelin.  /*       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]); */
      Look at hpijx to understand the reason of that which relies in memory size        if(globpr){
      and note for a fixed period like estepm months */          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the   %11.6f %11.6f %11.6f ", \
      survival function given by stepm (the optimization length). Unfortunately it                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
      means that if the survival funtion is printed only each two years of age and if                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
      results. So we changed our mind and took the option of the best precision.            llt +=ll[k]*gipmx/gsw;
   */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          }
           fprintf(ficresilk," %10.6f\n", -llt);
   agelim=AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      } /* end of wave */
     /* nhstepm age range expressed in number of stepm */    } /* end of individual */
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     /* if (stepm >= YEARM) hstepm=1;*/    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    if(globpr==0){ /* First time we count the contributions and weights */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gipmx=ipmx;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      gsw=sw;
     gp=matrix(0,nhstepm,1,nlstate*2);    }
     gm=matrix(0,nhstepm,1,nlstate*2);    return -l;
   }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    /*************** function likelione ***********/
    void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
     /* Computing Variances of health expectancies */       to check the exact contribution to the likelihood.
        Plotting could be done.
      for(theta=1; theta <=npar; theta++){     */
       for(i=1; i<=npar; i++){    int k;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    if(*globpri !=0){ /* Just counts and sums, no printings */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        strcpy(fileresilk,"ilk"); 
        strcat(fileresilk,fileres);
       cptj=0;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for(j=1; j<= nlstate; j++){        printf("Problem with resultfile: %s\n", fileresilk);
         for(i=1; i<=nlstate; i++){        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
           cptj=cptj+1;      }
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      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");
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
           }      /*  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(k=1; k<=nlstate; k++) 
       }        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
            fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
          }
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    *fretone=(*funcone)(p);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      if(*globpri !=0){
            fclose(ficresilk);
       cptj=0;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       for(j=1; j<= nlstate; j++){      fflush(fichtm); 
         for(i=1;i<=nlstate;i++){    } 
           cptj=cptj+1;    return;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  }
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  
         }  /*********** Maximum Likelihood Estimation ***************/
       }  
       for(j=1; j<= nlstate*2; j++)  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         for(h=0; h<=nhstepm-1; h++){  {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    int i,j, iter;
         }    double **xi;
      }    double fret;
        double fretone; /* Only one call to likelihood */
 /* End theta */    /*  char filerespow[FILENAMELENGTH];*/
     xi=matrix(1,npar,1,npar);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
      for(h=0; h<=nhstepm-1; h++)        xi[i][j]=(i==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate*2;j++)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         for(theta=1; theta <=npar; theta++)    strcpy(filerespow,"pow"); 
           trgradg[h][j][theta]=gradg[h][theta][j];    strcat(filerespow,fileres);
          if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
      for(i=1;i<=nlstate*2;i++)      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       for(j=1;j<=nlstate*2;j++)    }
         varhe[i][j][(int)age] =0.;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
      printf("%d|",(int)age);fflush(stdout);      for(j=1;j<=nlstate+ndeath;j++)
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      for(h=0;h<=nhstepm-1;h++){    fprintf(ficrespow,"\n");
       for(k=0;k<=nhstepm-1;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    powell(p,xi,npar,ftol,&iter,&fret,func);
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  
         for(i=1;i<=nlstate*2;i++)    free_matrix(xi,1,npar,1,npar);
           for(j=1;j<=nlstate*2;j++)    fclose(ficrespow);
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       }    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     /* Computing expectancies */  
     for(i=1; i<=nlstate;i++)  }
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  /**** Computes Hessian and covariance matrix ***/
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
            {
 /* 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]);*/    double  **a,**y,*x,pd;
     double **hess;
         }    int i, j,jk;
     int *indx;
     fprintf(ficreseij,"%3.0f",age );  
     cptj=0;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     for(i=1; i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       for(j=1; j<=nlstate;j++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
         cptj++;    void ludcmp(double **a, int npar, int *indx, double *d) ;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    double gompertz(double p[]);
       }    hess=matrix(1,npar,1,npar);
     fprintf(ficreseij,"\n");  
        printf("\nCalculation of the hessian matrix. Wait...\n");
     free_matrix(gm,0,nhstepm,1,nlstate*2);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     free_matrix(gp,0,nhstepm,1,nlstate*2);    for (i=1;i<=npar;i++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      printf("%d",i);fflush(stdout);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      fprintf(ficlog,"%d",i);fflush(ficlog);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     
   }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   printf("\n");      
   fprintf(ficlog,"\n");      /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   free_vector(xp,1,npar);    }
   free_matrix(dnewm,1,nlstate*2,1,npar);    
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    for (i=1;i<=npar;i++) {
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);      for (j=1;j<=npar;j++)  {
 }        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
 /************ Variance ******************/          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 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)          hess[i][j]=hessij(p,delti,i,j,func,npar);
 {          
   /* Variance of health expectancies */          hess[j][i]=hess[i][j];    
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          /*printf(" %lf ",hess[i][j]);*/
   /* double **newm;*/        }
   double **dnewm,**doldm;      }
   double **dnewmp,**doldmp;    }
   int i, j, nhstepm, hstepm, h, nstepm ;    printf("\n");
   int k, cptcode;    fprintf(ficlog,"\n");
   double *xp;  
   double **gp, **gm;  /* for var eij */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   double ***gradg, ***trgradg; /*for var eij */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   double **gradgp, **trgradgp; /* for var p point j */    
   double *gpp, *gmp; /* for var p point j */    a=matrix(1,npar,1,npar);
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */    y=matrix(1,npar,1,npar);
   double ***p3mat;    x=vector(1,npar);
   double age,agelim, hf;    indx=ivector(1,npar);
   int theta;    for (i=1;i<=npar;i++)
   char digit[4];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   char digitp[16];    ludcmp(a,npar,indx,&pd);
   
   char fileresprobmorprev[FILENAMELENGTH];    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   if(popbased==1)      x[j]=1;
     strcpy(digitp,"-populbased-");      lubksb(a,npar,indx,x);
   else      for (i=1;i<=npar;i++){ 
     strcpy(digitp,"-stablbased-");        matcov[i][j]=x[i];
       }
   strcpy(fileresprobmorprev,"prmorprev");    }
   sprintf(digit,"%-d",ij);  
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    printf("\n#Hessian matrix#\n");
   strcat(fileresprobmorprev,digit); /* Tvar to be done */    fprintf(ficlog,"\n#Hessian matrix#\n");
   strcat(fileresprobmorprev,digitp); /* Popbased or not */    for (i=1;i<=npar;i++) { 
   strcat(fileresprobmorprev,fileres);      for (j=1;j<=npar;j++) { 
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {        printf("%.3e ",hess[i][j]);
     printf("Problem with resultfile: %s\n", fileresprobmorprev);        fprintf(ficlog,"%.3e ",hess[i][j]);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);      }
   }      printf("\n");
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      fprintf(ficlog,"\n");
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    }
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");  
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    /* Recompute Inverse */
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    for (i=1;i<=npar;i++)
     fprintf(ficresprobmorprev," p.%-d SE",j);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     for(i=1; i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);  
   }      /*  printf("\n#Hessian matrix recomputed#\n");
   fprintf(ficresprobmorprev,"\n");  
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    for (j=1;j<=npar;j++) {
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);      for (i=1;i<=npar;i++) x[i]=0;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);      x[j]=1;
     exit(0);      lubksb(a,npar,indx,x);
   }      for (i=1;i<=npar;i++){ 
   else{        y[i][j]=x[i];
     fprintf(ficgp,"\n# Routine varevsij");        printf("%.3e ",y[i][j]);
   }        fprintf(ficlog,"%.3e ",y[i][j]);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {      }
     printf("Problem with html file: %s\n", optionfilehtm);      printf("\n");
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);      fprintf(ficlog,"\n");
     exit(0);    }
   }    */
   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");    free_matrix(a,1,npar,1,npar);
   }    free_matrix(y,1,npar,1,npar);
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
   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");    free_matrix(hess,1,npar,1,npar);
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)  }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  
   fprintf(ficresvij,"\n");  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   xp=vector(1,npar);  {
   dnewm=matrix(1,nlstate,1,npar);    int i;
   doldm=matrix(1,nlstate,1,nlstate);    int l=1, lmax=20;
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);    double k1,k2;
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    double p2[NPARMAX+1];
     double res;
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   gpp=vector(nlstate+1,nlstate+ndeath);    double fx;
   gmp=vector(nlstate+1,nlstate+ndeath);    int k=0,kmax=10;
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    double l1;
    
   if(estepm < stepm){    fx=func(x);
     printf ("Problem %d lower than %d\n",estepm, stepm);    for (i=1;i<=npar;i++) p2[i]=x[i];
   }    for(l=0 ; l <=lmax; l++){
   else  hstepm=estepm;        l1=pow(10,l);
   /* For example we decided to compute the life expectancy with the smallest unit */      delts=delt;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for(k=1 ; k <kmax; k=k+1){
      nhstepm is the number of hstepm from age to agelim        delt = delta*(l1*k);
      nstepm is the number of stepm from age to agelin.        p2[theta]=x[theta] +delt;
      Look at hpijx to understand the reason of that which relies in memory size        k1=func(p2)-fx;
      and note for a fixed period like k years */        p2[theta]=x[theta]-delt;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        k2=func(p2)-fx;
      survival function given by stepm (the optimization length). Unfortunately it        /*res= (k1-2.0*fx+k2)/delt/delt; */
      means that if the survival funtion is printed only each two years of age and if        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
      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.  #ifdef DEBUG
   */        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        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);
   agelim = AGESUP;  #endif
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          k=kmax;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     gp=matrix(0,nhstepm,1,nlstate);          k=kmax; l=lmax*10.;
     gm=matrix(0,nhstepm,1,nlstate);        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
     for(theta=1; theta <=npar; theta++){        }
       for(i=1; i<=npar; i++){ /* Computes gradient */      }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }    delti[theta]=delts;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      return res; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    
   }
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
           prlim[i][i]=probs[(int)age][i][ij];  {
       }    int i;
      int l=1, l1, lmax=20;
       for(j=1; j<= nlstate; j++){    double k1,k2,k3,k4,res,fx;
         for(h=0; h<=nhstepm; h++){    double p2[NPARMAX+1];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    int k;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }    fx=func(x);
       }    for (k=1; k<=2; k++) {
       /* This for computing forces of mortality (h=1)as a weighted average */      for (i=1;i<=npar;i++) p2[i]=x[i];
       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];      k1=func(p2)-fx;
       }        
       /* end force of mortality */      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(i=1; i<=npar; i++) /* Computes gradient */      k2=func(p2)-fx;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        p2[thetai]=x[thetai]-delti[thetai]/k;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k3=func(p2)-fx;
       if (popbased==1) {    
         for(i=1; i<=nlstate;i++)      p2[thetai]=x[thetai]-delti[thetai]/k;
           prlim[i][i]=probs[(int)age][i][ij];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       }      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       for(j=1; j<= nlstate; j++){  #ifdef DEBUG
         for(h=0; h<=nhstepm; h++){      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, gm[h][j]=0.;i<=nlstate;i++)      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);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  #endif
         }    }
       }    return res;
       /* This for computing force of mortality (h=1)as a weighted average */  }
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){  
         for(i=1; i<= nlstate; i++)  /************** Inverse of matrix **************/
           gmp[j] += prlim[i][i]*p3mat[i][j][1];  void ludcmp(double **a, int n, int *indx, double *d) 
       }      { 
       /* end force of mortality */    int i,imax,j,k; 
     double big,dum,sum,temp; 
       for(j=1; j<= nlstate; j++) /* vareij */    double *vv; 
         for(h=0; h<=nhstepm; h++){   
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    vv=vector(1,n); 
         }    *d=1.0; 
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */    for (i=1;i<=n;i++) { 
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];      big=0.0; 
       }      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
     } /* End theta */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */    } 
     for (j=1;j<=n;j++) { 
     for(h=0; h<=nhstepm; h++) /* veij */      for (i=1;i<j;i++) { 
       for(j=1; j<=nlstate;j++)        sum=a[i][j]; 
         for(theta=1; theta <=npar; theta++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           trgradg[h][j][theta]=gradg[h][theta][j];        a[i][j]=sum; 
       } 
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */      big=0.0; 
       for(theta=1; theta <=npar; theta++)      for (i=j;i<=n;i++) { 
         trgradgp[j][theta]=gradgp[theta][j];        sum=a[i][j]; 
         for (k=1;k<j;k++) 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          sum -= a[i][k]*a[k][j]; 
     for(i=1;i<=nlstate;i++)        a[i][j]=sum; 
       for(j=1;j<=nlstate;j++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         vareij[i][j][(int)age] =0.;          big=dum; 
           imax=i; 
     for(h=0;h<=nhstepm;h++){        } 
       for(k=0;k<=nhstepm;k++){      } 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      if (j != imax) { 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        for (k=1;k<=n;k++) { 
         for(i=1;i<=nlstate;i++)          dum=a[imax][k]; 
           for(j=1;j<=nlstate;j++)          a[imax][k]=a[j][k]; 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          a[j][k]=dum; 
       }        } 
     }        *d = -(*d); 
         vv[imax]=vv[j]; 
     /* pptj */      } 
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);      indx[j]=imax; 
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     for(j=nlstate+1;j<=nlstate+ndeath;j++)      if (j != n) { 
       for(i=nlstate+1;i<=nlstate+ndeath;i++)        dum=1.0/(a[j][j]); 
         varppt[j][i]=doldmp[j][i];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     /* end ppptj */      } 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);      } 
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    free_vector(vv,1,n);  /* Doesn't work */
    ;
     if (popbased==1) {  } 
       for(i=1; i<=nlstate;i++)  
         prlim[i][i]=probs[(int)age][i][ij];  void lubksb(double **a, int n, int *indx, double b[]) 
     }  { 
        int i,ii=0,ip,j; 
     /* This for computing force of mortality (h=1)as a weighted average */    double sum; 
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){   
       for(i=1; i<= nlstate; i++)    for (i=1;i<=n;i++) { 
         gmp[j] += prlim[i][i]*p3mat[i][j][1];      ip=indx[i]; 
     }          sum=b[ip]; 
     /* end force of mortality */      b[ip]=b[i]; 
       if (ii) 
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){      else if (sum) ii=i; 
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));      b[i]=sum; 
       for(i=1; i<=nlstate;i++){    } 
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);    for (i=n;i>=1;i--) { 
       }      sum=b[i]; 
     }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     fprintf(ficresprobmorprev,"\n");      b[i]=sum/a[i][i]; 
     } 
     fprintf(ficresvij,"%.0f ",age );  } 
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  void pstamp(FILE *fichier)
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  {
       }    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     fprintf(ficresvij,"\n");  }
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);  /************ Frequencies ********************/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  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[])
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  {  /* Some frequencies */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
   } /* End age */    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   free_vector(gpp,nlstate+1,nlstate+ndeath);    int first;
   free_vector(gmp,nlstate+1,nlstate+ndeath);    double ***freq; /* Frequencies */
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);    double *pp, **prop;
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");    char fileresp[FILENAMELENGTH];
   /* 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)\";");    pp=vector(1,nlstate);
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);    strcpy(fileresp,"p");
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);    strcat(fileresp,fileres);
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   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);      printf("Problem with prevalence resultfile: %s\n", fileresp);
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
   free_vector(xp,1,npar);    }
   free_matrix(doldm,1,nlstate,1,nlstate);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   free_matrix(dnewm,1,nlstate,1,npar);    j1=0;
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);    j=cptcoveff;
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   fclose(ficresprobmorprev);  
   fclose(ficgp);    first=1;
   fclose(fichtm);  
     for(k1=1; k1<=j;k1++){
 }      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
 /************ Variance of prevlim ******************/        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 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)          scanf("%d", i);*/
 {        for (i=-5; i<=nlstate+ndeath; i++)  
   /* Variance of prevalence limit */          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            for(m=iagemin; m <= iagemax+3; m++)
   double **newm;              freq[i][jk][m]=0;
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm;      for (i=1; i<=nlstate; i++)  
   int k, cptcode;        for(m=iagemin; m <= iagemax+3; m++)
   double *xp;          prop[i][m]=0;
   double *gp, *gm;        
   double **gradg, **trgradg;        dateintsum=0;
   double age,agelim;        k2cpt=0;
   int theta;        for (i=1; i<=imx; i++) {
              bool=1;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");          if  (cptcovn>0) {
   fprintf(ficresvpl,"# Age");            for (z1=1; z1<=cptcoveff; z1++) 
   for(i=1; i<=nlstate;i++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fprintf(ficresvpl," %1d-%1d",i,i);                bool=0;
   fprintf(ficresvpl,"\n");          }
           if (bool==1){
   xp=vector(1,npar);            for(m=firstpass; m<=lastpass; m++){
   dnewm=matrix(1,nlstate,1,npar);              k2=anint[m][i]+(mint[m][i]/12.);
   doldm=matrix(1,nlstate,1,nlstate);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                  if(agev[m][i]==0) agev[m][i]=iagemax+1;
   hstepm=1*YEARM; /* Every year of age */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   agelim = AGESUP;                if (m<lastpass) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     if (stepm >= YEARM) hstepm=1;                }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                
     gradg=matrix(1,npar,1,nlstate);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     gp=vector(1,nlstate);                  dateintsum=dateintsum+k2;
     gm=vector(1,nlstate);                  k2cpt++;
                 }
     for(theta=1; theta <=npar; theta++){                /*}*/
       for(i=1; i<=npar; i++){ /* Computes gradient */            }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
       }        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);         
       for(i=1;i<=nlstate;i++)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         gp[i] = prlim[i][i];        pstamp(ficresp);
            if  (cptcovn>0) {
       for(i=1; i<=npar; i++) /* Computes gradient */          fprintf(ficresp, "\n#********** Variable "); 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          fprintf(ficresp, "**********\n#");
       for(i=1;i<=nlstate;i++)        }
         gm[i] = prlim[i][i];        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       for(i=1;i<=nlstate;i++)        fprintf(ficresp, "\n");
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        
     } /* End theta */        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
     trgradg =matrix(1,nlstate,1,npar);            fprintf(ficlog,"Total");
           }else{
     for(j=1; j<=nlstate;j++)            if(first==1){
       for(theta=1; theta <=npar; theta++)              first=0;
         trgradg[j][theta]=gradg[theta][j];              printf("See log file for details...\n");
             }
     for(i=1;i<=nlstate;i++)            fprintf(ficlog,"Age %d", i);
       varpl[i][(int)age] =0.;          }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          for(jk=1; jk <=nlstate ; jk++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for(i=1;i<=nlstate;i++)              pp[jk] += freq[jk][m][i]; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          }
           for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficresvpl,"%.0f ",age );            for(m=-1, pos=0; m <=0 ; m++)
     for(i=1; i<=nlstate;i++)              pos += freq[jk][m][i];
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            if(pp[jk]>=1.e-10){
     fprintf(ficresvpl,"\n");              if(first==1){
     free_vector(gp,1,nlstate);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     free_vector(gm,1,nlstate);              }
     free_matrix(gradg,1,npar,1,nlstate);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     free_matrix(trgradg,1,nlstate,1,npar);            }else{
   } /* End age */              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   free_vector(xp,1,npar);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   free_matrix(doldm,1,nlstate,1,npar);            }
   free_matrix(dnewm,1,nlstate,1,nlstate);          }
   
 }          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 /************ Variance of one-step probabilities  ******************/              pp[jk] += freq[jk][m][i];
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          }       
 {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   int i, j=0,  i1, k1, l1, t, tj;            pos += pp[jk];
   int k2, l2, j1,  z1;            posprop += prop[jk][i];
   int k=0,l, cptcode;          }
   int first=1, first1;          for(jk=1; jk <=nlstate ; jk++){
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;            if(pos>=1.e-5){
   double **dnewm,**doldm;              if(first==1)
   double *xp;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double *gp, *gm;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double **gradg, **trgradg;            }else{
   double **mu;              if(first==1)
   double age,agelim, cov[NCOVMAX];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   int theta;            }
   char fileresprob[FILENAMELENGTH];            if( i <= iagemax){
   char fileresprobcov[FILENAMELENGTH];              if(pos>=1.e-5){
   char fileresprobcor[FILENAMELENGTH];                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
   double ***varpij;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
   strcpy(fileresprob,"prob");              else
   strcat(fileresprob,fileres);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            }
     printf("Problem with resultfile: %s\n", fileresprob);          }
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);          
   }          for(jk=-1; jk <=nlstate+ndeath; jk++)
   strcpy(fileresprobcov,"probcov");            for(m=-1; m <=nlstate+ndeath; m++)
   strcat(fileresprobcov,fileres);              if(freq[jk][m][i] !=0 ) {
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {              if(first==1)
     printf("Problem with resultfile: %s\n", fileresprobcov);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   }              }
   strcpy(fileresprobcor,"probcor");          if(i <= iagemax)
   strcat(fileresprobcor,fileres);            fprintf(ficresp,"\n");
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {          if(first==1)
     printf("Problem with resultfile: %s\n", fileresprobcor);            printf("Others in log...\n");
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);          fprintf(ficlog,"\n");
   }        }
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      }
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    }
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    dateintmean=dateintsum/k2cpt; 
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);   
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    fclose(ficresp);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
      free_vector(pp,1,nlstate);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   fprintf(ficresprob,"# Age");    /* End of Freq */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");  }
   fprintf(ficresprobcov,"# Age");  
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");  /************ Prevalence ********************/
   fprintf(ficresprobcov,"# Age");  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)
   {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   for(i=1; i<=nlstate;i++)       in each health status at the date of interview (if between dateprev1 and dateprev2).
     for(j=1; j<=(nlstate+ndeath);j++){       We still use firstpass and lastpass as another selection.
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);   
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     }      double ***freq; /* Frequencies */
   fprintf(ficresprob,"\n");    double *pp, **prop;
   fprintf(ficresprobcov,"\n");    double pos,posprop; 
   fprintf(ficresprobcor,"\n");    double  y2; /* in fractional years */
   xp=vector(1,npar);    int iagemin, iagemax;
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    iagemin= (int) agemin;
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    iagemax= (int) agemax;
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    /*pp=vector(1,nlstate);*/
   first=1;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    j1=0;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    
     exit(0);    j=cptcoveff;
   }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   else{    
     fprintf(ficgp,"\n# Routine varprob");    for(k1=1; k1<=j;k1++){
   }      for(i1=1; i1<=ncodemax[k1];i1++){
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {        j1++;
     printf("Problem with html file: %s\n", optionfilehtm);        
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);        for (i=1; i<=nlstate; i++)  
     exit(0);          for(m=iagemin; m <= iagemax+3; m++)
   }            prop[i][m]=0.0;
   else{       
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");        for (i=1; i<=imx; i++) { /* Each individual */
     fprintf(fichtm,"\n");          bool=1;
           if  (cptcovn>0) {
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");            for (z1=1; z1<=cptcoveff; z1++) 
     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");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     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");                bool=0;
           } 
   }          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   cov[1]=1;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   tj=cptcoveff;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   j1=0;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   for(t=1; t<=tj;t++){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     for(i1=1; i1<=ncodemax[t];i1++){                  /*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]]);*/
       j1++;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                        prop[s[m][i]][iagemax+3] += weight[i]; 
       if  (cptcovn>0) {                } 
         fprintf(ficresprob, "\n#********** Variable ");              }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            } /* end selection of waves */
         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]]);        for(i=iagemin; i <= iagemax+3; i++){  
         fprintf(ficresprobcov, "**********\n#");          
                  for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         fprintf(ficgp, "\n#********** Variable ");            posprop += prop[jk][i]; 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          } 
         fprintf(ficgp, "**********\n#");  
                  for(jk=1; jk <=nlstate ; jk++){     
                    if( i <=  iagemax){ 
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");              if(posprop>=1.e-5){ 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                probs[i][jk][j1]= prop[jk][i]/posprop;
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");              } 
                    } 
         fprintf(ficresprobcor, "\n#********** Variable ");              }/* end jk */ 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        }/* end i */ 
         fprintf(ficgp, "**********\n#");          } /* end i1 */
       }    } /* end k1 */
          
       for (age=bage; age<=fage; age ++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         cov[2]=age;    /*free_vector(pp,1,nlstate);*/
         for (k=1; k<=cptcovn;k++) {    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  }  /* End of prevalence */
         }  
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /************* Waves Concatenation ***************/
         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]]];  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)
          {
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);       Death is a valid wave (if date is known).
         gp=vector(1,(nlstate)*(nlstate+ndeath));       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         gm=vector(1,(nlstate)*(nlstate+ndeath));       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           and mw[mi+1][i]. dh depends on stepm.
         for(theta=1; theta <=npar; theta++){       */
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    int i, mi, m;
              /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);       double sum=0., jmean=0.;*/
              int first;
           k=0;    int j, k=0,jk, ju, jl;
           for(i=1; i<= (nlstate); i++){    double sum=0.;
             for(j=1; j<=(nlstate+ndeath);j++){    first=0;
               k=k+1;    jmin=1e+5;
               gp[k]=pmmij[i][j];    jmax=-1;
             }    jmean=0.;
           }    for(i=1; i<=imx; i++){
                mi=0;
           for(i=1; i<=npar; i++)      m=firstpass;
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      while(s[m][i] <= nlstate){
            if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          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++;
               gm[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<= (nlstate)*(nlstate+ndeath); i++)           /* Only death is a correct wave */
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          mw[mi][i]=m;
         }      }
   
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)      wav[i]=mi;
           for(theta=1; theta <=npar; theta++)      if(mi==0){
             trgradg[j][theta]=gradg[theta][j];        nbwarn++;
                if(first==0){
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);          first=1;
                }
         pmij(pmmij,cov,ncovmodel,x,nlstate);        if(first==1){
                  fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         k=0;        }
         for(i=1; i<=(nlstate); i++){      } /* end mi==0 */
           for(j=1; j<=(nlstate+ndeath);j++){    } /* End individuals */
             k=k+1;  
             mu[k][(int) age]=pmmij[i][j];    for(i=1; i<=imx; i++){
           }      for(mi=1; mi<wav[i];mi++){
         }        if (stepm <=0)
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)          dh[mi][i]=1;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)        else{
             varpij[i][j][(int)age] = doldm[i][j];          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
         /*printf("\n%d ",(int)age);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){              if(j==0) j=1;  /* Survives at least one month after exam */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              else if(j<0){
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));                nberr++;
      }*/                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 j=1; /* Temporary Dangerous patch */
         fprintf(ficresprob,"\n%d ",(int)age);                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(ficresprobcov,"\n%d ",(int)age);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         fprintf(ficresprobcor,"\n%d ",(int)age);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)              k=k+1;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));              if (j >= jmax){
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){                jmax=j;
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);                ijmax=i;
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);              }
         }              if (j <= jmin){
         i=0;                jmin=j;
         for (k=1; k<=(nlstate);k++){                ijmin=i;
           for (l=1; l<=(nlstate+ndeath);l++){              }
             i=i++;              sum=sum+j;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             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]));          else{
             }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           }  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
         }/* end of loop for state */  
       } /* end of loop for age */            k=k+1;
             if (j >= jmax) {
       /* Confidence intervalle of pij  */              jmax=j;
       /*              ijmax=i;
       fprintf(ficgp,"\nset noparametric;unset label");            }
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");            else if (j <= jmin){
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");              jmin=j;
       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);              ijmin=i;
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);            }
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);            /*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]);*/
       */            if(j<0){
               nberr++;
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/              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]);
       first1=1;              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]);
       for (k2=1; k2<=(nlstate);k2++){            }
         for (l2=1; l2<=(nlstate+ndeath);l2++){            sum=sum+j;
           if(l2==k2) continue;          }
           j=(k2-1)*(nlstate+ndeath)+l2;          jk= j/stepm;
           for (k1=1; k1<=(nlstate);k1++){          jl= j -jk*stepm;
             for (l1=1; l1<=(nlstate+ndeath);l1++){          ju= j -(jk+1)*stepm;
               if(l1==k1) continue;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
               i=(k1-1)*(nlstate+ndeath)+l1;            if(jl==0){
               if(i<=j) continue;              dh[mi][i]=jk;
               for (age=bage; age<=fage; age ++){              bh[mi][i]=0;
                 if ((int)age %5==0){            }else{ /* We want a negative bias in order to only have interpolation ie
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;                    * at the price of an extra matrix product in likelihood */
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;              dh[mi][i]=jk+1;
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;              bh[mi][i]=ju;
                   mu1=mu[i][(int) age]/stepm*YEARM ;            }
                   mu2=mu[j][(int) age]/stepm*YEARM;          }else{
                   c12=cv12/sqrt(v1*v2);            if(jl <= -ju){
                   /* Computing eigen value of matrix of covariance */              dh[mi][i]=jk;
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;              bh[mi][i]=jl;       /* bias is positive if real duration
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                                   * is higher than the multiple of stepm and negative otherwise.
                   /* Eigen vectors */                                   */
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));            }
                   /*v21=sqrt(1.-v11*v11); *//* error */            else{
                   v21=(lc1-v1)/cv12*v11;              dh[mi][i]=jk+1;
                   v12=-v21;              bh[mi][i]=ju;
                   v22=v11;            }
                   tnalp=v21/v11;            if(dh[mi][i]==0){
                   if(first1==1){              dh[mi][i]=1; /* At least one step */
                     first1=0;              bh[mi][i]=ju; /* At least one step */
                     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(" 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);*/
                   }            }
                   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);          } /* end if mle */
                   /*printf(fignu*/        }
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */      } /* end wave */
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */    }
                   if(first==1){    jmean=sum/k;
                     first=0;    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);
                     fprintf(ficgp,"\nset parametric;unset label");    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);
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);   }
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);  /*********** Tricode ****************************/
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);  void tricode(int *Tvar, int **nbcode, int imx)
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);  {
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);    
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    int Ndum[20],ij=1, k, j, i, maxncov=19;
                     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",\    int cptcode=0;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\    cptcoveff=0; 
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));   
                   }else{    for (k=0; k<maxncov; k++) Ndum[k]=0;
                     first=0;    for (k=1; k<=7; k++) ncodemax[k]=0;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);  
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\                                 modality*/ 
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                   }/* if first */        Ndum[ij]++; /*store the modality */
                 } /* age mod 5 */        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
               } /* end loop age */        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);                                         Tvar[j]. If V=sex and male is 0 and 
               first=1;                                         female is 1, then  cptcode=1.*/
             } /*l12 */      }
           } /* k12 */  
         } /*l1 */      for (i=0; i<=cptcode; i++) {
       }/* k1 */        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 */
     } /* loop covariates */      }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      ij=1; 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      for (i=1; i<=ncodemax[j]; i++) {
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);        for (k=0; k<= maxncov; k++) {
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          if (Ndum[k] != 0) {
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            nbcode[Tvar[j]][ij]=k; 
   }            /* 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; */
   free_vector(xp,1,npar);            
   fclose(ficresprob);            ij++;
   fclose(ficresprobcov);          }
   fclose(ficresprobcor);          if (ij > ncodemax[j]) break; 
   fclose(ficgp);        }  
   fclose(fichtm);      } 
 }    }  
   
    for (k=0; k< maxncov; k++) Ndum[k]=0;
 /******************* Printing html file ***********/  
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \   for (i=1; i<=ncovmodel-2; i++) { 
                   int lastpass, int stepm, int weightopt, char model[],\     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\     ij=Tvar[i];
                   int popforecast, int estepm ,\     Ndum[ij]++;
                   double jprev1, double mprev1,double anprev1, \   }
                   double jprev2, double mprev2,double anprev2){  
   int jj1, k1, i1, cpt;   ij=1;
   /*char optionfilehtm[FILENAMELENGTH];*/   for (i=1; i<= maxncov; i++) {
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {     if((Ndum[i]!=0) && (i<=ncovcol)){
     printf("Problem with %s \n",optionfilehtm), exit(0);       Tvaraff[ij]=i; /*For printing */
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);       ij++;
   }     }
    }
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n   
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n   cptcoveff=ij-1; /*Number of simple covariates*/
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n  }
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n  
  - Life expectancies by age and initial health status (estepm=%2d months):  /*********** Health Expectancies ****************/
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  {
     /* Health expectancies, no variances */
  m=cptcoveff;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
  jj1=0;    double ***p3mat;
  for(k1=1; k1<=m;k1++){    double eip;
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;    pstamp(ficreseij);
      if (cptcovn > 0) {    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    fprintf(ficreseij,"# Age");
        for (cpt=1; cpt<=cptcoveff;cpt++)    for(i=1; i<=nlstate;i++){
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      for(j=1; j<=nlstate;j++){
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        fprintf(ficreseij," e%1d%1d ",i,j);
      }      }
      /* Pij */      fprintf(ficreseij," e%1d. ",i);
      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);        fprintf(ficreseij,"\n");
      /* Quasi-incidences */  
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    if(estepm < stepm){
        /* Stable prevalence in each health state */      printf ("Problem %d lower than %d\n",estepm, stepm);
        for(cpt=1; cpt<nlstate;cpt++){    }
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    else  hstepm=estepm;   
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    /* We compute the life expectancy from trapezoids spaced every estepm months
        }     * This is mainly to measure the difference between two models: for example
      for(cpt=1; cpt<=nlstate;cpt++) {     * if stepm=24 months pijx are given only every 2 years and by summing them
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>     * we are calculating an estimate of the Life Expectancy assuming a linear 
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);     * progression in between and thus overestimating or underestimating according
      }     * to the curvature of the survival function. If, for the same date, we 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and     * estimate the model with stepm=1 month, we can keep estepm to 24 months
 health expectancies in states (1) and (2): e%s%d.png<br>     * to compare the new estimate of Life expectancy with the same linear 
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     * hypothesis. A more precise result, taking into account a more precise
    } /* end i1 */     * curvature will be obtained if estepm is as small as stepm. */
  }/* End k1 */  
  fprintf(fichtm,"</ul>");    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n       nstepm is the number of stepm from age to agelin. 
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n       Look at hpijx to understand the reason of that which relies in memory size
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n       and note for a fixed period like estepm months */
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n       survival function given by stepm (the optimization length). Unfortunately it
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n       means that if the survival funtion is printed only each two years of age and if
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  - 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);       results. So we changed our mind and took the option of the best precision.
     */
  if(popforecast==1) fprintf(fichtm,"\n    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  - 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    agelim=AGESUP;
         <br>",fileres,fileres,fileres,fileres);    /* If stepm=6 months */
  else      /* Computed by stepm unit matrices, product of hstepm matrices, stored
    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);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");      
   /* nhstepm age range expressed in number of stepm */
  m=cptcoveff;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
  jj1=0;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  for(k1=1; k1<=m;k1++){    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;    for (age=bage; age<=fage; age ++){ 
      if (cptcovn > 0) {      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        for (cpt=1; cpt<=cptcoveff;cpt++)      /* if (stepm >= YEARM) hstepm=1;*/
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
      }      /* If stepm=6 months */
      for(cpt=1; cpt<=nlstate;cpt++) {      /* Computed by stepm unit matrices, product of hstepma matrices, stored
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
 interval) in state (%d): v%s%d%d.png <br>      
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
      }      
    } /* end i1 */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  }/* End k1 */      
  fprintf(fichtm,"</ul>");      printf("%d|",(int)age);fflush(stdout);
 fclose(fichtm);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 }      
       /* Computing expectancies */
 /******************* Gnuplot file **************/      for(i=1; i<=nlstate;i++)
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   int ng;            
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            /* 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("Problem with file %s",optionfilegnuplot);  
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);          }
   }  
       fprintf(ficreseij,"%3.0f",age );
 #ifdef windows      for(i=1; i<=nlstate;i++){
     fprintf(ficgp,"cd \"%s\" \n",pathc);        eip=0;
 #endif        for(j=1; j<=nlstate;j++){
 m=pow(2,cptcoveff);          eip +=eij[i][j][(int)age];
            fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
  /* 1eme*/        }
   for (cpt=1; cpt<= nlstate ; cpt ++) {        fprintf(ficreseij,"%9.4f", eip );
    for (k1=1; k1<= m ; k1 ++) {      }
       fprintf(ficreseij,"\n");
 #ifdef windows      
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    }
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #endif    printf("\n");
 #ifdef unix    fprintf(ficlog,"\n");
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  }
 #endif  
   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  {
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* Covariances of health expectancies eij and of total life expectancies according
 }     to initial status i, ei. .
     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 ++) {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    int nhstepma, nstepma; /* Decreasing with age */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double age, agelim, hf;
 }    double ***p3matp, ***p3matm, ***varhe;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    double **dnewm,**doldm;
      for (i=1; i<= nlstate ; i ++) {    double *xp, *xm;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double **gp, **gm;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double ***gradg, ***trgradg;
 }      int theta;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix    double eip, vip;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");  
 #endif    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
    }    xp=vector(1,npar);
   }    xm=vector(1,npar);
   /*2 eme*/    dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   for (k1=1; k1<= m ; k1 ++) {    
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    pstamp(ficresstdeij);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
        fprintf(ficresstdeij,"# Age");
     for (i=1; i<= nlstate+1 ; i ++) {    for(i=1; i<=nlstate;i++){
       k=2*i;      for(j=1; j<=nlstate;j++)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       for (j=1; j<= nlstate+1 ; j ++) {      fprintf(ficresstdeij," e%1d. ",i);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficresstdeij,"\n");
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    pstamp(ficrescveij);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficrescveij,"# Age");
       for (j=1; j<= nlstate+1 ; j ++) {    for(i=1; i<=nlstate;i++)
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for(j=1; j<=nlstate;j++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");        cptj= (j-1)*nlstate+i;
 }          for(i2=1; i2<=nlstate;i2++)
       fprintf(ficgp,"\" t\"\" w l 0,");          for(j2=1; j2<=nlstate;j2++){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            cptj2= (j2-1)*nlstate+i2;
       for (j=1; j<= nlstate+1 ; j ++) {            if(cptj2 <= cptj)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }        }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    fprintf(ficrescveij,"\n");
       else fprintf(ficgp,"\" t\"\" w l 0,");    
     }    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   /*3eme*/    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   for (k1=1; k1<= m ; k1 ++) {     * This is mainly to measure the difference between two models: for example
     for (cpt=1; cpt<= nlstate ; cpt ++) {     * if stepm=24 months pijx are given only every 2 years and by summing them
       k=2+nlstate*(2*cpt-2);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);     * progression in between and thus overestimating or underestimating according
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);     * to the curvature of the survival function. If, for the same date, we 
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");     * to compare the new estimate of Life expectancy with the same linear 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);     * hypothesis. A more precise result, taking into account a more precise
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);     * curvature will be obtained if estepm is as small as stepm. */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 */       nhstepm is the number of hstepm from age to agelim 
       for (i=1; i< nlstate ; i ++) {       nstepm is the number of stepm from age to agelin. 
         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);       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
       }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     }       survival function given by stepm (the optimization length). Unfortunately it
   }       means that if the survival funtion is printed only each two years of age and if
         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   /* CV preval stat */       results. So we changed our mind and took the option of the best precision.
     for (k1=1; k1<= m ; k1 ++) {    */
     for (cpt=1; cpt<nlstate ; cpt ++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       k=3;  
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    /* If stepm=6 months */
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
       for (i=1; i< nlstate ; i ++)    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
         fprintf(ficgp,"+$%d",k+i+1);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    /* if (stepm >= YEARM) hstepm=1;*/
          nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       l=3+(nlstate+ndeath)*cpt;    
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for (i=1; i< nlstate ; i ++) {    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         l=3+(nlstate+ndeath)*cpt;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         fprintf(ficgp,"+$%d",l+i+1);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       }    gp=matrix(0,nhstepm,1,nlstate*nlstate);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     }  
   }      for (age=bage; age<=fage; age ++){ 
        nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   /* proba elementaires */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
    for(i=1,jk=1; i <=nlstate; i++){      /* if (stepm >= YEARM) hstepm=1;*/
     for(k=1; k <=(nlstate+ndeath); k++){      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){      /* If stepm=6 months */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           jk++;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           fprintf(ficgp,"\n");      
         }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       }  
     }      /* Computing  Variances of health expectancies */
    }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/      for(theta=1; theta <=npar; theta++){
      for(jk=1; jk <=m; jk++) {        for(i=1; i<=npar; i++){ 
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        if (ng==2)          xm[i] = x[i] - (i==theta ?delti[theta]:0);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");        }
        else        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
          fprintf(ficgp,"\nset title \"Probability\"\n");        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    
        i=1;        for(j=1; j<= nlstate; j++){
        for(k2=1; k2<=nlstate; k2++) {          for(i=1; i<=nlstate; i++){
          k3=i;            for(h=0; h<=nhstepm-1; h++){
          for(k=1; k<=(nlstate+ndeath); k++) {              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
            if (k != k2){              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
              if(ng==2)            }
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          }
              else        }
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);       
              ij=1;        for(ij=1; ij<= nlstate*nlstate; ij++)
              for(j=3; j <=ncovmodel; j++) {          for(h=0; h<=nhstepm-1; h++){
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          }
                  ij++;      }/* End theta */
                }      
                else      
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for(h=0; h<=nhstepm-1; h++)
              }        for(j=1; j<=nlstate*nlstate;j++)
              fprintf(ficgp,")/(1");          for(theta=1; theta <=npar; theta++)
                          trgradg[h][j][theta]=gradg[h][theta][j];
              for(k1=1; k1 <=nlstate; k1++){        
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
                ij=1;       for(ij=1;ij<=nlstate*nlstate;ij++)
                for(j=3; j <=ncovmodel; j++){        for(ji=1;ji<=nlstate*nlstate;ji++)
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          varhe[ij][ji][(int)age] =0.;
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
                    ij++;       printf("%d|",(int)age);fflush(stdout);
                  }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                  else       for(h=0;h<=nhstepm-1;h++){
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for(k=0;k<=nhstepm-1;k++){
                }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                fprintf(ficgp,")");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
              }          for(ij=1;ij<=nlstate*nlstate;ij++)
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);            for(ji=1;ji<=nlstate*nlstate;ji++)
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
              i=i+ncovmodel;        }
            }      }
          } /* end k */  
        } /* end k2 */      /* Computing expectancies */
      } /* end jk */      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
    } /* end ng */      for(i=1; i<=nlstate;i++)
    fclose(ficgp);        for(j=1; j<=nlstate;j++)
 }  /* end gnuplot */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
 /*************** Moving average **************/            /* 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]);*/
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  
           }
   int i, cpt, cptcod;  
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)      fprintf(ficresstdeij,"%3.0f",age );
       for (i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        eip=0.;
           mobaverage[(int)agedeb][i][cptcod]=0.;        vip=0.;
            for(j=1; j<=nlstate;j++){
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          eip += eij[i][j][(int)age];
       for (i=1; i<=nlstate;i++){          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           for (cpt=0;cpt<=4;cpt++){          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        }
           }        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      }
         }      fprintf(ficresstdeij,"\n");
       }  
     }      fprintf(ficrescveij,"%3.0f",age );
          for(i=1; i<=nlstate;i++)
 }        for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
 /************** Forecasting ******************/            for(j2=1; j2<=nlstate;j2++){
 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){              cptj2= (j2-1)*nlstate+i2;
                if(cptj2 <= cptj)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   int *popage;            }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        }
   double *popeffectif,*popcount;      fprintf(ficrescveij,"\n");
   double ***p3mat;     
   char fileresf[FILENAMELENGTH];    }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
  agelim=AGESUP;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      printf("\n");
   strcpy(fileresf,"f");    fprintf(ficlog,"\n");
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {    free_vector(xm,1,npar);
     printf("Problem with forecast resultfile: %s\n", fileresf);    free_vector(xp,1,npar);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);  }
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   if (mobilav==1) {  {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* Variance of health expectancies */
     movingaverage(agedeb, fage, ageminpar, mobaverage);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   }    /* double **newm;*/
     double **dnewm,**doldm;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double **dnewmp,**doldmp;
   if (stepm<=12) stepsize=1;    int i, j, nhstepm, hstepm, h, nstepm ;
      int k, cptcode;
   agelim=AGESUP;    double *xp;
      double **gp, **gm;  /* for var eij */
   hstepm=1;    double ***gradg, ***trgradg; /*for var eij */
   hstepm=hstepm/stepm;    double **gradgp, **trgradgp; /* for var p point j */
   yp1=modf(dateintmean,&yp);    double *gpp, *gmp; /* for var p point j */
   anprojmean=yp;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   yp2=modf((yp1*12),&yp);    double ***p3mat;
   mprojmean=yp;    double age,agelim, hf;
   yp1=modf((yp2*30.5),&yp);    double ***mobaverage;
   jprojmean=yp;    int theta;
   if(jprojmean==0) jprojmean=1;    char digit[4];
   if(mprojmean==0) jprojmean=1;    char digitp[25];
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    char fileresprobmorprev[FILENAMELENGTH];
    
   for(cptcov=1;cptcov<=i2;cptcov++){    if(popbased==1){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      if(mobilav!=0)
       k=k+1;        strcpy(digitp,"-populbased-mobilav-");
       fprintf(ficresf,"\n#******");      else strcpy(digitp,"-populbased-nomobil-");
       for(j=1;j<=cptcoveff;j++) {    }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    else 
       }      strcpy(digitp,"-stablbased-");
       fprintf(ficresf,"******\n");  
       fprintf(ficresf,"# StartingAge FinalAge");    if (mobilav!=0) {
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      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);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         fprintf(ficresf,"\n");      }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      }
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    strcpy(fileresprobmorprev,"prmorprev"); 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    sprintf(digit,"%-d",ij);
           nhstepm = nhstepm/hstepm;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
              strcat(fileresprobmorprev,digit); /* Tvar to be done */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           oldm=oldms;savm=savms;    strcat(fileresprobmorprev,fileres);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
              printf("Problem with resultfile: %s\n", fileresprobmorprev);
           for (h=0; h<=nhstepm; h++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
             if (h==(int) (calagedate+YEARM*cpt)) {    }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             }   
             for(j=1; j<=nlstate+ndeath;j++) {    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
               kk1=0.;kk2=0;    pstamp(ficresprobmorprev);
               for(i=1; i<=nlstate;i++) {                  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);
                 if (mobilav==1)    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                 else {      fprintf(ficresprobmorprev," p.%-d SE",j);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for(i=1; i<=nlstate;i++)
                 }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
                    }  
               }    fprintf(ficresprobmorprev,"\n");
               if (h==(int)(calagedate+12*cpt)){    fprintf(ficgp,"\n# Routine varevsij");
                 fprintf(ficresf," %.3f", kk1);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
                            fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
               }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
             }  /*   } */
           }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    pstamp(ficresvij);
         }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
       }    if(popbased==1)
     }      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
   }    else
              fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
   fclose(ficresf);      for(j=1; j<=nlstate;j++)
 }        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
 /************** Forecasting ******************/    fprintf(ficresvij,"\n");
 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){  
      xp=vector(1,npar);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    dnewm=matrix(1,nlstate,1,npar);
   int *popage;    doldm=matrix(1,nlstate,1,nlstate);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   double *popeffectif,*popcount;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    gmp=vector(nlstate+1,nlstate+ndeath);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   agelim=AGESUP;    
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    }
      else  hstepm=estepm;   
      /* For example we decided to compute the life expectancy with the smallest unit */
   strcpy(filerespop,"pop");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   strcat(filerespop,fileres);       nhstepm is the number of hstepm from age to agelim 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {       nstepm is the number of stepm from age to agelin. 
     printf("Problem with forecast resultfile: %s\n", filerespop);       Look at hpijx to understand the reason of that which relies in memory size
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);       and note for a fixed period like k years */
   }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   printf("Computing forecasting: result on file '%s' \n", filerespop);       survival function given by stepm (the optimization length). Unfortunately it
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);       means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       results. So we changed our mind and took the option of the best precision.
     */
   if (mobilav==1) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    agelim = AGESUP;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   stepsize=(int) (stepm+YEARM-1)/YEARM;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (stepm<=12) stepsize=1;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        gp=matrix(0,nhstepm,1,nlstate);
   agelim=AGESUP;      gm=matrix(0,nhstepm,1,nlstate);
    
   hstepm=1;  
   hstepm=hstepm/stepm;      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   if (popforecast==1) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     if((ficpop=fopen(popfile,"r"))==NULL) {        }
       printf("Problem with population file : %s\n",popfile);exit(0);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }  
     popage=ivector(0,AGESUP);        if (popbased==1) {
     popeffectif=vector(0,AGESUP);          if(mobilav ==0){
     popcount=vector(0,AGESUP);            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=probs[(int)age][i][ij];
     i=1;            }else{ /* mobilav */ 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=mobaverage[(int)age][i][ij];
     imx=i;          }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        }
   }    
         for(j=1; j<= nlstate; j++){
   for(cptcov=1;cptcov<=i2;cptcov++){          for(h=0; h<=nhstepm; h++){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       k=k+1;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       fprintf(ficrespop,"\n#******");          }
       for(j=1;j<=cptcoveff;j++) {        }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        /* This for computing probability of death (h=1 means
       }           computed over hstepm matrices product = hstepm*stepm months) 
       fprintf(ficrespop,"******\n");           as a weighted average of prlim.
       fprintf(ficrespop,"# Age");        */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       if (popforecast==1)  fprintf(ficrespop," [Population]");          for(i=1,gpp[j]=0.; i<= nlstate; i++)
                  gpp[j] += prlim[i][i]*p3mat[i][j][1];
       for (cpt=0; cpt<=0;cpt++) {        }    
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          /* end probability of death */
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           nhstepm = nhstepm/hstepm;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                  prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   
           oldm=oldms;savm=savms;        if (popbased==1) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            if(mobilav ==0){
                    for(i=1; i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){              prlim[i][i]=probs[(int)age][i][ij];
             if (h==(int) (calagedate+YEARM*cpt)) {          }else{ /* mobilav */ 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            for(i=1; i<=nlstate;i++)
             }              prlim[i][i]=mobaverage[(int)age][i][ij];
             for(j=1; j<=nlstate+ndeath;j++) {          }
               kk1=0.;kk2=0;        }
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)        for(j=1; j<= nlstate; j++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          for(h=0; h<=nhstepm; h++){
                 else {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
                 }          }
               }        }
               if (h==(int)(calagedate+12*cpt)){        /* This for computing probability of death (h=1 means
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;           computed over hstepm matrices product = hstepm*stepm months) 
                   /*fprintf(ficrespop," %.3f", kk1);           as a weighted average of prlim.
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        */
               }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
             for(i=1; i<=nlstate;i++){           gmp[j] += prlim[i][i]*p3mat[i][j][1];
               kk1=0.;        }    
                 for(j=1; j<=nlstate;j++){        /* end probability of death */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  
                 }        for(j=1; j<= nlstate; j++) /* vareij */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          for(h=0; h<=nhstepm; h++){
             }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }  
       }      } /* End theta */
    
   /******/      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      for(h=0; h<=nhstepm; h++) /* veij */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          for(j=1; j<=nlstate;j++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          for(theta=1; theta <=npar; theta++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            trgradg[h][j][theta]=gradg[h][theta][j];
           nhstepm = nhstepm/hstepm;  
                for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(theta=1; theta <=npar; theta++)
           oldm=oldms;savm=savms;          trgradgp[j][theta]=gradgp[theta][j];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      for(i=1;i<=nlstate;i++)
             }        for(j=1;j<=nlstate;j++)
             for(j=1; j<=nlstate+ndeath;j++) {          vareij[i][j][(int)age] =0.;
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                    for(h=0;h<=nhstepm;h++){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            for(k=0;k<=nhstepm;k++){
               }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
             }          for(i=1;i<=nlstate;i++)
           }            for(j=1;j<=nlstate;j++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }        }
       }      }
    }    
   }      /* pptj */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
   if (popforecast==1) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     free_ivector(popage,0,AGESUP);          varppt[j][i]=doldmp[j][i];
     free_vector(popeffectif,0,AGESUP);      /* end ppptj */
     free_vector(popcount,0,AGESUP);      /*  x centered again */
   }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   fclose(ficrespop);      if (popbased==1) {
 }        if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
 /***********************************************/            prlim[i][i]=probs[(int)age][i][ij];
 /**************** Main Program *****************/        }else{ /* mobilav */ 
 /***********************************************/          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
 int main(int argc, char *argv[])        }
 {      }
                
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      /* This for computing probability of death (h=1 means
   double agedeb, agefin,hf;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;         as a weighted average of prlim.
       */
   double fret;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   double **xi,tmp,delta;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   double dum; /* Dummy variable */      }    
   double ***p3mat;      /* end probability of death */
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   int firstobs=1, lastobs=10;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   int sdeb, sfin; /* Status at beginning and end */        for(i=1; i<=nlstate;i++){
   int c,  h , cpt,l;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   int ju,jl, mi;        }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      } 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      fprintf(ficresprobmorprev,"\n");
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;      fprintf(ficresvij,"%.0f ",age );
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   double bage, fage, age, agelim, agebase;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   double ftolpl=FTOL;        }
   double **prlim;      fprintf(ficresvij,"\n");
   double *severity;      free_matrix(gp,0,nhstepm,1,nlstate);
   double ***param; /* Matrix of parameters */      free_matrix(gm,0,nhstepm,1,nlstate);
   double  *p;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   double **matcov; /* Matrix of covariance */      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   double ***delti3; /* Scale */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double *delti; /* Scale */    } /* End age */
   double ***eij, ***vareij;    free_vector(gpp,nlstate+1,nlstate+ndeath);
   double **varpl; /* Variances of prevalence limits by age */    free_vector(gmp,nlstate+1,nlstate+ndeath);
   double *epj, vepp;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   double kk1, kk2;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
      /* 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)\";");
   char *alph[]={"a","a","b","c","d","e"}, str[4];  /*   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); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   char z[1]="c", occ;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
 #include <sys/time.h>    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
 #include <time.h>    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   /* long total_usecs;    /*  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);
   struct timeval start_time, end_time;  */
    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   getcwd(pathcd, size);  
     free_vector(xp,1,npar);
   printf("\n%s",version);    free_matrix(doldm,1,nlstate,1,nlstate);
   if(argc <=1){    free_matrix(dnewm,1,nlstate,1,npar);
     printf("\nEnter the parameter file name: ");    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     scanf("%s",pathtot);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   else{    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     strcpy(pathtot,argv[1]);    fclose(ficresprobmorprev);
   }    fflush(ficgp);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    fflush(fichtm); 
   /*cygwin_split_path(pathtot,path,optionfile);  }  /* end varevsij */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/  /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  {
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    /* Variance of prevalence limit */
   chdir(path);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   replace(pathc,path);    double **newm;
     double **dnewm,**doldm;
 /*-------- arguments in the command line --------*/    int i, j, nhstepm, hstepm;
     int k, cptcode;
   /* Log file */    double *xp;
   strcat(filelog, optionfilefiname);    double *gp, *gm;
   strcat(filelog,".log");    /* */    double **gradg, **trgradg;
   if((ficlog=fopen(filelog,"w"))==NULL)    {    double age,agelim;
     printf("Problem with logfile %s\n",filelog);    int theta;
     goto end;    
   }    pstamp(ficresvpl);
   fprintf(ficlog,"Log filename:%s\n",filelog);    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   fprintf(ficlog,"\n%s",version);    fprintf(ficresvpl,"# Age");
   fprintf(ficlog,"\nEnter the parameter file name: ");    for(i=1; i<=nlstate;i++)
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        fprintf(ficresvpl," %1d-%1d",i,i);
   fflush(ficlog);    fprintf(ficresvpl,"\n");
   
   /* */    xp=vector(1,npar);
   strcpy(fileres,"r");    dnewm=matrix(1,nlstate,1,npar);
   strcat(fileres, optionfilefiname);    doldm=matrix(1,nlstate,1,nlstate);
   strcat(fileres,".txt");    /* Other files have txt extension */    
     hstepm=1*YEARM; /* Every year of age */
   /*---------arguments file --------*/    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     printf("Problem with optionfile %s\n",optionfile);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);      if (stepm >= YEARM) hstepm=1;
     goto end;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   }      gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
   strcpy(filereso,"o");      gm=vector(1,nlstate);
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {      for(theta=1; theta <=npar; theta++){
     printf("Problem with Output resultfile: %s\n", filereso);        for(i=1; i<=npar; i++){ /* Computes gradient */
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     goto end;        }
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */          gp[i] = prlim[i][i];
   while((c=getc(ficpar))=='#' && c!= EOF){      
     ungetc(c,ficpar);        for(i=1; i<=npar; i++) /* Computes gradient */
     fgets(line, MAXLINE, ficpar);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     puts(line);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     fputs(line,ficparo);        for(i=1;i<=nlstate;i++)
   }          gm[i] = prlim[i][i];
   ungetc(c,ficpar);  
         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);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   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);      } /* End theta */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);  
 while((c=getc(ficpar))=='#' && c!= EOF){      trgradg =matrix(1,nlstate,1,npar);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      for(j=1; j<=nlstate;j++)
     puts(line);        for(theta=1; theta <=npar; theta++)
     fputs(line,ficparo);          trgradg[j][theta]=gradg[theta][j];
   }  
   ungetc(c,ficpar);      for(i=1;i<=nlstate;i++)
          varpl[i][(int)age] =0.;
          matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   covar=matrix(0,NCOVMAX,1,n);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   cptcovn=0;      for(i=1;i<=nlstate;i++)
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
   ncovmodel=2+cptcovn;      fprintf(ficresvpl,"%.0f ",age );
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   /* Read guess parameters */      fprintf(ficresvpl,"\n");
   /* Reads comments: lines beginning with '#' */      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);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)  }
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);  /************ Variance of one-step probabilities  ******************/
       fprintf(ficparo,"%1d%1d",i1,j1);  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[])
       if(mle==1)  {
         printf("%1d%1d",i,j);    int i, j=0,  i1, k1, l1, t, tj;
       fprintf(ficlog,"%1d%1d",i,j);    int k2, l2, j1,  z1;
       for(k=1; k<=ncovmodel;k++){    int k=0,l, cptcode;
         fscanf(ficpar," %lf",&param[i][j][k]);    int first=1, first1;
         if(mle==1){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           printf(" %lf",param[i][j][k]);    double **dnewm,**doldm;
           fprintf(ficlog," %lf",param[i][j][k]);    double *xp;
         }    double *gp, *gm;
         else    double **gradg, **trgradg;
           fprintf(ficlog," %lf",param[i][j][k]);    double **mu;
         fprintf(ficparo," %lf",param[i][j][k]);    double age,agelim, cov[NCOVMAX];
       }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       fscanf(ficpar,"\n");    int theta;
       if(mle==1)    char fileresprob[FILENAMELENGTH];
         printf("\n");    char fileresprobcov[FILENAMELENGTH];
       fprintf(ficlog,"\n");    char fileresprobcor[FILENAMELENGTH];
       fprintf(ficparo,"\n");  
     }    double ***varpij;
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
   p=param[1][1];    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
   /* Reads comments: lines beginning with '#' */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    strcpy(fileresprobcov,"probcov"); 
     fgets(line, MAXLINE, ficpar);    strcat(fileresprobcov,fileres);
     puts(line);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     fputs(line,ficparo);      printf("Problem with resultfile: %s\n", fileresprobcov);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   ungetc(c,ficpar);    }
     strcpy(fileresprobcor,"probcor"); 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    strcat(fileresprobcor,fileres);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   for(i=1; i <=nlstate; i++){      printf("Problem with resultfile: %s\n", fileresprobcor);
     for(j=1; j <=nlstate+ndeath-1; j++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    }
       printf("%1d%1d",i,j);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       fprintf(ficparo,"%1d%1d",i1,j1);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       for(k=1; k<=ncovmodel;k++){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         fscanf(ficpar,"%le",&delti3[i][j][k]);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         printf(" %le",delti3[i][j][k]);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         fprintf(ficparo," %le",delti3[i][j][k]);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       }    pstamp(ficresprob);
       fscanf(ficpar,"\n");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       printf("\n");    fprintf(ficresprob,"# Age");
       fprintf(ficparo,"\n");    pstamp(ficresprobcov);
     }    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   }    fprintf(ficresprobcov,"# Age");
   delti=delti3[1][1];    pstamp(ficresprobcor);
      fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   /* Reads comments: lines beginning with '#' */    fprintf(ficresprobcor,"# Age");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    for(i=1; i<=nlstate;i++)
     puts(line);      for(j=1; j<=(nlstate+ndeath);j++){
     fputs(line,ficparo);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   ungetc(c,ficpar);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
   matcov=matrix(1,npar,1,npar);   /* fprintf(ficresprob,"\n");
   for(i=1; i <=npar; i++){    fprintf(ficresprobcov,"\n");
     fscanf(ficpar,"%s",&str);    fprintf(ficresprobcor,"\n");
     if(mle==1)   */
       printf("%s",str);   xp=vector(1,npar);
     fprintf(ficlog,"%s",str);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     fprintf(ficparo,"%s",str);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     for(j=1; j <=i; j++){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       fscanf(ficpar," %le",&matcov[i][j]);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       if(mle==1){    first=1;
         printf(" %.5le",matcov[i][j]);    fprintf(ficgp,"\n# Routine varprob");
         fprintf(ficlog," %.5le",matcov[i][j]);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       }    fprintf(fichtm,"\n");
       else  
         fprintf(ficlog," %.5le",matcov[i][j]);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       fprintf(ficparo," %.5le",matcov[i][j]);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     }    file %s<br>\n",optionfilehtmcov);
     fscanf(ficpar,"\n");    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     if(mle==1)  and drawn. It helps understanding how is the covariance between two incidences.\
       printf("\n");   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(ficlog,"\n");    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
     fprintf(ficparo,"\n");  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   for(i=1; i <=npar; i++)  standard deviations wide on each axis. <br>\
     for(j=i+1;j<=npar;j++)   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
       matcov[i][j]=matcov[j][i];   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
      To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   if(mle==1)  
     printf("\n");    cov[1]=1;
   fprintf(ficlog,"\n");    tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     /*-------- Rewriting paramater file ----------*/    for(t=1; t<=tj;t++){
      strcpy(rfileres,"r");    /* "Rparameterfile */      for(i1=1; i1<=ncodemax[t];i1++){ 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        j1++;
      strcat(rfileres,".");    /* */        if  (cptcovn>0) {
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          fprintf(ficresprob, "\n#********** Variable "); 
     if((ficres =fopen(rfileres,"w"))==NULL) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          fprintf(ficresprob, "**********\n#\n");
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;          fprintf(ficresprobcov, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficres,"#%s\n",version);          fprintf(ficresprobcov, "**********\n#\n");
              
     /*-------- data file ----------*/          fprintf(ficgp, "\n#********** Variable "); 
     if((fic=fopen(datafile,"r"))==NULL)    {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       printf("Problem with datafile: %s\n", datafile);goto end;          fprintf(ficgp, "**********\n#\n");
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;          
     }          
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     n= lastobs;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     severity = vector(1,maxwav);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     outcome=imatrix(1,maxwav+1,1,n);          
     num=ivector(1,n);          fprintf(ficresprobcor, "\n#********** Variable ");    
     moisnais=vector(1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     annais=vector(1,n);          fprintf(ficresprobcor, "**********\n#");    
     moisdc=vector(1,n);        }
     andc=vector(1,n);        
     agedc=vector(1,n);        for (age=bage; age<=fage; age ++){ 
     cod=ivector(1,n);          cov[2]=age;
     weight=vector(1,n);          for (k=1; k<=cptcovn;k++) {
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     mint=matrix(1,maxwav,1,n);          }
     anint=matrix(1,maxwav,1,n);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     s=imatrix(1,maxwav+1,1,n);          for (k=1; k<=cptcovprod;k++)
     adl=imatrix(1,maxwav+1,1,n);                cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     tab=ivector(1,NCOVMAX);          
     ncodemax=ivector(1,8);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     i=1;          gp=vector(1,(nlstate)*(nlstate+ndeath));
     while (fgets(line, MAXLINE, fic) != NULL)    {          gm=vector(1,(nlstate)*(nlstate+ndeath));
       if ((i >= firstobs) && (i <=lastobs)) {      
                  for(theta=1; theta <=npar; theta++){
         for (j=maxwav;j>=1;j--){            for(i=1; i<=npar; i++)
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
           strcpy(line,stra);            
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            
         }            k=0;
                    for(i=1; i<= (nlstate); i++){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              for(j=1; j<=(nlstate+ndeath);j++){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                k=k+1;
                 gp[k]=pmmij[i][j];
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            }
             
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            for(i=1; i<=npar; i++)
         for (j=ncovcol;j>=1;j--){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      
         }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         num[i]=atol(stra);            k=0;
                    for(i=1; i<=(nlstate); i++){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              for(j=1; j<=(nlstate+ndeath);j++){
           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;}*/                k=k+1;
                 gm[k]=pmmij[i][j];
         i=i+1;              }
       }            }
     }       
     /* printf("ii=%d", ij);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
        scanf("%d",i);*/              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   imx=i-1; /* Number of individuals */          }
   
   /* for (i=1; i<=imx; i++){          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;            for(theta=1; theta <=npar; theta++)
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              trgradg[j][theta]=gradg[theta][j];
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          
     }*/          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
    /*  for (i=1; i<=imx; i++){          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
      if (s[4][i]==9)  s[4][i]=-1;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
      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]));}*/          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
            free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
            free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   /* 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 */          pmij(pmmij,cov,ncovmodel,x,nlstate);
   Tprod=ivector(1,15);          
   Tvaraff=ivector(1,15);          k=0;
   Tvard=imatrix(1,15,1,2);          for(i=1; i<=(nlstate); i++){
   Tage=ivector(1,15);                  for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
   if (strlen(model) >1){              mu[k][(int) age]=pmmij[i][j];
     j=0, j1=0, k1=1, k2=1;            }
     j=nbocc(model,'+');          }
     j1=nbocc(model,'*');          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     cptcovn=j+1;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     cptcovprod=j1;              varpij[i][j][(int)age] = doldm[i][j];
      
     strcpy(modelsav,model);          /*printf("\n%d ",(int)age);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       printf("Error. Non available option model=%s ",model);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       fprintf(ficlog,"Error. Non available option model=%s ",model);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       goto end;            }*/
     }  
              fprintf(ficresprob,"\n%d ",(int)age);
     for(i=(j+1); i>=1;i--){          fprintf(ficresprobcov,"\n%d ",(int)age);
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */          fprintf(ficresprobcor,"\n%d ",(int)age);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       /*scanf("%d",i);*/            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       if (strchr(strb,'*')) {  /* Model includes a product */          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
         if (strcmp(strc,"age")==0) { /* Vn*age */            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           cptcovprod--;          }
           cutv(strb,stre,strd,'V');          i=0;
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/          for (k=1; k<=(nlstate);k++){
           cptcovage++;            for (l=1; l<=(nlstate+ndeath);l++){ 
             Tage[cptcovage]=i;              i=i++;
             /*printf("stre=%s ", stre);*/              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
         }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
         else if (strcmp(strd,"age")==0) { /* or age*Vn */              for (j=1; j<=i;j++){
           cptcovprod--;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
           cutv(strb,stre,strc,'V');                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
           Tvar[i]=atoi(stre);              }
           cptcovage++;            }
           Tage[cptcovage]=i;          }/* end of loop for state */
         }        } /* end of loop for age */
         else {  /* Age is not in the model */  
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/        /* Confidence intervalle of pij  */
           Tvar[i]=ncovcol+k1;        /*
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */          fprintf(ficgp,"\nset noparametric;unset label");
           Tprod[k1]=i;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           Tvard[k1][1]=atoi(strc); /* m*/          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           Tvard[k1][2]=atoi(stre); /* n */          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);
           Tvar[cptcovn+k2]=Tvard[k1][1];          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           for (k=1; k<=lastobs;k++)          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        */
           k1++;  
           k2=k2+2;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         }        first1=1;
       }        for (k2=1; k2<=(nlstate);k2++){
       else { /* no more sum */          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            if(l2==k2) continue;
        /*  scanf("%d",i);*/            j=(k2-1)*(nlstate+ndeath)+l2;
       cutv(strd,strc,strb,'V');            for (k1=1; k1<=(nlstate);k1++){
       Tvar[i]=atoi(strc);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       }                if(l1==k1) continue;
       strcpy(modelsav,stra);                  i=(k1-1)*(nlstate+ndeath)+l1;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                if(i<=j) continue;
         scanf("%d",i);*/                for (age=bage; age<=fage; age ++){ 
     } /* end of loop + */                  if ((int)age %5==0){
   } /* end model */                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                      v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   printf("cptcovprod=%d ", cptcovprod);                    mu1=mu[i][(int) age]/stepm*YEARM ;
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);                    mu2=mu[j][(int) age]/stepm*YEARM;
   scanf("%d ",i);*/                    c12=cv12/sqrt(v1*v2);
     fclose(fic);                    /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     /*  if(mle==1){*/                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     if (weightopt != 1) { /* Maximisation without weights*/                    /* Eigen vectors */
       for(i=1;i<=n;i++) weight[i]=1.0;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     }                    /*v21=sqrt(1.-v11*v11); *//* error */
     /*-calculation of age at interview from date of interview and age at death -*/                    v21=(lc1-v1)/cv12*v11;
     agev=matrix(1,maxwav,1,imx);                    v12=-v21;
                     v22=v11;
     for (i=1; i<=imx; i++) {                    tnalp=v21/v11;
       for(m=2; (m<= maxwav); m++) {                    if(first1==1){
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                      first1=0;
          anint[m][i]=9999;                      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);
          s[m][i]=-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);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;                    /*printf(fignu*/
       }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     }                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
     for (i=1; i<=imx; i++)  {                      first=0;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                      fprintf(ficgp,"\nset parametric;unset label");
       for(m=1; (m<= maxwav); m++){                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
         if(s[m][i] >0){                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           if (s[m][i] >= nlstate+1) {                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
             if(agedc[i]>0)   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
               if(moisdc[i]!=99 && andc[i]!=9999)  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                 agev[m][i]=agedc[i];                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
            else {                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
               if (andc[i]!=9999){                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
               agev[m][i]=-1;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
               }                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
             }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
           }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           else if(s[m][i] !=9){ /* Should no more exist */                    }else{
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                      first=0;
             if(mint[m][i]==99 || anint[m][i]==9999)                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
               agev[m][i]=1;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
             else if(agev[m][i] <agemin){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
               agemin=agev[m][i];                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
             }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
             else if(agev[m][i] >agemax){                    }/* if first */
               agemax=agev[m][i];                  } /* age mod 5 */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                } /* end loop age */
             }                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
             /*agev[m][i]=anint[m][i]-annais[i];*/                first=1;
             /*   agev[m][i] = age[i]+2*m;*/              } /*l12 */
           }            } /* k12 */
           else { /* =9 */          } /*l1 */
             agev[m][i]=1;        }/* k1 */
             s[m][i]=-1;      } /* loop covariates */
           }    }
         }    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         else /*= 0 Unknown */    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));
       }    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
        free_vector(xp,1,npar);
     }    fclose(ficresprob);
     for (i=1; i<=imx; i++)  {    fclose(ficresprobcov);
       for(m=1; (m<= maxwav); m++){    fclose(ficresprobcor);
         if (s[m][i] > (nlstate+ndeath)) {    fflush(ficgp);
           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);      fflush(fichtmcov);
           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;  
         }  
       }  /******************* Printing html file ***********/
     }  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                    int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
     free_vector(severity,1,maxwav);                    double jprev2, double mprev2,double anprev2){
     free_imatrix(outcome,1,maxwav+1,1,n);    int jj1, k1, i1, cpt;
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     /* free_matrix(mint,1,maxwav,1,n);     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
        free_matrix(anint,1,maxwav,1,n);*/  </ul>");
     free_vector(moisdc,1,n);     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
     free_vector(andc,1,n);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
         fprintf(fichtm,"\
     wav=ivector(1,imx);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
     dh=imatrix(1,lastpass-firstpass+1,1,imx);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
     mw=imatrix(1,lastpass-firstpass+1,1,imx);     fprintf(fichtm,"\
       - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
     /* Concatenates waves */             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);     fprintf(fichtm,"\
    - (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",
       Tcode=ivector(1,100);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     fprintf(fichtm,"\
       ncodemax[1]=1;   - Population projections by age and states: \
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
        
    codtab=imatrix(1,100,1,10);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    h=0;  
    m=pow(2,cptcoveff);   m=cptcoveff;
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){   jj1=0;
        for(j=1; j <= ncodemax[k]; j++){   for(k1=1; k1<=m;k1++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){     for(i1=1; i1<=ncodemax[k1];i1++){
            h++;       jj1++;
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;       if (cptcovn > 0) {
            /*  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,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          }         for (cpt=1; cpt<=cptcoveff;cpt++) 
        }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
      }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
    }       }
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);       /* Pij */
       codtab[1][2]=1;codtab[2][2]=2; */       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> \
    /* for(i=1; i <=m ;i++){  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
       for(k=1; k <=cptcovn; k++){       /* Quasi-incidences */
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
       }   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
       printf("\n");  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
       }         /* Period (stable) prevalence in each health state */
       scanf("%d",i);*/         for(cpt=1; cpt<nlstate;cpt++){
               fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
    /* Calculates basic frequencies. Computes observed prevalence at single age  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
        and prints on file fileres'p'. */         }
        for(cpt=1; cpt<=nlstate;cpt++) {
              fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <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);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     } /* end i1 */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   }/* End k1 */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   fprintf(fichtm,"</ul>");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
        
     /* For Powell, parameters are in a vector p[] starting at p[1]   fprintf(fichtm,"\
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
     if(mle==1){   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
     }   fprintf(fichtm,"\
       - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     /*--------- results files --------------*/           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
     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,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
    jk=1;           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");   fprintf(fichtm,"\
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");   - 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): \
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");     <a href=\"%s\">%s</a> <br>\n</li>",
    for(i=1,jk=1; i <=nlstate; i++){             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
      for(k=1; k <=(nlstate+ndeath); k++){   fprintf(fichtm,"\
        if (k != i)   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
          {     <a href=\"%s\">%s</a> <br>\n</li>",
            printf("%d%d ",i,k);             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
            fprintf(ficlog,"%d%d ",i,k);   fprintf(fichtm,"\
            fprintf(ficres,"%1d%1d ",i,k);   - 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",
            for(j=1; j <=ncovmodel; j++){           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
              printf("%f ",p[jk]);   fprintf(fichtm,"\
              fprintf(ficlog,"%f ",p[jk]);   - 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",
              fprintf(ficres,"%f ",p[jk]);           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
              jk++;   fprintf(fichtm,"\
            }   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            printf("\n");           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
            fprintf(ficlog,"\n");  
            fprintf(ficres,"\n");  /*  if(popforecast==1) fprintf(fichtm,"\n */
          }  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
      }  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
    }  /*      <br>",fileres,fileres,fileres,fileres); */
    if(mle==1){  /*  else  */
      /* Computing hessian and covariance matrix */  /*    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); */
      ftolhess=ftol; /* Usually correct */   fflush(fichtm);
      hesscov(matcov, p, npar, delti, ftolhess, func);   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
    }  
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");   m=cptcoveff;
    printf("# Scales (for hessian or gradient estimation)\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");  
    for(i=1,jk=1; i <=nlstate; i++){   jj1=0;
      for(j=1; j <=nlstate+ndeath; j++){   for(k1=1; k1<=m;k1++){
        if (j!=i) {     for(i1=1; i1<=ncodemax[k1];i1++){
          fprintf(ficres,"%1d%1d",i,j);       jj1++;
          printf("%1d%1d",i,j);       if (cptcovn > 0) {
          fprintf(ficlog,"%1d%1d",i,j);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for(k=1; k<=ncovmodel;k++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
            printf(" %.5e",delti[jk]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
            fprintf(ficlog," %.5e",delti[jk]);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
            fprintf(ficres," %.5e",delti[jk]);       }
            jk++;       for(cpt=1; cpt<=nlstate;cpt++) {
          }         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
          printf("\n");  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
          fprintf(ficlog,"\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
          fprintf(ficres,"\n");       }
        }       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
      }  health expectancies in states (1) and (2): %s%d.png<br>\
    }  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
         } /* end i1 */
    k=1;   }/* End k1 */
    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");   fprintf(fichtm,"</ul>");
    if(mle==1)   fflush(fichtm);
      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");  
    for(i=1;i<=npar;i++){  /******************* Gnuplot file **************/
      /*  if (k>nlstate) k=1;  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
          i1=(i-1)/(ncovmodel*nlstate)+1;  
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    char dirfileres[132],optfileres[132];
          printf("%s%d%d",alph[k],i1,tab[i]);*/    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
      fprintf(ficres,"%3d",i);    int ng;
      if(mle==1)  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
        printf("%3d",i);  /*     printf("Problem with file %s",optionfilegnuplot); */
      fprintf(ficlog,"%3d",i);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
      for(j=1; j<=i;j++){  /*   } */
        fprintf(ficres," %.5e",matcov[i][j]);  
        if(mle==1)    /*#ifdef windows */
          printf(" %.5e",matcov[i][j]);    fprintf(ficgp,"cd \"%s\" \n",pathc);
        fprintf(ficlog," %.5e",matcov[i][j]);      /*#endif */
      }    m=pow(2,cptcoveff);
      fprintf(ficres,"\n");  
      if(mle==1)    strcpy(dirfileres,optionfilefiname);
        printf("\n");    strcpy(optfileres,"vpl");
      fprintf(ficlog,"\n");   /* 1eme*/
      k++;    for (cpt=1; cpt<= nlstate ; cpt ++) {
    }     for (k1=1; k1<= m ; k1 ++) {
           fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
    while((c=getc(ficpar))=='#' && c!= EOF){       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
      ungetc(c,ficpar);       fprintf(ficgp,"set xlabel \"Age\" \n\
      fgets(line, MAXLINE, ficpar);  set ylabel \"Probability\" \n\
      puts(line);  set ter png small\n\
      fputs(line,ficparo);  set size 0.65,0.65\n\
    }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
    ungetc(c,ficpar);  
    estepm=0;       for (i=1; i<= nlstate ; i ++) {
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
    if (estepm==0 || estepm < stepm) estepm=stepm;         else fprintf(ficgp," \%%*lf (\%%*lf)");
    if (fage <= 2) {       }
      bage = ageminpar;       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);
      fage = agemaxpar;       for (i=1; i<= nlstate ; i ++) {
    }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             else fprintf(ficgp," \%%*lf (\%%*lf)");
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");       } 
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);       for (i=1; i<= nlstate ; i ++) {
             if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
    while((c=getc(ficpar))=='#' && c!= EOF){         else fprintf(ficgp," \%%*lf (\%%*lf)");
      ungetc(c,ficpar);       }  
      fgets(line, MAXLINE, ficpar);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      puts(line);     }
      fputs(line,ficparo);    }
    }    /*2 eme*/
    ungetc(c,ficpar);    
      for (k1=1; k1<= m ; k1 ++) { 
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      
          for (i=1; i<= nlstate+1 ; i ++) {
    while((c=getc(ficpar))=='#' && c!= EOF){        k=2*i;
      ungetc(c,ficpar);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
      fgets(line, MAXLINE, ficpar);        for (j=1; j<= nlstate+1 ; j ++) {
      puts(line);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
      fputs(line,ficparo);          else fprintf(ficgp," \%%*lf (\%%*lf)");
    }        }   
    ungetc(c,ficpar);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
          else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        for (j=1; j<= nlstate+1 ; j ++) {
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   fscanf(ficpar,"pop_based=%d\n",&popbased);        }   
   fprintf(ficparo,"pop_based=%d\n",popbased);          fprintf(ficgp,"\" t\"\" w l 0,");
   fprintf(ficres,"pop_based=%d\n",popbased);          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
          for (j=1; j<= nlstate+1 ; j ++) {
   while((c=getc(ficpar))=='#' && c!= EOF){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     ungetc(c,ficpar);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     fgets(line, MAXLINE, ficpar);        }   
     puts(line);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     fputs(line,ficparo);        else fprintf(ficgp,"\" t\"\" w l 0,");
   }      }
   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);    /*3eme*/
 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(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
 while((c=getc(ficpar))=='#' && c!= EOF){        k=2+(nlstate+1)*(cpt-1);
     ungetc(c,ficpar);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
     fgets(line, MAXLINE, ficpar);        fprintf(ficgp,"set ter png small\n\
     puts(line);  set size 0.65,0.65\n\
     fputs(line,ficparo);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
   }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   ungetc(c,ficpar);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   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,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        */
         for (i=1; i< nlstate ; i ++) {
 /*------------ gnuplot -------------*/          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);
   strcpy(optionfilegnuplot,optionfilefiname);          /*      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);*/
   strcat(optionfilegnuplot,".gp");          
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        } 
     printf("Problem with file %s",optionfilegnuplot);        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
   }      }
   fclose(ficgp);    }
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    
 /*--------- index.htm --------*/    /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
   strcpy(optionfilehtm,optionfile);      for (cpt=1; cpt<=nlstate ; cpt ++) {
   strcat(optionfilehtm,".htm");        k=3;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
     printf("Problem with %s \n",optionfilehtm), exit(0);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   }  set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        
 \n        for (i=1; i< nlstate ; i ++)
 Total number of observations=%d <br>\n          fprintf(ficgp,"+$%d",k+i+1);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
 <hr  size=\"2\" color=\"#EC5E5E\">        
  <ul><li><h4>Parameter files</h4>\n        l=3+(nlstate+ndeath)*cpt;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
  - Log file of the run: <a href=\"%s\">%s</a><br>\n        for (i=1; i< nlstate ; i ++) {
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);          l=3+(nlstate+ndeath)*cpt;
   fclose(fichtm);          fprintf(ficgp,"+$%d",l+i+1);
         }
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
        } 
 /*------------ free_vector  -------------*/    }  
  chdir(path);    
      /* proba elementaires */
  free_ivector(wav,1,imx);    for(i=1,jk=1; i <=nlstate; i++){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      for(k=1; k <=(nlstate+ndeath); k++){
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          if (k != i) {
  free_ivector(num,1,n);          for(j=1; j <=ncovmodel; j++){
  free_vector(agedc,1,n);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            jk++; 
  fclose(ficparo);            fprintf(ficgp,"\n");
  fclose(ficres);          }
         }
       }
   /*--------------- Prevalence limit --------------*/     }
    
   strcpy(filerespl,"pl");     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   strcat(filerespl,fileres);       for(jk=1; jk <=m; jk++) {
   if((ficrespl=fopen(filerespl,"w"))==NULL) {         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;         if (ng==2)
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   }         else
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);           fprintf(ficgp,"\nset title \"Probability\"\n");
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   fprintf(ficrespl,"#Prevalence limit\n");         i=1;
   fprintf(ficrespl,"#Age ");         for(k2=1; k2<=nlstate; k2++) {
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);           k3=i;
   fprintf(ficrespl,"\n");           for(k=1; k<=(nlstate+ndeath); k++) {
               if (k != k2){
   prlim=matrix(1,nlstate,1,nlstate);               if(ng==2)
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               else
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */               ij=1;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */               for(j=3; j <=ncovmodel; j++) {
   k=0;                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   agebase=ageminpar;                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   agelim=agemaxpar;                   ij++;
   ftolpl=1.e-10;                 }
   i1=cptcoveff;                 else
   if (cptcovn < 1){i1=1;}                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
   for(cptcov=1;cptcov<=i1;cptcov++){               fprintf(ficgp,")/(1");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){               
         k=k+1;               for(k1=1; k1 <=nlstate; k1++){   
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
         fprintf(ficrespl,"\n#******");                 ij=1;
         printf("\n#******");                 for(j=3; j <=ncovmodel; j++){
         fprintf(ficlog,"\n#******");                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
         for(j=1;j<=cptcoveff;j++) {                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                     ij++;
           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]]);                   else
         }                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         fprintf(ficrespl,"******\n");                 }
         printf("******\n");                 fprintf(ficgp,")");
         fprintf(ficlog,"******\n");               }
                       fprintf(ficgp,") t \"p%d%d\" ", k2,k);
         for (age=agebase; age<=agelim; age++){               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);               i=i+ncovmodel;
           fprintf(ficrespl,"%.0f",age );             }
           for(i=1; i<=nlstate;i++)           } /* end k */
           fprintf(ficrespl," %.5f", prlim[i][i]);         } /* end k2 */
           fprintf(ficrespl,"\n");       } /* end jk */
         }     } /* end ng */
       }     fflush(ficgp); 
     }  }  /* end gnuplot */
   fclose(ficrespl);  
   
   /*------------- h Pij x at various ages ------------*/  /*************** Moving average **************/
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    int i, cpt, cptcod;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    int modcovmax =1;
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;    int mobilavrange, mob;
   }    double age;
   printf("Computing pij: result on file '%s' \n", filerespij);  
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                               a covariate has 2 modalities */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   /*if (stepm<=24) stepsize=2;*/  
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   agelim=AGESUP;      if(mobilav==1) mobilavrange=5; /* default */
   hstepm=stepsize*YEARM; /* Every year of age */      else mobilavrange=mobilav;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
   /* hstepm=1;   aff par mois*/          for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   k=0;      /* We keep the original values on the extreme ages bage, fage and for 
   for(cptcov=1;cptcov<=i1;cptcov++){         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         we use a 5 terms etc. until the borders are no more concerned. 
       k=k+1;      */ 
         fprintf(ficrespij,"\n#****** ");      for (mob=3;mob <=mobilavrange;mob=mob+2){
         for(j=1;j<=cptcoveff;j++)        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (i=1; i<=nlstate;i++){
         fprintf(ficrespij,"******\n");            for (cptcod=1;cptcod<=modcovmax;cptcod++){
                      mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                for (cpt=1;cpt<=(mob-1)/2;cpt++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
           /*      nhstepm=nhstepm*YEARM; aff par mois*/              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
           oldm=oldms;savm=savms;        }/* end age */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        }/* end mob */
           fprintf(ficrespij,"# Age");    }else return -1;
           for(i=1; i<=nlstate;i++)    return 0;
             for(j=1; j<=nlstate+ndeath;j++)  }/* End movingaverage */
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");  
            for (h=0; h<=nhstepm; h++){  /************** Forecasting ******************/
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  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){
             for(i=1; i<=nlstate;i++)    /* proj1, year, month, day of starting projection 
               for(j=1; j<=nlstate+ndeath;j++)       agemin, agemax range of age
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);       dateprev1 dateprev2 range of dates during which prevalence is computed
             fprintf(ficrespij,"\n");       anproj2 year of en of projection (same day and month as proj1).
              }    */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
           fprintf(ficrespij,"\n");    int *popage;
         }    double agec; /* generic age */
     }    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   }    double *popeffectif,*popcount;
     double ***p3mat;
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   fclose(ficrespij);  
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   /*---------- Forecasting ------------------*/   
   if((stepm == 1) && (strcmp(model,".")==0)){    strcpy(fileresf,"f"); 
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    strcat(fileresf,fileres);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    if((ficresf=fopen(fileresf,"w"))==NULL) {
   }      printf("Problem with forecast resultfile: %s\n", fileresf);
   else{      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     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);    printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   }  
      if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   /*---------- Health expectancies and variances ------------*/    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(filerest,"t");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   strcat(filerest,fileres);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   if((ficrest=fopen(filerest,"w"))==NULL) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     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 LEs with variances: file '%s' \n", filerest);    stepsize=(int) (stepm+YEARM-1)/YEARM;
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);    if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   strcpy(filerese,"e");    }
   strcat(filerese,fileres);    else  hstepm=estepm;   
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    hstepm=hstepm/stepm; 
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   }                                 fractional in yp1 */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    anprojmean=yp;
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);    yp2=modf((yp1*12),&yp);
     mprojmean=yp;
   strcpy(fileresv,"v");    yp1=modf((yp2*30.5),&yp);
   strcat(fileresv,fileres);    jprojmean=yp;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    if(jprojmean==0) jprojmean=1;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    if(mprojmean==0) jprojmean=1;
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    i1=cptcoveff;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    if (cptcovn < 1){i1=1;}
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    
   calagedate=-1;    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){  /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       k=k+1;      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       fprintf(ficrest,"\n#****** ");        k=k+1;
       for(j=1;j<=cptcoveff;j++)        fprintf(ficresf,"\n#******");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1;j<=cptcoveff;j++) {
       fprintf(ficrest,"******\n");          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
       fprintf(ficreseij,"\n#****** ");        fprintf(ficresf,"******\n");
       for(j=1;j<=cptcoveff;j++)        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<=nlstate+ndeath;j++){ 
       fprintf(ficreseij,"******\n");          for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
       fprintf(ficresvij,"\n#****** ");          fprintf(ficresf," p.%d",j);
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
       fprintf(ficresvij,"******\n");          fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;          for (agec=fage; agec>=(ageminpar-1); agec--){ 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);              nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
              nhstepm = nhstepm/hstepm; 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       oldm=oldms;savm=savms;            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);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
       if(popbased==1){          
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);            for (h=0; h<=nhstepm; h++){
        }              if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                  for(j=1;j<=cptcoveff;j++) 
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
       fprintf(ficrest,"\n");              } 
               for(j=1; j<=nlstate+ndeath;j++) {
       epj=vector(1,nlstate+1);                ppij=0.;
       for(age=bage; age <=fage ;age++){                for(i=1; i<=nlstate;i++) {
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                  if (mobilav==1) 
         if (popbased==1) {                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
           for(i=1; i<=nlstate;i++)                  else {
             prlim[i][i]=probs[(int)age][i][k];                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
         }                  }
                          if (h*hstepm/YEARM*stepm== yearp) {
         fprintf(ficrest," %4.0f",age);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                  }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                } /* end i */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                if (h*hstepm/YEARM*stepm==yearp) {
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                  fprintf(ficresf," %.3f", ppij);
           }                }
           epj[nlstate+1] +=epj[j];              }/* end j */
         }            } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(i=1, vepp=0.;i <=nlstate;i++)          } /* end agec */
           for(j=1;j <=nlstate;j++)        } /* end yearp */
             vepp += vareij[i][j][(int)age];      } /* end cptcod */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    } /* end  cptcov */
         for(j=1;j <=nlstate;j++){         
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         }  
         fprintf(ficrest,"\n");    fclose(ficresf);
       }  }
     }  
   }  /************** Forecasting *****not tested NB*************/
 free_matrix(mint,1,maxwav,1,n);  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){
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    
     free_vector(weight,1,n);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   fclose(ficreseij);    int *popage;
   fclose(ficresvij);    double calagedatem, agelim, kk1, kk2;
   fclose(ficrest);    double *popeffectif,*popcount;
   fclose(ficpar);    double ***p3mat,***tabpop,***tabpopprev;
   free_vector(epj,1,nlstate+1);    double ***mobaverage;
      char filerespop[FILENAMELENGTH];
   /*------- Variance limit prevalence------*/    
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(fileresvpl,"vpl");    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(fileresvpl,fileres);    agelim=AGESUP;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    
     exit(0);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   }    
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    
     strcpy(filerespop,"pop"); 
   k=0;    strcat(filerespop,fileres);
   for(cptcov=1;cptcov<=i1;cptcov++){    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf("Problem with forecast resultfile: %s\n", filerespop);
       k=k+1;      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficresvpl,"\n#****** ");    }
       for(j=1;j<=cptcoveff;j++)    printf("Computing forecasting: result on file '%s' \n", filerespop);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
       fprintf(ficresvpl,"******\n");  
          if (cptcoveff==0) ncodemax[cptcoveff]=1;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    if (mobilav!=0) {
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
  }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
   fclose(ficresvpl);      }
     }
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    stepsize=(int) (stepm+YEARM-1)/YEARM;
      if (stepm<=12) stepsize=1;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    agelim=AGESUP;
      
      hstepm=1;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    hstepm=hstepm/stepm; 
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    if (popforecast==1) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      if((ficpop=fopen(popfile,"r"))==NULL) {
          printf("Problem with population file : %s\n",popfile);exit(0);
   free_matrix(matcov,1,npar,1,npar);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
   free_vector(delti,1,npar);      } 
   free_matrix(agev,1,maxwav,1,imx);      popage=ivector(0,AGESUP);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
   fprintf(fichtm,"\n</body>");      
   fclose(fichtm);      i=1;   
   fclose(ficgp);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
       
       imx=i;
   if(erreur >0){      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     printf("End of Imach with error or warning %d\n",erreur);    }
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);  
   }else{    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
    printf("End of Imach\n");     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
    fprintf(ficlog,"End of Imach\n");        k=k+1;
   }        fprintf(ficrespop,"\n#******");
   printf("See log file on %s\n",filelog);        for(j=1;j<=cptcoveff;j++) {
   fclose(ficlog);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        }
          fprintf(ficrespop,"******\n");
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        fprintf(ficrespop,"# Age");
   /*printf("Total time was %d uSec.\n", total_usecs);*/        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   /*------ End -----------*/        if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
  end:          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
 #ifdef windows          
   /* chdir(pathcd);*/          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
 #endif            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
  /*system("wgnuplot graph.plt");*/            nhstepm = nhstepm/hstepm; 
  /*system("../gp37mgw/wgnuplot graph.plt");*/            
  /*system("cd ../gp37mgw");*/            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            oldm=oldms;savm=savms;
  strcpy(plotcmd,GNUPLOTPROGRAM);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
  strcat(plotcmd," ");          
  strcat(plotcmd,optionfilegnuplot);            for (h=0; h<=nhstepm; h++){
  system(plotcmd);              if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
 #ifdef windows              } 
   while (z[0] != 'q') {              for(j=1; j<=nlstate+ndeath;j++) {
     /* chdir(path); */                kk1=0.;kk2=0;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");                for(i=1; i<=nlstate;i++) {              
     scanf("%s",z);                  if (mobilav==1) 
     if (z[0] == 'c') system("./imach");                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
     else if (z[0] == 'e') system(optionfilehtm);                  else {
     else if (z[0] == 'g') system(plotcmd);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     else if (z[0] == 'q') exit(0);                  }
   }                }
 #endif                if (h==(int)(calagedatem+12*cpt)){
 }                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* 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); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           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(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           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(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.1.51  
changed lines
  Added in v.1.127


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