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version 1.50, 2002/06/26 23:25:02 version 1.136, 2010/04/26 20:30:53
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.136  2010/04/26 20:30:53  brouard
      (Module): merging some libgsl code. Fixing computation
   This program computes Healthy Life Expectancies from    of likelione (using inter/intrapolation if mle = 0) in order to
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    get same likelihood as if mle=1.
   first survey ("cross") where individuals from different ages are    Some cleaning of code and comments added.
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.135  2009/10/29 15:33:14  brouard
   second wave of interviews ("longitudinal") which measure each change    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.134  2009/10/29 13:18:53  brouard
   model. More health states you consider, more time is necessary to reach the    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.133  2009/07/06 10:21:25  brouard
   probability to be observed in state j at the second wave    just nforces
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.132  2009/07/06 08:22:05  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Many tings
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.131  2009/06/20 16:22:47  brouard
   you to do it.  More covariates you add, slower the    Some dimensions resccaled
   convergence.  
     Revision 1.130  2009/05/26 06:44:34  brouard
   The advantage of this computer programme, compared to a simple    (Module): Max Covariate is now set to 20 instead of 8. A
   multinomial logistic model, is clear when the delay between waves is not    lot of cleaning with variables initialized to 0. Trying to make
   identical for each individual. Also, if a individual missed an    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.128  2006/06/30 13:02:05  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    (Module): Clarifications on computing e.j
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.127  2006/04/28 18:11:50  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Yes the sum of survivors was wrong since
   and the contribution of each individual to the likelihood is simply    imach-114 because nhstepm was no more computed in the age
   hPijx.    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
   Also this programme outputs the covariance matrix of the parameters but also    compute health expectancies (without variances) in a first step
   of the life expectancies. It also computes the prevalence limits.    and then all the health expectancies with variances or standard
      deviation (needs data from the Hessian matrices) which slows the
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    computation.
            Institut national d'études démographiques, Paris.    In the future we should be able to stop the program is only health
   This software have been partly granted by Euro-REVES, a concerted action    expectancies and graph are needed without standard deviations.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.126  2006/04/28 17:23:28  brouard
   software can be distributed freely for non commercial use. Latest version    (Module): Yes the sum of survivors was wrong since
   can be accessed at http://euroreves.ined.fr/imach .    imach-114 because nhstepm was no more computed in the age
   **********************************************************************/    loop. Now we define nhstepma in the age loop.
      Version 0.98h
 #include <math.h>  
 #include <stdio.h>    Revision 1.125  2006/04/04 15:20:31  lievre
 #include <stdlib.h>    Errors in calculation of health expectancies. Age was not initialized.
 #include <unistd.h>    Forecasting file added.
   
 #define MAXLINE 256    Revision 1.124  2006/03/22 17:13:53  lievre
 #define GNUPLOTPROGRAM "gnuplot"    Parameters are printed with %lf instead of %f (more numbers after the comma).
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    The log-likelihood is printed in the log file
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.123  2006/03/20 10:52:43  brouard
 #define windows    * imach.c (Module): <title> changed, corresponds to .htm file
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    name. <head> headers where missing.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     * imach.c (Module): Weights can have a decimal point as for
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    English (a comma might work with a correct LC_NUMERIC environment,
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define NINTERVMAX 8    1.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Version 0.98g
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.122  2006/03/20 09:45:41  brouard
 #define MAXN 20000    (Module): Weights can have a decimal point as for
 #define YEARM 12. /* Number of months per year */    English (a comma might work with a correct LC_NUMERIC environment,
 #define AGESUP 130    otherwise the weight is truncated).
 #define AGEBASE 40    Modification of warning when the covariates values are not 0 or
 #ifdef windows    1.
 #define DIRSEPARATOR '\\'    Version 0.98g
 #define ODIRSEPARATOR '/'  
 #else    Revision 1.121  2006/03/16 17:45:01  lievre
 #define DIRSEPARATOR '/'    * imach.c (Module): Comments concerning covariates added
 #define ODIRSEPARATOR '\\'  
 #endif    * imach.c (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    not 1 month. Version 0.98f
 int erreur; /* Error number */  
 int nvar;    Revision 1.120  2006/03/16 15:10:38  lievre
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    (Module): refinements in the computation of lli if
 int npar=NPARMAX;    status=-2 in order to have more reliable computation if stepm is
 int nlstate=2; /* Number of live states */    not 1 month. Version 0.98f
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.119  2006/03/15 17:42:26  brouard
 int popbased=0;    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.118  2006/03/14 18:20:07  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): varevsij Comments added explaining the second
 int mle, weightopt;    table of variances if popbased=1 .
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): Function pstamp added
 double jmean; /* Mean space between 2 waves */    (Module): Version 0.98d
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.117  2006/03/14 17:16:22  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Module): varevsij Comments added explaining the second
 FILE *ficlog;    table of variances if popbased=1 .
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 FILE *ficresprobmorprev;    (Module): Function pstamp added
 FILE *fichtm; /* Html File */    (Module): Version 0.98d
 FILE *ficreseij;  
 char filerese[FILENAMELENGTH];    Revision 1.116  2006/03/06 10:29:27  brouard
 FILE  *ficresvij;    (Module): Variance-covariance wrong links and
 char fileresv[FILENAMELENGTH];    varian-covariance of ej. is needed (Saito).
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    Revision 1.115  2006/02/27 12:17:45  brouard
 char title[MAXLINE];    (Module): One freematrix added in mlikeli! 0.98c
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    Revision 1.114  2006/02/26 12:57:58  brouard
     (Module): Some improvements in processing parameter
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    filename with strsep.
 char filelog[FILENAMELENGTH]; /* Log file */  
 char filerest[FILENAMELENGTH];    Revision 1.113  2006/02/24 14:20:24  brouard
 char fileregp[FILENAMELENGTH];    (Module): Memory leaks checks with valgrind and:
 char popfile[FILENAMELENGTH];    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  
     Revision 1.112  2006/01/30 09:55:26  brouard
 #define NR_END 1    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 #define NRANSI    (Module): Comments can be added in data file. Missing date values
 #define ITMAX 200    can be a simple dot '.'.
   
 #define TOL 2.0e-4    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.109  2006/01/24 19:37:15  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): Comments (lines starting with a #) are allowed in data.
   
 #define GOLD 1.618034    Revision 1.108  2006/01/19 18:05:42  lievre
 #define GLIMIT 100.0    Gnuplot problem appeared...
 #define TINY 1.0e-20    To be fixed
   
 static double maxarg1,maxarg2;    Revision 1.107  2006/01/19 16:20:37  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Test existence of gnuplot in imach path
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.106  2006/01/19 13:24:36  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Some cleaning and links added in html output
 #define rint(a) floor(a+0.5)  
     Revision 1.105  2006/01/05 20:23:19  lievre
 static double sqrarg;    *** empty log message ***
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 int imx;    (Module): If the status is missing at the last wave but we know
 int stepm;    that the person is alive, then we can code his/her status as -2
 /* Stepm, step in month: minimum step interpolation*/    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 int estepm;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    the healthy state at last known wave). Version is 0.98
   
 int m,nb;    Revision 1.103  2005/09/30 15:54:49  lievre
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): sump fixed, loop imx fixed, and simplifications.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.102  2004/09/15 17:31:30  brouard
 double dateintmean=0;    Add the possibility to read data file including tab characters.
   
 double *weight;    Revision 1.101  2004/09/15 10:38:38  brouard
 int **s; /* Status */    Fix on curr_time
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.98  2004/05/16 15:05:56  brouard
 {    New version 0.97 . First attempt to estimate force of mortality
    char *s;                             /* pointer */    directly from the data i.e. without the need of knowing the health
    int  l1, l2;                         /* length counters */    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
    l1 = strlen( path );                 /* length of path */    other analysis, in order to test if the mortality estimated from the
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    cross-longitudinal survey is different from the mortality estimated
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    from other sources like vital statistic data.
    if ( s == NULL ) {                   /* no directory, so use current */  
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    The same imach parameter file can be used but the option for mle should be -3.
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  
 #if     defined(__bsd__)                /* get current working directory */    Agnès, who wrote this part of the code, tried to keep most of the
       extern char       *getwd( );    former routines in order to include the new code within the former code.
   
       if ( getwd( dirc ) == NULL ) {    The output is very simple: only an estimate of the intercept and of
 #else    the slope with 95% confident intervals.
       extern char       *getcwd( );  
     Current limitations:
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    A) Even if you enter covariates, i.e. with the
 #endif    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
          return( GLOCK_ERROR_GETCWD );    B) There is no computation of Life Expectancy nor Life Table.
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.97  2004/02/20 13:25:42  lievre
    } else {                             /* strip direcotry from path */    Version 0.96d. Population forecasting command line is (temporarily)
       s++;                              /* after this, the filename */    suppressed.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.96  2003/07/15 15:38:55  brouard
       strcpy( name, s );                /* save file name */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    rewritten within the same printf. Workaround: many printfs.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.95  2003/07/08 07:54:34  brouard
    l1 = strlen( dirc );                 /* length of directory */    * imach.c (Repository):
 #ifdef windows    (Repository): Using imachwizard code to output a more meaningful covariance
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    matrix (cov(a12,c31) instead of numbers.
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.94  2003/06/27 13:00:02  brouard
 #endif    Just cleaning
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.93  2003/06/25 16:33:55  brouard
    strcpy(ext,s);                       /* save extension */    (Module): On windows (cygwin) function asctime_r doesn't
    l1= strlen( name);    exist so I changed back to asctime which exists.
    l2= strlen( s)+1;    (Module): Version 0.96b
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.92  2003/06/25 16:30:45  brouard
    return( 0 );                         /* we're done */    (Module): On windows (cygwin) function asctime_r doesn't
 }    exist so I changed back to asctime which exists.
   
     Revision 1.91  2003/06/25 15:30:29  brouard
 /******************************************/    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 void replace(char *s, char*t)    helps to forecast when convergence will be reached. Elapsed time
 {    is stamped in powell.  We created a new html file for the graphs
   int i;    concerning matrix of covariance. It has extension -cov.htm.
   int lg=20;  
   i=0;    Revision 1.90  2003/06/24 12:34:15  brouard
   lg=strlen(t);    (Module): Some bugs corrected for windows. Also, when
   for(i=0; i<= lg; i++) {    mle=-1 a template is output in file "or"mypar.txt with the design
     (s[i] = t[i]);    of the covariance matrix to be input.
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.89  2003/06/24 12:30:52  brouard
 }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 int nbocc(char *s, char occ)    of the covariance matrix to be input.
 {  
   int i,j=0;    Revision 1.88  2003/06/23 17:54:56  brouard
   int lg=20;    * 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.
   i=0;  
   lg=strlen(s);    Revision 1.87  2003/06/18 12:26:01  brouard
   for(i=0; i<= lg; i++) {    Version 0.96
   if  (s[i] == occ ) j++;  
   }    Revision 1.86  2003/06/17 20:04:08  brouard
   return j;    (Module): Change position of html and gnuplot routines and added
 }    routine fileappend.
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.85  2003/06/17 13:12:43  brouard
 {    * imach.c (Repository): Check when date of death was earlier that
   /* cuts string t into u and v where u is ended by char occ excluding it    current date of interview. It may happen when the death was just
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    prior to the death. In this case, dh was negative and likelihood
      gives u="abcedf" and v="ghi2j" */    was wrong (infinity). We still send an "Error" but patch by
   int i,lg,j,p=0;    assuming that the date of death was just one stepm after the
   i=0;    interview.
   for(j=0; j<=strlen(t)-1; j++) {    (Repository): Because some people have very long ID (first column)
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    we changed int to long in num[] and we added a new lvector for
   }    memory allocation. But we also truncated to 8 characters (left
     truncation)
   lg=strlen(t);    (Repository): No more line truncation errors.
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Revision 1.84  2003/06/13 21:44:43  brouard
   }    * imach.c (Repository): Replace "freqsummary" at a correct
      u[p]='\0';    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
    for(j=0; j<= lg; j++) {    parcimony.
     if (j>=(p+1))(v[j-p-1] = t[j]);    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   }  
 }    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 /********************** nrerror ********************/  
     Revision 1.82  2003/06/05 15:57:20  brouard
 void nrerror(char error_text[])    Add log in  imach.c and  fullversion number is now printed.
 {  
   fprintf(stderr,"ERREUR ...\n");  */
   fprintf(stderr,"%s\n",error_text);  /*
   exit(1);     Interpolated Markov Chain
 }  
 /*********************** vector *******************/    Short summary of the programme:
 double *vector(int nl, int nh)    
 {    This program computes Healthy Life Expectancies from
   double *v;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    first survey ("cross") where individuals from different ages are
   if (!v) nrerror("allocation failure in vector");    interviewed on their health status or degree of disability (in the
   return v-nl+NR_END;    case of a health survey which is our main interest) -2- at least a
 }    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 /************************ free vector ******************/    computed from the time spent in each health state according to a
 void free_vector(double*v, int nl, int nh)    model. More health states you consider, more time is necessary to reach the
 {    Maximum Likelihood of the parameters involved in the model.  The
   free((FREE_ARG)(v+nl-NR_END));    simplest model is the multinomial logistic model where pij is the
 }    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
 /************************ivector *******************************/    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 int *ivector(long nl,long nh)    'age' is age and 'sex' is a covariate. If you want to have a more
 {    complex model than "constant and age", you should modify the program
   int *v;    where the markup *Covariates have to be included here again* invites
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    you to do it.  More covariates you add, slower the
   if (!v) nrerror("allocation failure in ivector");    convergence.
   return v-nl+NR_END;  
 }    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 /******************free ivector **************************/    identical for each individual. Also, if a individual missed an
 void free_ivector(int *v, long nl, long nh)    intermediate interview, the information is lost, but taken into
 {    account using an interpolation or extrapolation.  
   free((FREE_ARG)(v+nl-NR_END));  
 }    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
 /******************* imatrix *******************************/    split into an exact number (nh*stepm) of unobserved intermediate
 int **imatrix(long nrl, long nrh, long ncl, long nch)    states. This elementary transition (by month, quarter,
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    semester or year) is modelled as a multinomial logistic.  The hPx
 {    matrix is simply the matrix product of nh*stepm elementary matrices
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    and the contribution of each individual to the likelihood is simply
   int **m;    hPijx.
    
   /* allocate pointers to rows */    Also this programme outputs the covariance matrix of the parameters but also
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    of the life expectancies. It also computes the period (stable) prevalence. 
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m -= nrl;             Institut national d'études démographiques, Paris.
      This software have been partly granted by Euro-REVES, a concerted action
      from the European Union.
   /* allocate rows and set pointers to them */    It is copyrighted identically to a GNU software product, ie programme and
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    software can be distributed freely for non commercial use. Latest version
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    can be accessed at http://euroreves.ined.fr/imach .
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    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
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    
      **********************************************************************/
   /* return pointer to array of pointers to rows */  /*
   return m;    main
 }    read parameterfile
     read datafile
 /****************** free_imatrix *************************/    concatwav
 void free_imatrix(m,nrl,nrh,ncl,nch)    freqsummary
       int **m;    if (mle >= 1)
       long nch,ncl,nrh,nrl;      mlikeli
      /* free an int matrix allocated by imatrix() */    print results files
 {    if mle==1 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));       computes hessian
   free((FREE_ARG) (m+nrl-NR_END));    read end of parameter file: agemin, agemax, bage, fage, estepm
 }        begin-prev-date,...
     open gnuplot file
 /******************* matrix *******************************/    open html file
 double **matrix(long nrl, long nrh, long ncl, long nch)    period (stable) prevalence
 {     for age prevalim()
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    h Pij x
   double **m;    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    health expectancies
   if (!m) nrerror("allocation failure 1 in matrix()");    Variance-covariance of DFLE
   m += NR_END;    prevalence()
   m -= nrl;     movingaverage()
     varevsij() 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    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 m;  
 }  
    
 /*************************free matrix ************************/  #include <math.h>
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #include <stdio.h>
 {  #include <stdlib.h>
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #include <string.h>
   free((FREE_ARG)(m+nrl-NR_END));  #include <unistd.h>
 }  
   #include <limits.h>
 /******************* ma3x *******************************/  #include <sys/types.h>
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #include <sys/stat.h>
 {  #include <errno.h>
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  extern int errno;
   double ***m;  
   /* #include <sys/time.h> */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #include <time.h>
   if (!m) nrerror("allocation failure 1 in matrix()");  #include "timeval.h"
   m += NR_END;  
   m -= nrl;  #ifdef GSL
   #include <gsl/gsl_errno.h>
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <gsl/gsl_multimin.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #endif
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   #define MAXLINE 256
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define GNUPLOTPROGRAM "gnuplot"
   m[nrl][ncl] += NR_END;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   m[nrl][ncl] -= nll;  #define FILENAMELENGTH 132
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
    #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
     for (j=ncl+1; j<=nch; j++)  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
       m[i][j]=m[i][j-1]+nlay;  
   }  #define NINTERVMAX 8
   return m;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 20 /* Maximum number of covariates */
 /*************************free ma3x ************************/  #define MAXN 20000
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define YEARM 12. /* Number of months per year */
 {  #define AGESUP 130
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define AGEBASE 40
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   free((FREE_ARG)(m+nrl-NR_END));  #ifdef UNIX
 }  #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
 /***************** f1dim *************************/  #define ODIRSEPARATOR '\\'
 extern int ncom;  #else
 extern double *pcom,*xicom;  #define DIRSEPARATOR '\\'
 extern double (*nrfunc)(double []);  #define CHARSEPARATOR "\\"
    #define ODIRSEPARATOR '/'
 double f1dim(double x)  #endif
 {  
   int j;  /* $Id$ */
   double f;  /* $State$ */
   double *xt;  
    char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
   xt=vector(1,ncom);  char fullversion[]="$Revision$ $Date$"; 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  char strstart[80];
   f=(*nrfunc)(xt);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   free_vector(xt,1,ncom);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   return f;  int nvar=0, nforce=0; /* Number of variables, number of forces */
 }  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
   int npar=NPARMAX;
 /*****************brent *************************/  int nlstate=2; /* Number of live states */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int ndeath=1; /* Number of dead states */
 {  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int iter;  int popbased=0;
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  int *wav; /* Number of waves for this individuual 0 is possible */
   double ftemp;  int maxwav=0; /* Maxim number of waves */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   double e=0.0;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
    int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   a=(ax < cx ? ax : cx);                     to the likelihood and the sum of weights (done by funcone)*/
   b=(ax > cx ? ax : cx);  int mle=1, weightopt=0;
   x=w=v=bx;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   fw=fv=fx=(*f)(x);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   for (iter=1;iter<=ITMAX;iter++) {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     xm=0.5*(a+b);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  double jmean=1; /* Mean space between 2 waves */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  double **oldm, **newm, **savm; /* Working pointers to matrices */
     printf(".");fflush(stdout);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     fprintf(ficlog,".");fflush(ficlog);  /*FILE *fic ; */ /* Used in readdata only */
 #ifdef DEBUG  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     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);  FILE *ficlog, *ficrespow;
     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);  int globpr=0; /* Global variable for printing or not */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  double fretone; /* Only one call to likelihood */
 #endif  long ipmx=0; /* Number of contributions */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  double sw; /* Sum of weights */
       *xmin=x;  char filerespow[FILENAMELENGTH];
       return fx;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     }  FILE *ficresilk;
     ftemp=fu;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     if (fabs(e) > tol1) {  FILE *ficresprobmorprev;
       r=(x-w)*(fx-fv);  FILE *fichtm, *fichtmcov; /* Html File */
       q=(x-v)*(fx-fw);  FILE *ficreseij;
       p=(x-v)*q-(x-w)*r;  char filerese[FILENAMELENGTH];
       q=2.0*(q-r);  FILE *ficresstdeij;
       if (q > 0.0) p = -p;  char fileresstde[FILENAMELENGTH];
       q=fabs(q);  FILE *ficrescveij;
       etemp=e;  char filerescve[FILENAMELENGTH];
       e=d;  FILE  *ficresvij;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  char fileresv[FILENAMELENGTH];
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE  *ficresvpl;
       else {  char fileresvpl[FILENAMELENGTH];
         d=p/q;  char title[MAXLINE];
         u=x+d;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
         if (u-a < tol2 || b-u < tol2)  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
           d=SIGN(tol1,xm-x);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       }  char command[FILENAMELENGTH];
     } else {  int  outcmd=0;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  char filelog[FILENAMELENGTH]; /* Log file */
     if (fu <= fx) {  char filerest[FILENAMELENGTH];
       if (u >= x) a=x; else b=x;  char fileregp[FILENAMELENGTH];
       SHFT(v,w,x,u)  char popfile[FILENAMELENGTH];
         SHFT(fv,fw,fx,fu)  
         } else {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
             v=w;  struct timezone tzp;
             w=u;  extern int gettimeofday();
             fv=fw;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
             fw=fu;  long time_value;
           } else if (fu <= fv || v == x || v == w) {  extern long time();
             v=u;  char strcurr[80], strfor[80];
             fv=fu;  
           }  char *endptr;
         }  long lval;
   }  double dval;
   nrerror("Too many iterations in brent");  
   *xmin=x;  #define NR_END 1
   return fx;  #define FREE_ARG char*
 }  #define FTOL 1.0e-10
   
 /****************** mnbrak ***********************/  #define NRANSI 
   #define ITMAX 200 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  #define TOL 2.0e-4 
 {  
   double ulim,u,r,q, dum;  #define CGOLD 0.3819660 
   double fu;  #define ZEPS 1.0e-10 
    #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  #define GOLD 1.618034 
   if (*fb > *fa) {  #define GLIMIT 100.0 
     SHFT(dum,*ax,*bx,dum)  #define TINY 1.0e-20 
       SHFT(dum,*fb,*fa,dum)  
       }  static double maxarg1,maxarg2;
   *cx=(*bx)+GOLD*(*bx-*ax);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   *fc=(*func)(*cx);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   while (*fb > *fc) {    
     r=(*bx-*ax)*(*fb-*fc);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     q=(*bx-*cx)*(*fb-*fa);  #define rint(a) floor(a+0.5)
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  static double sqrarg;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     if ((*bx-u)*(u-*cx) > 0.0) {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       fu=(*func)(u);  int agegomp= AGEGOMP;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  int imx; 
       if (fu < *fc) {  int stepm=1;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /* Stepm, step in month: minimum step interpolation*/
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  int estepm;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       u=ulim;  
       fu=(*func)(u);  int m,nb;
     } else {  long *num;
       u=(*cx)+GOLD*(*cx-*bx);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       fu=(*func)(u);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     }  double **pmmij, ***probs;
     SHFT(*ax,*bx,*cx,u)  double *ageexmed,*agecens;
       SHFT(*fa,*fb,*fc,fu)  double dateintmean=0;
       }  
 }  double *weight;
   int **s; /* Status */
 /*************** linmin ************************/  double *agedc, **covar, idx;
   int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 int ncom;  double *lsurv, *lpop, *tpop;
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
    double ftolhess; /* Tolerance for computing hessian */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  /**************** split *************************/
   double brent(double ax, double bx, double cx,  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
                double (*f)(double), double tol, double *xmin);  {
   double f1dim(double x);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,       the name of the file (name), its extension only (ext) and its first part of the name (finame)
               double *fc, double (*func)(double));    */ 
   int j;    char  *ss;                            /* pointer */
   double xx,xmin,bx,ax;    int   l1, l2;                         /* length counters */
   double fx,fb,fa;  
      l1 = strlen(path );                   /* length of path */
   ncom=n;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   pcom=vector(1,n);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   xicom=vector(1,n);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   nrfunc=func;      strcpy( name, path );               /* we got the fullname name because no directory */
   for (j=1;j<=n;j++) {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     pcom[j]=p[j];        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     xicom[j]=xi[j];      /* get current working directory */
   }      /*    extern  char* getcwd ( char *buf , int len);*/
   ax=0.0;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   xx=1.0;        return( GLOCK_ERROR_GETCWD );
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      }
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      /* got dirc from getcwd*/
 #ifdef DEBUG      printf(" DIRC = %s \n",dirc);
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    } else {                              /* strip direcotry from path */
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      ss++;                               /* after this, the filename */
 #endif      l2 = strlen( ss );                  /* length of filename */
   for (j=1;j<=n;j++) {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     xi[j] *= xmin;      strcpy( name, ss );         /* save file name */
     p[j] += xi[j];      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   }      dirc[l1-l2] = 0;                    /* add zero */
   free_vector(xicom,1,n);      printf(" DIRC2 = %s \n",dirc);
   free_vector(pcom,1,n);    }
 }    /* We add a separator at the end of dirc if not exists */
     l1 = strlen( dirc );                  /* length of directory */
 /*************** powell ************************/    if( dirc[l1-1] != DIRSEPARATOR ){
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      dirc[l1] =  DIRSEPARATOR;
             double (*func)(double []))      dirc[l1+1] = 0; 
 {      printf(" DIRC3 = %s \n",dirc);
   void linmin(double p[], double xi[], int n, double *fret,    }
               double (*func)(double []));    ss = strrchr( name, '.' );            /* find last / */
   int i,ibig,j;    if (ss >0){
   double del,t,*pt,*ptt,*xit;      ss++;
   double fp,fptt;      strcpy(ext,ss);                     /* save extension */
   double *xits;      l1= strlen( name);
   pt=vector(1,n);      l2= strlen(ss)+1;
   ptt=vector(1,n);      strncpy( finame, name, l1-l2);
   xit=vector(1,n);      finame[l1-l2]= 0;
   xits=vector(1,n);    }
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];    return( 0 );                          /* we're done */
   for (*iter=1;;++(*iter)) {  }
     fp=(*fret);  
     ibig=0;  
     del=0.0;  /******************************************/
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  void replace_back_to_slash(char *s, char*t)
     for (i=1;i<=n;i++)  {
       printf(" %d %.12f",i, p[i]);    int i;
     fprintf(ficlog," %d %.12f",i, p[i]);    int lg=0;
     printf("\n");    i=0;
     fprintf(ficlog,"\n");    lg=strlen(t);
     for (i=1;i<=n;i++) {    for(i=0; i<= lg; i++) {
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      (s[i] = t[i]);
       fptt=(*fret);      if (t[i]== '\\') s[i]='/';
 #ifdef DEBUG    }
       printf("fret=%lf \n",*fret);  }
       fprintf(ficlog,"fret=%lf \n",*fret);  
 #endif  char *trimbb(char *out, char *in)
       printf("%d",i);fflush(stdout);  { /* Trim multiple blanks in line */
       fprintf(ficlog,"%d",i);fflush(ficlog);    char *s;
       linmin(p,xit,n,fret,func);    s=out;
       if (fabs(fptt-(*fret)) > del) {    while (*in != '\0'){
         del=fabs(fptt-(*fret));      while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
         ibig=i;        in++;
       }      }
 #ifdef DEBUG      *out++ = *in++;
       printf("%d %.12e",i,(*fret));    }
       fprintf(ficlog,"%d %.12e",i,(*fret));    *out='\0';
       for (j=1;j<=n;j++) {    return s;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  }
         printf(" x(%d)=%.12e",j,xit[j]);  
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  int nbocc(char *s, char occ)
       }  {
       for(j=1;j<=n;j++) {    int i,j=0;
         printf(" p=%.12e",p[j]);    int lg=20;
         fprintf(ficlog," p=%.12e",p[j]);    i=0;
       }    lg=strlen(s);
       printf("\n");    for(i=0; i<= lg; i++) {
       fprintf(ficlog,"\n");    if  (s[i] == occ ) j++;
 #endif    }
     }    return j;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  }
 #ifdef DEBUG  
       int k[2],l;  void cutv(char *u,char *v, char*t, char occ)
       k[0]=1;  {
       k[1]=-1;    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       printf("Max: %.12e",(*func)(p));       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       fprintf(ficlog,"Max: %.12e",(*func)(p));       gives u="abcedf" and v="ghi2j" */
       for (j=1;j<=n;j++) {    int i,lg,j,p=0;
         printf(" %.12e",p[j]);    i=0;
         fprintf(ficlog," %.12e",p[j]);    for(j=0; j<=strlen(t)-1; j++) {
       }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       printf("\n");    }
       fprintf(ficlog,"\n");  
       for(l=0;l<=1;l++) {    lg=strlen(t);
         for (j=1;j<=n;j++) {    for(j=0; j<p; j++) {
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      (u[j] = t[j]);
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    }
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);       u[p]='\0';
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));     for(j=0; j<= lg; j++) {
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      if (j>=(p+1))(v[j-p-1] = t[j]);
       }    }
 #endif  }
   
   /********************** nrerror ********************/
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  void nrerror(char error_text[])
       free_vector(ptt,1,n);  {
       free_vector(pt,1,n);    fprintf(stderr,"ERREUR ...\n");
       return;    fprintf(stderr,"%s\n",error_text);
     }    exit(EXIT_FAILURE);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  }
     for (j=1;j<=n;j++) {  /*********************** vector *******************/
       ptt[j]=2.0*p[j]-pt[j];  double *vector(int nl, int nh)
       xit[j]=p[j]-pt[j];  {
       pt[j]=p[j];    double *v;
     }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     fptt=(*func)(ptt);    if (!v) nrerror("allocation failure in vector");
     if (fptt < fp) {    return v-nl+NR_END;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  }
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  /************************ free vector ******************/
         for (j=1;j<=n;j++) {  void free_vector(double*v, int nl, int nh)
           xi[j][ibig]=xi[j][n];  {
           xi[j][n]=xit[j];    free((FREE_ARG)(v+nl-NR_END));
         }  }
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /************************ivector *******************************/
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int *ivector(long nl,long nh)
         for(j=1;j<=n;j++){  {
           printf(" %.12e",xit[j]);    int *v;
           fprintf(ficlog," %.12e",xit[j]);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         }    if (!v) nrerror("allocation failure in ivector");
         printf("\n");    return v-nl+NR_END;
         fprintf(ficlog,"\n");  }
 #endif  
       }  /******************free ivector **************************/
     }  void free_ivector(int *v, long nl, long nh)
   }  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /**** Prevalence limit ****************/  
   /************************lvector *******************************/
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  long *lvector(long nl,long nh)
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    long *v;
      matrix by transitions matrix until convergence is reached */    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
   int i, ii,j,k;    return v-nl+NR_END;
   double min, max, maxmin, maxmax,sumnew=0.;  }
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  /******************free lvector **************************/
   double **newm;  void free_lvector(long *v, long nl, long nh)
   double agefin, delaymax=50 ; /* Max number of years to converge */  {
     free((FREE_ARG)(v+nl-NR_END));
   for (ii=1;ii<=nlstate+ndeath;ii++)  }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /******************* imatrix *******************************/
     }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
    cov[1]=1.;  { 
      long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    int **m; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    
     newm=savm;    /* allocate pointers to rows */ 
     /* Covariates have to be included here again */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
      cov[2]=agefin;    if (!m) nrerror("allocation failure 1 in matrix()"); 
      m += NR_END; 
       for (k=1; k<=cptcovn;k++) {    m -= nrl; 
         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]]);*/    
       }    /* allocate rows and set pointers to them */ 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       for (k=1; k<=cptcovprod;k++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    /* return pointer to array of pointers to rows */ 
     return m; 
     savm=oldm;  } 
     oldm=newm;  
     maxmax=0.;  /****************** free_imatrix *************************/
     for(j=1;j<=nlstate;j++){  void free_imatrix(m,nrl,nrh,ncl,nch)
       min=1.;        int **m;
       max=0.;        long nch,ncl,nrh,nrl; 
       for(i=1; i<=nlstate; i++) {       /* free an int matrix allocated by imatrix() */ 
         sumnew=0;  { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         prlim[i][j]= newm[i][j]/(1-sumnew);    free((FREE_ARG) (m+nrl-NR_END)); 
         max=FMAX(max,prlim[i][j]);  } 
         min=FMIN(min,prlim[i][j]);  
       }  /******************* matrix *******************************/
       maxmin=max-min;  double **matrix(long nrl, long nrh, long ncl, long nch)
       maxmax=FMAX(maxmax,maxmin);  {
     }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     if(maxmax < ftolpl){    double **m;
       return prlim;  
     }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   }    if (!m) nrerror("allocation failure 1 in matrix()");
 }    m += NR_END;
     m -= nrl;
 /*************** transition probabilities ***************/  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 {    m[nrl] += NR_END;
   double s1, s2;    m[nrl] -= ncl;
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
     for(i=1; i<= nlstate; i++){    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     for(j=1; j<i;j++){     */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  }
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /*************************free matrix ************************/
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       }  {
       ps[i][j]=s2;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    free((FREE_ARG)(m+nrl-NR_END));
     }  }
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /******************* ma3x *******************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  {
       }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       ps[i][j]=s2;    double ***m;
     }  
   }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     /*ps[3][2]=1;*/    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   for(i=1; i<= nlstate; i++){    m -= nrl;
      s1=0;  
     for(j=1; j<i; j++)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       s1+=exp(ps[i][j]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for(j=i+1; j<=nlstate+ndeath; j++)    m[nrl] += NR_END;
       s1+=exp(ps[i][j]);    m[nrl] -= ncl;
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       ps[i][j]= exp(ps[i][j])*ps[i][i];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    m[nrl][ncl] += NR_END;
   } /* end i */    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      m[nrl][j]=m[nrl][j-1]+nlay;
     for(jj=1; jj<= nlstate+ndeath; jj++){    
       ps[ii][jj]=0;    for (i=nrl+1; i<=nrh; i++) {
       ps[ii][ii]=1;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     }      for (j=ncl+1; j<=nch; j++) 
   }        m[i][j]=m[i][j-1]+nlay;
     }
     return m; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for(jj=1; jj<= nlstate+ndeath; jj++){             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
      printf("%lf ",ps[ii][jj]);    */
    }  }
     printf("\n ");  
     }  /*************************free ma3x ************************/
     printf("\n ");printf("%lf ",cov[2]);*/  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 /*  {
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   goto end;*/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     return ps;    free((FREE_ARG)(m+nrl-NR_END));
 }  }
   
 /**************** Product of 2 matrices ******************/  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  {
 {    /* Caution optionfilefiname is hidden */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    strcpy(tmpout,optionfilefiname);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    strcat(tmpout,"/"); /* Add to the right */
   /* in, b, out are matrice of pointers which should have been initialized    strcat(tmpout,fileres);
      before: only the contents of out is modified. The function returns    return tmpout;
      a pointer to pointers identical to out */  }
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /*************** function subdirf2 ***********/
     for(k=ncolol; k<=ncoloh; k++)  char *subdirf2(char fileres[], char *preop)
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  {
         out[i][k] +=in[i][j]*b[j][k];    
     /* Caution optionfilefiname is hidden */
   return out;    strcpy(tmpout,optionfilefiname);
 }    strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,fileres);
 /************* Higher Matrix Product ***************/    return tmpout;
   }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  /*************** function subdirf3 ***********/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  char *subdirf3(char fileres[], char *preop, char *preop2)
      duration (i.e. until  {
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    /* Caution optionfilefiname is hidden */
      (typically every 2 years instead of every month which is too big).    strcpy(tmpout,optionfilefiname);
      Model is determined by parameters x and covariates have to be    strcat(tmpout,"/");
      included manually here.    strcat(tmpout,preop);
     strcat(tmpout,preop2);
      */    strcat(tmpout,fileres);
     return tmpout;
   int i, j, d, h, k;  }
   double **out, cov[NCOVMAX];  
   double **newm;  /***************** f1dim *************************/
   extern int ncom; 
   /* Hstepm could be zero and should return the unit matrix */  extern double *pcom,*xicom;
   for (i=1;i<=nlstate+ndeath;i++)  extern double (*nrfunc)(double []); 
     for (j=1;j<=nlstate+ndeath;j++){   
       oldm[i][j]=(i==j ? 1.0 : 0.0);  double f1dim(double x) 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  { 
     }    int j; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double f;
   for(h=1; h <=nhstepm; h++){    double *xt; 
     for(d=1; d <=hstepm; d++){   
       newm=savm;    xt=vector(1,ncom); 
       /* Covariates have to be included here again */    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       cov[1]=1.;    f=(*nrfunc)(xt); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    free_vector(xt,1,ncom); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    return f; 
       for (k=1; k<=cptcovage;k++)  } 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /*****************brent *************************/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
     int iter; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    double a,b,d,etemp;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    double fu,fv,fw,fx;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    double ftemp;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       savm=oldm;    double e=0.0; 
       oldm=newm;   
     }    a=(ax < cx ? ax : cx); 
     for(i=1; i<=nlstate+ndeath; i++)    b=(ax > cx ? ax : cx); 
       for(j=1;j<=nlstate+ndeath;j++) {    x=w=v=bx; 
         po[i][j][h]=newm[i][j];    fw=fv=fx=(*f)(x); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    for (iter=1;iter<=ITMAX;iter++) { 
          */      xm=0.5*(a+b); 
       }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   } /* end h */      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   return po;      printf(".");fflush(stdout);
 }      fprintf(ficlog,".");fflush(ficlog);
   #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);
 /*************** log-likelihood *************/      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 double func( double *x)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 {  #endif
   int i, ii, j, k, mi, d, kk;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        *xmin=x; 
   double **out;        return fx; 
   double sw; /* Sum of weights */      } 
   double lli; /* Individual log likelihood */      ftemp=fu;
   long ipmx;      if (fabs(e) > tol1) { 
   /*extern weight */        r=(x-w)*(fx-fv); 
   /* We are differentiating ll according to initial status */        q=(x-v)*(fx-fw); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        p=(x-v)*q-(x-w)*r; 
   /*for(i=1;i<imx;i++)        q=2.0*(q-r); 
     printf(" %d\n",s[4][i]);        if (q > 0.0) p = -p; 
   */        q=fabs(q); 
   cov[1]=1.;        etemp=e; 
         e=d; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        else { 
     for(mi=1; mi<= wav[i]-1; mi++){          d=p/q; 
       for (ii=1;ii<=nlstate+ndeath;ii++)          u=x+d; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          if (u-a < tol2 || b-u < tol2) 
       for(d=0; d<dh[mi][i]; d++){            d=SIGN(tol1,xm-x); 
         newm=savm;        } 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      } else { 
         for (kk=1; kk<=cptcovage;kk++) {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      } 
         }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
              fu=(*f)(u); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      if (fu <= fx) { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        if (u >= x) a=x; else b=x; 
         savm=oldm;        SHFT(v,w,x,u) 
         oldm=newm;          SHFT(fv,fw,fx,fu) 
                  } else { 
                    if (u < x) a=u; else b=u; 
       } /* end mult */            if (fu <= fw || w == x) { 
                    v=w; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);              w=u; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/              fv=fw; 
       ipmx +=1;              fw=fu; 
       sw += weight[i];            } else if (fu <= fv || v == x || v == w) { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;              v=u; 
     } /* end of wave */              fv=fu; 
   } /* end of individual */            } 
           } 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    } 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    nrerror("Too many iterations in brent"); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    *xmin=x; 
   return -l;    return fx; 
 }  } 
   
   /****************** mnbrak ***********************/
 /*********** Maximum Likelihood Estimation ***************/  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))              double (*func)(double)) 
 {  { 
   int i,j, iter;    double ulim,u,r,q, dum;
   double **xi,*delti;    double fu; 
   double fret;   
   xi=matrix(1,npar,1,npar);    *fa=(*func)(*ax); 
   for (i=1;i<=npar;i++)    *fb=(*func)(*bx); 
     for (j=1;j<=npar;j++)    if (*fb > *fa) { 
       xi[i][j]=(i==j ? 1.0 : 0.0);      SHFT(dum,*ax,*bx,dum) 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");        SHFT(dum,*fb,*fa,dum) 
   powell(p,xi,npar,ftol,&iter,&fret,func);        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    *fc=(*func)(*cx); 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    while (*fb > *fc) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 /**** Computes Hessian and covariance matrix ***/      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   double  **a,**y,*x,pd;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double **hess;        fu=(*func)(u); 
   int i, j,jk;        if (fu < *fc) { 
   int *indx;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
   double hessii(double p[], double delta, int theta, double delti[]);            } 
   double hessij(double p[], double delti[], int i, int j);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   void lubksb(double **a, int npar, int *indx, double b[]) ;        u=ulim; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;        fu=(*func)(u); 
       } else { 
   hess=matrix(1,npar,1,npar);        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
   printf("\nCalculation of the hessian matrix. Wait...\n");      } 
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");      SHFT(*ax,*bx,*cx,u) 
   for (i=1;i<=npar;i++){        SHFT(*fa,*fb,*fc,fu) 
     printf("%d",i);fflush(stdout);        } 
     fprintf(ficlog,"%d",i);fflush(ficlog);  } 
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/  /*************** linmin ************************/
     /*printf(" %lf ",hess[i][i]);*/  
   }  int ncom; 
    double *pcom,*xicom;
   for (i=1;i<=npar;i++) {  double (*nrfunc)(double []); 
     for (j=1;j<=npar;j++)  {   
       if (j>i) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         printf(".%d%d",i,j);fflush(stdout);  { 
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    double brent(double ax, double bx, double cx, 
         hess[i][j]=hessij(p,delti,i,j);                 double (*f)(double), double tol, double *xmin); 
         hess[j][i]=hess[i][j];        double f1dim(double x); 
         /*printf(" %lf ",hess[i][j]);*/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       }                double *fc, double (*func)(double)); 
     }    int j; 
   }    double xx,xmin,bx,ax; 
   printf("\n");    double fx,fb,fa;
   fprintf(ficlog,"\n");   
     ncom=n; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    pcom=vector(1,n); 
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    xicom=vector(1,n); 
      nrfunc=func; 
   a=matrix(1,npar,1,npar);    for (j=1;j<=n;j++) { 
   y=matrix(1,npar,1,npar);      pcom[j]=p[j]; 
   x=vector(1,npar);      xicom[j]=xi[j]; 
   indx=ivector(1,npar);    } 
   for (i=1;i<=npar;i++)    ax=0.0; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    xx=1.0; 
   ludcmp(a,npar,indx,&pd);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for (j=1;j<=npar;j++) {  #ifdef DEBUG
     for (i=1;i<=npar;i++) x[i]=0;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     x[j]=1;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     lubksb(a,npar,indx,x);  #endif
     for (i=1;i<=npar;i++){    for (j=1;j<=n;j++) { 
       matcov[i][j]=x[i];      xi[j] *= xmin; 
     }      p[j] += xi[j]; 
   }    } 
     free_vector(xicom,1,n); 
   printf("\n#Hessian matrix#\n");    free_vector(pcom,1,n); 
   fprintf(ficlog,"\n#Hessian matrix#\n");  } 
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++) {  char *asc_diff_time(long time_sec, char ascdiff[])
       printf("%.3e ",hess[i][j]);  {
       fprintf(ficlog,"%.3e ",hess[i][j]);    long sec_left, days, hours, minutes;
     }    days = (time_sec) / (60*60*24);
     printf("\n");    sec_left = (time_sec) % (60*60*24);
     fprintf(ficlog,"\n");    hours = (sec_left) / (60*60) ;
   }    sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
   /* Recompute Inverse */    sec_left = (sec_left) % (60);
   for (i=1;i<=npar;i++)    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    return ascdiff;
   ludcmp(a,npar,indx,&pd);  }
   
   /*  printf("\n#Hessian matrix recomputed#\n");  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   for (j=1;j<=npar;j++) {              double (*func)(double [])) 
     for (i=1;i<=npar;i++) x[i]=0;  { 
     x[j]=1;    void linmin(double p[], double xi[], int n, double *fret, 
     lubksb(a,npar,indx,x);                double (*func)(double [])); 
     for (i=1;i<=npar;i++){    int i,ibig,j; 
       y[i][j]=x[i];    double del,t,*pt,*ptt,*xit;
       printf("%.3e ",y[i][j]);    double fp,fptt;
       fprintf(ficlog,"%.3e ",y[i][j]);    double *xits;
     }    int niterf, itmp;
     printf("\n");  
     fprintf(ficlog,"\n");    pt=vector(1,n); 
   }    ptt=vector(1,n); 
   */    xit=vector(1,n); 
     xits=vector(1,n); 
   free_matrix(a,1,npar,1,npar);    *fret=(*func)(p); 
   free_matrix(y,1,npar,1,npar);    for (j=1;j<=n;j++) pt[j]=p[j]; 
   free_vector(x,1,npar);    for (*iter=1;;++(*iter)) { 
   free_ivector(indx,1,npar);      fp=(*fret); 
   free_matrix(hess,1,npar,1,npar);      ibig=0; 
       del=0.0; 
       last_time=curr_time;
 }      (void) gettimeofday(&curr_time,&tzp);
       printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
 /*************** hessian matrix ****************/      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);
 double hessii( double x[], double delta, int theta, double delti[])  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
 {     for (i=1;i<=n;i++) {
   int i;        printf(" %d %.12f",i, p[i]);
   int l=1, lmax=20;        fprintf(ficlog," %d %.12lf",i, p[i]);
   double k1,k2;        fprintf(ficrespow," %.12lf", p[i]);
   double p2[NPARMAX+1];      }
   double res;      printf("\n");
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      fprintf(ficlog,"\n");
   double fx;      fprintf(ficrespow,"\n");fflush(ficrespow);
   int k=0,kmax=10;      if(*iter <=3){
   double l1;        tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tm));
   fx=func(x);  /*       asctime_r(&tm,strcurr); */
   for (i=1;i<=npar;i++) p2[i]=x[i];        forecast_time=curr_time; 
   for(l=0 ; l <=lmax; l++){        itmp = strlen(strcurr);
     l1=pow(10,l);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     delts=delt;          strcurr[itmp-1]='\0';
     for(k=1 ; k <kmax; k=k+1){        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       delt = delta*(l1*k);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       p2[theta]=x[theta] +delt;        for(niterf=10;niterf<=30;niterf+=10){
       k1=func(p2)-fx;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       p2[theta]=x[theta]-delt;          tmf = *localtime(&forecast_time.tv_sec);
       k2=func(p2)-fx;  /*      asctime_r(&tmf,strfor); */
       /*res= (k1-2.0*fx+k2)/delt/delt; */          strcpy(strfor,asctime(&tmf));
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          itmp = strlen(strfor);
                if(strfor[itmp-1]=='\n')
 #ifdef DEBUG          strfor[itmp-1]='\0';
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       fprintf(ficlog,"%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,"   - 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);
 #endif        }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      for (i=1;i<=n;i++) { 
         k=kmax;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       }        fptt=(*fret); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  #ifdef DEBUG
         k=kmax; l=lmax*10.;        printf("fret=%lf \n",*fret);
       }        fprintf(ficlog,"fret=%lf \n",*fret);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  #endif
         delts=delt;        printf("%d",i);fflush(stdout);
       }        fprintf(ficlog,"%d",i);fflush(ficlog);
     }        linmin(p,xit,n,fret,func); 
   }        if (fabs(fptt-(*fret)) > del) { 
   delti[theta]=delts;          del=fabs(fptt-(*fret)); 
   return res;          ibig=i; 
          } 
 }  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
 double hessij( double x[], double delti[], int thetai,int thetaj)        fprintf(ficlog,"%d %.12e",i,(*fret));
 {        for (j=1;j<=n;j++) {
   int i;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   int l=1, l1, lmax=20;          printf(" x(%d)=%.12e",j,xit[j]);
   double k1,k2,k3,k4,res,fx;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double p2[NPARMAX+1];        }
   int k;        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
   fx=func(x);          fprintf(ficlog," p=%.12e",p[j]);
   for (k=1; k<=2; k++) {        }
     for (i=1;i<=npar;i++) p2[i]=x[i];        printf("\n");
     p2[thetai]=x[thetai]+delti[thetai]/k;        fprintf(ficlog,"\n");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  #endif
     k1=func(p2)-fx;      } 
        if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     p2[thetai]=x[thetai]+delti[thetai]/k;  #ifdef DEBUG
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        int k[2],l;
     k2=func(p2)-fx;        k[0]=1;
          k[1]=-1;
     p2[thetai]=x[thetai]-delti[thetai]/k;        printf("Max: %.12e",(*func)(p));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        fprintf(ficlog,"Max: %.12e",(*func)(p));
     k3=func(p2)-fx;        for (j=1;j<=n;j++) {
            printf(" %.12e",p[j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;          fprintf(ficlog," %.12e",p[j]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        }
     k4=func(p2)-fx;        printf("\n");
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        fprintf(ficlog,"\n");
 #ifdef DEBUG        for(l=0;l<=1;l++) {
     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 (j=1;j<=n;j++) {
     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);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 #endif            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   return res;          }
 }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 /************** Inverse of matrix **************/        }
 void ludcmp(double **a, int n, int *indx, double *d)  #endif
 {  
   int i,imax,j,k;  
   double big,dum,sum,temp;        free_vector(xit,1,n); 
   double *vv;        free_vector(xits,1,n); 
          free_vector(ptt,1,n); 
   vv=vector(1,n);        free_vector(pt,1,n); 
   *d=1.0;        return; 
   for (i=1;i<=n;i++) {      } 
     big=0.0;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++)      for (j=1;j<=n;j++) { 
       if ((temp=fabs(a[i][j])) > big) big=temp;        ptt[j]=2.0*p[j]-pt[j]; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        xit[j]=p[j]-pt[j]; 
     vv[i]=1.0/big;        pt[j]=p[j]; 
   }      } 
   for (j=1;j<=n;j++) {      fptt=(*func)(ptt); 
     for (i=1;i<j;i++) {      if (fptt < fp) { 
       sum=a[i][j];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        if (t < 0.0) { 
       a[i][j]=sum;          linmin(p,xit,n,fret,func); 
     }          for (j=1;j<=n;j++) { 
     big=0.0;            xi[j][ibig]=xi[j][n]; 
     for (i=j;i<=n;i++) {            xi[j][n]=xit[j]; 
       sum=a[i][j];          }
       for (k=1;k<j;k++)  #ifdef DEBUG
         sum -= a[i][k]*a[k][j];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       a[i][j]=sum;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       if ( (dum=vv[i]*fabs(sum)) >= big) {          for(j=1;j<=n;j++){
         big=dum;            printf(" %.12e",xit[j]);
         imax=i;            fprintf(ficlog," %.12e",xit[j]);
       }          }
     }          printf("\n");
     if (j != imax) {          fprintf(ficlog,"\n");
       for (k=1;k<=n;k++) {  #endif
         dum=a[imax][k];        }
         a[imax][k]=a[j][k];      } 
         a[j][k]=dum;    } 
       }  } 
       *d = -(*d);  
       vv[imax]=vv[j];  /**** Prevalence limit (stable or period prevalence)  ****************/
     }  
     indx[j]=imax;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     if (a[j][j] == 0.0) a[j][j]=TINY;  {
     if (j != n) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       dum=1.0/(a[j][j]);       matrix by transitions matrix until convergence is reached */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }    int i, ii,j,k;
   }    double min, max, maxmin, maxmax,sumnew=0.;
   free_vector(vv,1,n);  /* Doesn't work */    double **matprod2();
 ;    double **out, cov[NCOVMAX+1], **pmij();
 }    double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
 void lubksb(double **a, int n, int *indx, double b[])  
 {    for (ii=1;ii<=nlstate+ndeath;ii++)
   int i,ii=0,ip,j;      for (j=1;j<=nlstate+ndeath;j++){
   double sum;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        }
   for (i=1;i<=n;i++) {  
     ip=indx[i];     cov[1]=1.;
     sum=b[ip];   
     b[ip]=b[i];   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     if (ii)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      newm=savm;
     else if (sum) ii=i;      /* Covariates have to be included here again */
     b[i]=sum;       cov[2]=agefin;
   }    
   for (i=n;i>=1;i--) {        for (k=1; k<=cptcovn;k++) {
     sum=b[i];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          /*      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]]);*/
     b[i]=sum/a[i][i];        }
   }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 }        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]]];
 /************ 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)        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 {  /* Some frequencies */        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
          /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   int first;  
   double ***freq; /* Frequencies */      savm=oldm;
   double *pp;      oldm=newm;
   double pos, k2, dateintsum=0,k2cpt=0;      maxmax=0.;
   FILE *ficresp;      for(j=1;j<=nlstate;j++){
   char fileresp[FILENAMELENGTH];        min=1.;
          max=0.;
   pp=vector(1,nlstate);        for(i=1; i<=nlstate; i++) {
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          sumnew=0;
   strcpy(fileresp,"p");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   strcat(fileresp,fileres);          prlim[i][j]= newm[i][j]/(1-sumnew);
   if((ficresp=fopen(fileresp,"w"))==NULL) {          max=FMAX(max,prlim[i][j]);
     printf("Problem with prevalence resultfile: %s\n", fileresp);          min=FMIN(min,prlim[i][j]);
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);        }
     exit(0);        maxmin=max-min;
   }        maxmax=FMAX(maxmax,maxmin);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      }
   j1=0;      if(maxmax < ftolpl){
          return prlim;
   j=cptcoveff;      }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    }
   }
   first=1;  
   /*************** transition probabilities ***************/ 
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       j1++;  {
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double s1, s2;
         scanf("%d", i);*/    /*double t34;*/
       for (i=-1; i<=nlstate+ndeath; i++)      int i,j,j1, nc, ii, jj;
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)      for(i=1; i<= nlstate; i++){
             freq[i][jk][m]=0;        for(j=1; j<i;j++){
                for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       dateintsum=0;            /*s2 += param[i][j][nc]*cov[nc];*/
       k2cpt=0;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for (i=1; i<=imx; i++) {  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
         bool=1;          }
         if  (cptcovn>0) {          ps[i][j]=s2;
           for (z1=1; z1<=cptcoveff; z1++)  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        }
               bool=0;        for(j=i+1; j<=nlstate+ndeath;j++){
         }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         if (bool==1) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           for(m=firstpass; m<=lastpass; m++){  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
             k2=anint[m][i]+(mint[m][i]/12.);          }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          ps[i][j]=s2;
               if(agev[m][i]==0) agev[m][i]=agemax+1;        }
               if(agev[m][i]==1) agev[m][i]=agemax+2;      }
               if (m<lastpass) {      /*ps[3][2]=1;*/
                 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];      for(i=1; i<= nlstate; i++){
               }        s1=0;
                      for(j=1; j<i; j++){
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          s1+=exp(ps[i][j]);
                 dateintsum=dateintsum+k2;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                 k2cpt++;        }
               }        for(j=i+1; j<=nlstate+ndeath; j++){
             }          s1+=exp(ps[i][j]);
           }          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }        }
       }        ps[i][i]=1./(s1+1.);
                for(j=1; j<i; j++)
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
       if  (cptcovn>0) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
         fprintf(ficresp, "\n#********** Variable ");        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      } /* end i */
         fprintf(ficresp, "**********\n#");      
       }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(i=1; i<=nlstate;i++)        for(jj=1; jj<= nlstate+ndeath; jj++){
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          ps[ii][jj]=0;
       fprintf(ficresp, "\n");          ps[ii][ii]=1;
              }
       for(i=(int)agemin; i <= (int)agemax+3; i++){      }
         if(i==(int)agemax+3){      
           fprintf(ficlog,"Total");  
         }else{  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
           if(first==1){  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
             first=0;  /*         printf("ddd %lf ",ps[ii][jj]); */
             printf("See log file for details...\n");  /*       } */
           }  /*       printf("\n "); */
           fprintf(ficlog,"Age %d", i);  /*        } */
         }  /*        printf("\n ");printf("%lf ",cov[2]); */
         for(jk=1; jk <=nlstate ; jk++){         /*
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
             pp[jk] += freq[jk][m][i];        goto end;*/
         }      return ps;
         for(jk=1; jk <=nlstate ; jk++){  }
           for(m=-1, pos=0; m <=0 ; m++)  
             pos += freq[jk][m][i];  /**************** Product of 2 matrices ******************/
           if(pp[jk]>=1.e-10){  
             if(first==1){  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  {
             }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
           }else{    /* in, b, out are matrice of pointers which should have been initialized 
             if(first==1)       before: only the contents of out is modified. The function returns
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       a pointer to pointers identical to out */
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    long i, j, k;
           }    for(i=nrl; i<= nrh; i++)
         }      for(k=ncolol; k<=ncoloh; k++)
         for(j=ncl,out[i][k]=0.; j<=nch; j++)
         for(jk=1; jk <=nlstate ; jk++){          out[i][k] +=in[i][j]*b[j][k];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];    return out;
         }  }
   
         for(jk=1,pos=0; jk <=nlstate ; jk++)  
           pos += pp[jk];  /************* Higher Matrix Product ***************/
         for(jk=1; jk <=nlstate ; jk++){  
           if(pos>=1.e-5){  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
             if(first==1)  {
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    /* Computes the transition matrix starting at age 'age' over 
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);       'nhstepm*hstepm*stepm' months (i.e. until
           }else{       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
             if(first==1)       nhstepm*hstepm matrices. 
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);       (typically every 2 years instead of every month which is too big 
           }       for the memory).
           if( i <= (int) agemax){       Model is determined by parameters x and covariates have to be 
             if(pos>=1.e-5){       included manually here. 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
               probs[i][jk][j1]= pp[jk]/pos;       */
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  
             }    int i, j, d, h, k;
             else    double **out, cov[NCOVMAX+1];
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    double **newm;
           }  
         }    /* Hstepm could be zero and should return the unit matrix */
            for (i=1;i<=nlstate+ndeath;i++)
         for(jk=-1; jk <=nlstate+ndeath; jk++)      for (j=1;j<=nlstate+ndeath;j++){
           for(m=-1; m <=nlstate+ndeath; m++)        oldm[i][j]=(i==j ? 1.0 : 0.0);
             if(freq[jk][m][i] !=0 ) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
             if(first==1)      }
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);    for(h=1; h <=nhstepm; h++){
             }      for(d=1; d <=hstepm; d++){
         if(i <= (int) agemax)        newm=savm;
           fprintf(ficresp,"\n");        /* Covariates have to be included here again */
         if(first==1)        cov[1]=1.;
           printf("Others in log...\n");        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         fprintf(ficlog,"\n");        for (k=1; k<=cptcovn;k++) 
       }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     }        for (k=1; k<=cptcovage;k++)
   }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   dateintmean=dateintsum/k2cpt;        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]]];
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
          /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   /* End of Freq */        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
 /************ Prevalence ********************/        oldm=newm;
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      }
 {  /* Some frequencies */      for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          po[i][j][h]=newm[i][j];
   double ***freq; /* Frequencies */          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   double *pp;        }
   double pos, k2;      /*printf("h=%d ",h);*/
     } /* end h */
   pp=vector(1,nlstate);  /*     printf("\n H=%d \n",h); */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    return po;
    }
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  
    /*************** log-likelihood *************/
   j=cptcoveff;  double func( double *x)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  {
      int i, ii, j, k, mi, d, kk;
   for(k1=1; k1<=j;k1++){    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     for(i1=1; i1<=ncodemax[k1];i1++){    double **out;
       j1++;    double sw; /* Sum of weights */
          double lli; /* Individual log likelihood */
       for (i=-1; i<=nlstate+ndeath; i++)      int s1, s2;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double bbh, survp;
           for(m=agemin; m <= agemax+3; m++)    long ipmx;
             freq[i][jk][m]=0;    /*extern weight */
          /* We are differentiating ll according to initial status */
       for (i=1; i<=imx; i++) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         bool=1;    /*for(i=1;i<imx;i++) 
         if  (cptcovn>0) {      printf(" %d\n",s[4][i]);
           for (z1=1; z1<=cptcoveff; z1++)    */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    cov[1]=1.;
               bool=0;  
         }    for(k=1; k<=nlstate; k++) ll[k]=0.;
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){    if(mle==1){
             k2=anint[m][i]+(mint[m][i]/12.);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               if(agev[m][i]==0) agev[m][i]=agemax+1;        for(mi=1; mi<= wav[i]-1; mi++){
               if(agev[m][i]==1) agev[m][i]=agemax+2;          for (ii=1;ii<=nlstate+ndeath;ii++)
               if (m<lastpass) {            for (j=1;j<=nlstate+ndeath;j++){
                 if (calagedate>0)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                 else            }
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          for(d=0; d<dh[mi][i]; d++){
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];            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];
         }            }
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=(int)agemin; i <= (int)agemax+3; i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(jk=1; jk <=nlstate ; jk++){            savm=oldm;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            oldm=newm;
             pp[jk] += freq[jk][m][i];          } /* end mult */
         }        
         for(jk=1; jk <=nlstate ; jk++){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           for(m=-1, pos=0; m <=0 ; m++)          /* But now since version 0.9 we anticipate for bias at large stepm.
             pos += freq[jk][m][i];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         }           * (in months) between two waves is not a multiple of stepm, we rounded to 
                   * the nearest (and in case of equal distance, to the lowest) interval but now
         for(jk=1; jk <=nlstate ; jk++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
             pp[jk] += freq[jk][m][i];           * probability in order to take into account the bias as a fraction of the way
         }           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
                   * -stepm/2 to stepm/2 .
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];           * For stepm=1 the results are the same as for previous versions of Imach.
                   * For stepm > 1 the results are less biased than in previous versions. 
         for(jk=1; jk <=nlstate ; jk++){               */
           if( i <= (int) agemax){          s1=s[mw[mi][i]][i];
             if(pos>=1.e-5){          s2=s[mw[mi+1][i]][i];
               probs[i][jk][j1]= pp[jk]/pos;          bbh=(double)bh[mi][i]/(double)stepm; 
             }          /* bias bh is positive if real duration
           }           * is higher than the multiple of stepm and negative otherwise.
         }/* end jk */           */
       }/* end i */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     } /* end i1 */          if( s2 > nlstate){ 
   } /* end k1 */            /* i.e. if s2 is a death state and if the date of death is known 
                then the contribution to the likelihood is the probability to 
                 die between last step unit time and current  step unit time, 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);               which is also equal to probability to die before dh 
   free_vector(pp,1,nlstate);               minus probability to die before dh-stepm . 
                 In version up to 0.92 likelihood was computed
 }  /* End of Freq */          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
 /************* Waves Concatenation ***************/          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          (healthy, disable or death) and IMaCh was corrected; but when we
 {          introduced the exact date of death then we should have modified
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          the contribution of an exact death to the likelihood. This new
      Death is a valid wave (if date is known).          contribution is smaller and very dependent of the step unit
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          stepm. It is no more the probability to die between last interview
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          and month of death but the probability to survive from last
      and mw[mi+1][i]. dh depends on stepm.          interview up to one month before death multiplied by the
      */          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
   int i, mi, m;          mortality artificially. The bad side is that we add another loop
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          which slows down the processing. The difference can be up to 10%
      double sum=0., jmean=0.;*/          lower mortality.
   int first;            */
   int j, k=0,jk, ju, jl;            lli=log(out[s1][s2] - savm[s1][s2]);
   double sum=0.;  
   first=0;  
   jmin=1e+5;          } else if  (s2==-2) {
   jmax=-1;            for (j=1,survp=0. ; j<=nlstate; j++) 
   jmean=0.;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   for(i=1; i<=imx; i++){            /*survp += out[s1][j]; */
     mi=0;            lli= log(survp);
     m=firstpass;          }
     while(s[m][i] <= nlstate){          
       if(s[m][i]>=1)          else if  (s2==-4) { 
         mw[++mi][i]=m;            for (j=3,survp=0. ; j<=nlstate; j++)  
       if(m >=lastpass)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         break;            lli= log(survp); 
       else          } 
         m++;  
     }/* end while */          else if  (s2==-5) { 
     if (s[m][i] > nlstate){            for (j=1,survp=0. ; j<=2; j++)  
       mi++;     /* Death is another wave */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       /* if(mi==0)  never been interviewed correctly before death */            lli= log(survp); 
          /* Only death is a correct wave */          } 
       mw[mi][i]=m;          
     }          else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     wav[i]=mi;            /*  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 */
     if(mi==0){          } 
       if(first==0){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);          /*if(lli ==000.0)*/
         first=1;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       }          ipmx +=1;
       if(first==1){          sw += weight[i];
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        } /* end of wave */
     } /* end mi==0 */      } /* end of individual */
   }    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for(i=1; i<=imx; i++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(mi=1; mi<wav[i];mi++){        for(mi=1; mi<= wav[i]-1; mi++){
       if (stepm <=0)          for (ii=1;ii<=nlstate+ndeath;ii++)
         dh[mi][i]=1;            for (j=1;j<=nlstate+ndeath;j++){
       else{              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (s[mw[mi+1][i]][i] > nlstate) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           if (agedc[i] < 2*AGESUP) {            }
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          for(d=0; d<=dh[mi][i]; d++){
           if(j==0) j=1;  /* Survives at least one month after exam */            newm=savm;
           k=k+1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           if (j >= jmax) jmax=j;            for (kk=1; kk<=cptcovage;kk++) {
           if (j <= jmin) jmin=j;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           sum=sum+j;            }
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
         else{            oldm=newm;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          } /* end mult */
           k=k+1;        
           if (j >= jmax) jmax=j;          s1=s[mw[mi][i]][i];
           else if (j <= jmin)jmin=j;          s2=s[mw[mi+1][i]][i];
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          bbh=(double)bh[mi][i]/(double)stepm; 
           sum=sum+j;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         }          ipmx +=1;
         jk= j/stepm;          sw += weight[i];
         jl= j -jk*stepm;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         ju= j -(jk+1)*stepm;        } /* end of wave */
         if(jl <= -ju)      } /* end of individual */
           dh[mi][i]=jk;    }  else if(mle==3){  /* exponential inter-extrapolation */
         else      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           dh[mi][i]=jk+1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if(dh[mi][i]==0)        for(mi=1; mi<= wav[i]-1; mi++){
           dh[mi][i]=1; /* At least one step */          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   jmean=sum/k;            }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          for(d=0; d<dh[mi][i]; d++){
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            newm=savm;
  }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 /*********** Tricode ****************************/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 void tricode(int *Tvar, int **nbcode, int imx)            }
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int Ndum[20],ij=1, k, j, i;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int cptcode=0;            savm=oldm;
   cptcoveff=0;            oldm=newm;
            } /* end mult */
   for (k=0; k<19; k++) Ndum[k]=0;        
   for (k=1; k<=7; k++) ncodemax[k]=0;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=1; i<=imx; i++) {          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       ij=(int)(covar[Tvar[j]][i]);          ipmx +=1;
       Ndum[ij]++;          sw += weight[i];
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       if (ij > cptcode) cptcode=ij;        } /* end of wave */
     }      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
     for (i=0; i<=cptcode; i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if(Ndum[i]!=0) ncodemax[j]++;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
     ij=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1; i<=ncodemax[j]; i++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (k=0; k<=19; k++) {            }
         if (Ndum[k] != 0) {          for(d=0; d<dh[mi][i]; d++){
           nbcode[Tvar[j]][ij]=k;            newm=savm;
                      cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           ij++;            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         if (ij > ncodemax[j]) break;            }
       }            
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
  for (k=0; k<19; k++) Ndum[k]=0;            oldm=newm;
           } /* end mult */
  for (i=1; i<=ncovmodel-2; i++) {        
    ij=Tvar[i];          s1=s[mw[mi][i]][i];
    Ndum[ij]++;          s2=s[mw[mi+1][i]][i];
  }          if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
  ij=1;          }else{
  for (i=1; i<=10; i++) {            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
    if((Ndum[i]!=0) && (i<=ncovcol)){          }
      Tvaraff[ij]=i;          ipmx +=1;
      ij++;          sw += weight[i];
    }          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 */
  cptcoveff=ij-1;      } /* end of individual */
 }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       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,
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   xp=vector(1,npar);            savm=oldm;
   dnewm=matrix(1,nlstate*2,1,npar);            oldm=newm;
   doldm=matrix(1,nlstate*2,1,nlstate*2);          } /* end mult */
          
   fprintf(ficreseij,"# Health expectancies\n");          s1=s[mw[mi][i]][i];
   fprintf(ficreseij,"# Age");          s2=s[mw[mi+1][i]][i];
   for(i=1; i<=nlstate;i++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(j=1; j<=nlstate;j++)          ipmx +=1;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          sw += weight[i];
   fprintf(ficreseij,"\n");          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]);*/
   if(estepm < stepm){        } /* end of wave */
     printf ("Problem %d lower than %d\n",estepm, stepm);      } /* end of individual */
   }    } /* End of if */
   else  hstepm=estepm;      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* We compute the life expectancy from trapezoids spaced every estepm months    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
    * This is mainly to measure the difference between two models: for example    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
    * if stepm=24 months pijx are given only every 2 years and by summing them    return -l;
    * we are calculating an estimate of the Life Expectancy assuming a linear  }
    * progression inbetween and thus overestimating or underestimating according  
    * to the curvature of the survival function. If, for the same date, we  /*************** log-likelihood *************/
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  double funcone( double *x)
    * to compare the new estimate of Life expectancy with the same linear  {
    * hypothesis. A more precise result, taking into account a more precise    /* Same as likeli but slower because of a lot of printf and if */
    * curvature will be obtained if estepm is as small as stepm. */    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   /* For example we decided to compute the life expectancy with the smallest unit */    double **out;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double lli; /* Individual log likelihood */
      nhstepm is the number of hstepm from age to agelim    double llt;
      nstepm is the number of stepm from age to agelin.    int s1, s2;
      Look at hpijx to understand the reason of that which relies in memory size    double bbh, survp;
      and note for a fixed period like estepm months */    /*extern weight */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* We are differentiating ll according to initial status */
      survival function given by stepm (the optimization length). Unfortunately it    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      means that if the survival funtion is printed only each two years of age and if    /*for(i=1;i<imx;i++) 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      printf(" %d\n",s[4][i]);
      results. So we changed our mind and took the option of the best precision.    */
   */    cov[1]=1.;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     /* nhstepm age range expressed in number of stepm */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      for(mi=1; mi<= wav[i]-1; mi++){
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        for (ii=1;ii<=nlstate+ndeath;ii++)
     /* if (stepm >= YEARM) hstepm=1;*/          for (j=1;j<=nlstate+ndeath;j++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          }
     gp=matrix(0,nhstepm,1,nlstate*2);        for(d=0; d<dh[mi][i]; d++){
     gm=matrix(0,nhstepm,1,nlstate*2);          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          for (kk=1; kk<=cptcovage;kk++) {
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          savm=oldm;
           oldm=newm;
     /* Computing Variances of health expectancies */        } /* end mult */
         
      for(theta=1; theta <=npar; theta++){        s1=s[mw[mi][i]][i];
       for(i=1; i<=npar; i++){        s2=s[mw[mi+1][i]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        bbh=(double)bh[mi][i]/(double)stepm; 
       }        /* bias is positive if real duration
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);           * is higher than the multiple of stepm and negative otherwise.
           */
       cptj=0;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       for(j=1; j<= nlstate; j++){          lli=log(out[s1][s2] - savm[s1][s2]);
         for(i=1; i<=nlstate; i++){        } else if  (s2==-2) {
           cptj=cptj+1;          for (j=1,survp=0. ; j<=nlstate; j++) 
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          lli= log(survp);
           }        }else if (mle==1){
         }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }        } else if(mle==2){
                lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
              } else if(mle==3){  /* exponential inter-extrapolation */
       for(i=1; i<=npar; i++)          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 */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            lli=log(out[s1][s2]); /* Original formula */
              } else{  /* mle=0 back to 1 */
       cptj=0;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for(j=1; j<= nlstate; j++){          /*lli=log(out[s1][s2]); */ /* Original formula */
         for(i=1;i<=nlstate;i++){        } /* End of if */
           cptj=cptj+1;        ipmx +=1;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){        sw += weight[i];
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        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]); */
         }        if(globpr){
       }          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       for(j=1; j<= nlstate*2; j++)   %11.6f %11.6f %11.6f ", \
         for(h=0; h<=nhstepm-1; h++){                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
      }            llt +=ll[k]*gipmx/gsw;
                fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
 /* End theta */          }
           fprintf(ficresilk," %10.6f\n", -llt);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);        }
       } /* end of wave */
      for(h=0; h<=nhstepm-1; h++)    } /* end of individual */
       for(j=1; j<=nlstate*2;j++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         for(theta=1; theta <=npar; theta++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           trgradg[h][j][theta]=gradg[h][theta][j];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
          if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
      for(i=1;i<=nlstate*2;i++)      gsw=sw;
       for(j=1;j<=nlstate*2;j++)    }
         varhe[i][j][(int)age] =0.;    return -l;
   }
      printf("%d|",(int)age);fflush(stdout);  
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);  
      for(h=0;h<=nhstepm-1;h++){  /*************** function likelione ***********/
       for(k=0;k<=nhstepm-1;k++){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  {
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    /* This routine should help understanding what is done with 
         for(i=1;i<=nlstate*2;i++)       the selection of individuals/waves and
           for(j=1;j<=nlstate*2;j++)       to check the exact contribution to the likelihood.
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;       Plotting could be done.
       }     */
     }    int k;
     /* Computing expectancies */  
     for(i=1; i<=nlstate;i++)    if(*globpri !=0){ /* Just counts and sums, no printings */
       for(j=1; j<=nlstate;j++)      strcpy(fileresilk,"ilk"); 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      strcat(fileresilk,fileres);
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
                  printf("Problem with resultfile: %s\n", fileresilk);
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
         }      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     fprintf(ficreseij,"%3.0f",age );      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     cptj=0;      for(k=1; k<=nlstate; k++) 
     for(i=1; i<=nlstate;i++)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       for(j=1; j<=nlstate;j++){      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         cptj++;    }
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );  
       }    *fretone=(*funcone)(p);
     fprintf(ficreseij,"\n");    if(*globpri !=0){
          fclose(ficresilk);
     free_matrix(gm,0,nhstepm,1,nlstate*2);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     free_matrix(gp,0,nhstepm,1,nlstate*2);      fflush(fichtm); 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    } 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    return;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
   }  
   printf("\n");  
   fprintf(ficlog,"\n");  /*********** Maximum Likelihood Estimation ***************/
   
   free_vector(xp,1,npar);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   free_matrix(dnewm,1,nlstate*2,1,npar);  {
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    int i,j, iter;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    double **xi;
 }    double fret;
     double fretone; /* Only one call to likelihood */
 /************ Variance ******************/    /*  char filerespow[FILENAMELENGTH];*/
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased)    xi=matrix(1,npar,1,npar);
 {    for (i=1;i<=npar;i++)
   /* Variance of health expectancies */      for (j=1;j<=npar;j++)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        xi[i][j]=(i==j ? 1.0 : 0.0);
   /* double **newm;*/    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double **dnewm,**doldm;    strcpy(filerespow,"pow"); 
   double **dnewmp,**doldmp;    strcat(filerespow,fileres);
   int i, j, nhstepm, hstepm, h, nstepm ;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   int k, cptcode;      printf("Problem with resultfile: %s\n", filerespow);
   double *xp;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   double **gp, **gm;  /* for var eij */    }
   double ***gradg, ***trgradg; /*for var eij */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   double **gradgp, **trgradgp; /* for var p point j */    for (i=1;i<=nlstate;i++)
   double *gpp, *gmp; /* for var p point j */      for(j=1;j<=nlstate+ndeath;j++)
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   double ***p3mat;    fprintf(ficrespow,"\n");
   double age,agelim, hf;  
   int theta;    powell(p,xi,npar,ftol,&iter,&fret,func);
   char digit[4];  
   char digitp[16];    free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
   char fileresprobmorprev[FILENAMELENGTH];    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));
   if(popbased==1)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     strcpy(digitp,"-populbased-");  
   else  }
     strcpy(digitp,"-stablbased-");  
   /**** Computes Hessian and covariance matrix ***/
   strcpy(fileresprobmorprev,"prmorprev");  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   sprintf(digit,"%-d",ij);  {
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    double  **a,**y,*x,pd;
   strcat(fileresprobmorprev,digit); /* Tvar to be done */    double **hess;
   strcat(fileresprobmorprev,digitp); /* Popbased or not */    int i, j,jk;
   strcat(fileresprobmorprev,fileres);    int *indx;
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobmorprev);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   }    void lubksb(double **a, int npar, int *indx, double b[]) ;
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    double gompertz(double p[]);
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");    hess=matrix(1,npar,1,npar);
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);  
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficresprobmorprev," p.%-d SE",j);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++){
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);      printf("%d",i);fflush(stdout);
   }        fprintf(ficlog,"%d",i);fflush(ficlog);
   fprintf(ficresprobmorprev,"\n");     
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);      
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);      /*  printf(" %f ",p[i]);
     exit(0);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   }    }
   else{    
     fprintf(ficgp,"\n# Routine varevsij");    for (i=1;i<=npar;i++) {
   }      for (j=1;j<=npar;j++)  {
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {        if (j>i) { 
     printf("Problem with html file: %s\n", optionfilehtm);          printf(".%d%d",i,j);fflush(stdout);
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     exit(0);          hess[i][j]=hessij(p,delti,i,j,func,npar);
   }          
   else{          hess[j][i]=hess[i][j];    
     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");          /*printf(" %lf ",hess[i][j]);*/
   }        }
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      }
     }
   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");    printf("\n");
   fprintf(ficresvij,"# Age");    fprintf(ficlog,"\n");
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   fprintf(ficresvij,"\n");    
     a=matrix(1,npar,1,npar);
   xp=vector(1,npar);    y=matrix(1,npar,1,npar);
   dnewm=matrix(1,nlstate,1,npar);    x=vector(1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    indx=ivector(1,npar);
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);    for (i=1;i<=npar;i++)
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);  
   gpp=vector(nlstate+1,nlstate+ndeath);    for (j=1;j<=npar;j++) {
   gmp=vector(nlstate+1,nlstate+ndeath);      for (i=1;i<=npar;i++) x[i]=0;
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/      x[j]=1;
        lubksb(a,npar,indx,x);
   if(estepm < stepm){      for (i=1;i<=npar;i++){ 
     printf ("Problem %d lower than %d\n",estepm, stepm);        matcov[i][j]=x[i];
   }      }
   else  hstepm=estepm;      }
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    printf("\n#Hessian matrix#\n");
      nhstepm is the number of hstepm from age to agelim    fprintf(ficlog,"\n#Hessian matrix#\n");
      nstepm is the number of stepm from age to agelin.    for (i=1;i<=npar;i++) { 
      Look at hpijx to understand the reason of that which relies in memory size      for (j=1;j<=npar;j++) { 
      and note for a fixed period like k years */        printf("%.3e ",hess[i][j]);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        fprintf(ficlog,"%.3e ",hess[i][j]);
      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      printf("\n");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      fprintf(ficlog,"\n");
      results. So we changed our mind and took the option of the best precision.    }
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    /* Recompute Inverse */
   agelim = AGESUP;    for (i=1;i<=npar;i++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    ludcmp(a,npar,indx,&pd);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*  printf("\n#Hessian matrix recomputed#\n");
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);    for (j=1;j<=npar;j++) {
     gm=matrix(0,nhstepm,1,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
       lubksb(a,npar,indx,x);
     for(theta=1; theta <=npar; theta++){      for (i=1;i<=npar;i++){ 
       for(i=1; i<=npar; i++){ /* Computes gradient */        y[i][j]=x[i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        printf("%.3e ",y[i][j]);
       }        fprintf(ficlog,"%.3e ",y[i][j]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      printf("\n");
       fprintf(ficlog,"\n");
       if (popbased==1) {    }
         for(i=1; i<=nlstate;i++)    */
           prlim[i][i]=probs[(int)age][i][ij];  
       }    free_matrix(a,1,npar,1,npar);
      free_matrix(y,1,npar,1,npar);
       for(j=1; j<= nlstate; j++){    free_vector(x,1,npar);
         for(h=0; h<=nhstepm; h++){    free_ivector(indx,1,npar);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    free_matrix(hess,1,npar,1,npar);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  
       }  }
       /* This for computing forces of mortality (h=1)as a weighted average */  
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){  /*************** hessian matrix ****************/
         for(i=1; i<= nlstate; i++)  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           gpp[j] += prlim[i][i]*p3mat[i][j][1];  {
       }        int i;
       /* end force of mortality */    int l=1, lmax=20;
     double k1,k2;
       for(i=1; i<=npar; i++) /* Computes gradient */    double p2[MAXPARM+1]; /* identical to x */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double res;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double fx;
      int k=0,kmax=10;
       if (popbased==1) {    double l1;
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    fx=func(x);
       }    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
       for(j=1; j<= nlstate; j++){      l1=pow(10,l);
         for(h=0; h<=nhstepm; h++){      delts=delt;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for(k=1 ; k <kmax; k=k+1){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        delt = delta*(l1*k);
         }        p2[theta]=x[theta] +delt;
       }        k1=func(p2)-fx;
       /* This for computing force of mortality (h=1)as a weighted average */        p2[theta]=x[theta]-delt;
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){        k2=func(p2)-fx;
         for(i=1; i<= nlstate; i++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
           gmp[j] += prlim[i][i]*p3mat[i][j][1];        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       }            
       /* end force of mortality */  #ifdef DEBUGHESS
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       for(j=1; j<= nlstate; j++) /* vareij */        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);
         for(h=0; h<=nhstepm; h++){  #endif
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          k=kmax;
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];        }
       }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
     } /* End theta */        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */          delts=delt;
         }
     for(h=0; h<=nhstepm; h++) /* veij */      }
       for(j=1; j<=nlstate;j++)    }
         for(theta=1; theta <=npar; theta++)    delti[theta]=delts;
           trgradg[h][j][theta]=gradg[h][theta][j];    return res; 
     
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */  }
       for(theta=1; theta <=npar; theta++)  
         trgradgp[j][theta]=gradgp[theta][j];  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   {
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    int i;
     for(i=1;i<=nlstate;i++)    int l=1, l1, lmax=20;
       for(j=1;j<=nlstate;j++)    double k1,k2,k3,k4,res,fx;
         vareij[i][j][(int)age] =0.;    double p2[MAXPARM+1];
     int k;
     for(h=0;h<=nhstepm;h++){  
       for(k=0;k<=nhstepm;k++){    fx=func(x);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    for (k=1; k<=2; k++) {
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      for (i=1;i<=npar;i++) p2[i]=x[i];
         for(i=1;i<=nlstate;i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
           for(j=1;j<=nlstate;j++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      k1=func(p2)-fx;
       }    
     }      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     /* pptj */      k2=func(p2)-fx;
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);    
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);      p2[thetai]=x[thetai]-delti[thetai]/k;
     for(j=nlstate+1;j<=nlstate+ndeath;j++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       for(i=nlstate+1;i<=nlstate+ndeath;i++)      k3=func(p2)-fx;
         varppt[j][i]=doldmp[j][i];    
     /* end ppptj */      p2[thetai]=x[thetai]-delti[thetai]/k;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);      k4=func(p2)-fx;
        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     if (popbased==1) {  #ifdef DEBUG
       for(i=1; i<=nlstate;i++)      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);
         prlim[i][i]=probs[(int)age][i][ij];      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
        }
     /* This for computing force of mortality (h=1)as a weighted average */    return res;
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){  }
       for(i=1; i<= nlstate; i++)  
         gmp[j] += prlim[i][i]*p3mat[i][j][1];  /************** Inverse of matrix **************/
     }      void ludcmp(double **a, int n, int *indx, double *d) 
     /* end force of mortality */  { 
     int i,imax,j,k; 
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);    double big,dum,sum,temp; 
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){    double *vv; 
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));   
       for(i=1; i<=nlstate;i++){    vv=vector(1,n); 
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);    *d=1.0; 
       }    for (i=1;i<=n;i++) { 
     }      big=0.0; 
     fprintf(ficresprobmorprev,"\n");      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
     fprintf(ficresvij,"%.0f ",age );      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     for(i=1; i<=nlstate;i++)      vv[i]=1.0/big; 
       for(j=1; j<=nlstate;j++){    } 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    for (j=1;j<=n;j++) { 
       }      for (i=1;i<j;i++) { 
     fprintf(ficresvij,"\n");        sum=a[i][j]; 
     free_matrix(gp,0,nhstepm,1,nlstate);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     free_matrix(gm,0,nhstepm,1,nlstate);        a[i][j]=sum; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      } 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      big=0.0; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=j;i<=n;i++) { 
   } /* End age */        sum=a[i][j]; 
   free_vector(gpp,nlstate+1,nlstate+ndeath);        for (k=1;k<j;k++) 
   free_vector(gmp,nlstate+1,nlstate+ndeath);          sum -= a[i][k]*a[k][j]; 
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);        a[i][j]=sum; 
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");          big=dum; 
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */          imax=i; 
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");        } 
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);      } 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);      if (j != imax) { 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);        for (k=1;k<=n;k++) { 
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);          dum=a[imax][k]; 
   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);          a[imax][k]=a[j][k]; 
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);          a[j][k]=dum; 
         } 
   free_vector(xp,1,npar);        *d = -(*d); 
   free_matrix(doldm,1,nlstate,1,nlstate);        vv[imax]=vv[j]; 
   free_matrix(dnewm,1,nlstate,1,npar);      } 
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      indx[j]=imax; 
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);      if (a[j][j] == 0.0) a[j][j]=TINY; 
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      if (j != n) { 
   fclose(ficresprobmorprev);        dum=1.0/(a[j][j]); 
   fclose(ficgp);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   fclose(fichtm);      } 
     } 
 }    free_vector(vv,1,n);  /* Doesn't work */
   ;
 /************ 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)  
 {  void lubksb(double **a, int n, int *indx, double b[]) 
   /* Variance of prevalence limit */  { 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    int i,ii=0,ip,j; 
   double **newm;    double sum; 
   double **dnewm,**doldm;   
   int i, j, nhstepm, hstepm;    for (i=1;i<=n;i++) { 
   int k, cptcode;      ip=indx[i]; 
   double *xp;      sum=b[ip]; 
   double *gp, *gm;      b[ip]=b[i]; 
   double **gradg, **trgradg;      if (ii) 
   double age,agelim;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   int theta;      else if (sum) ii=i; 
          b[i]=sum; 
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    } 
   fprintf(ficresvpl,"# Age");    for (i=n;i>=1;i--) { 
   for(i=1; i<=nlstate;i++)      sum=b[i]; 
       fprintf(ficresvpl," %1d-%1d",i,i);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   fprintf(ficresvpl,"\n");      b[i]=sum/a[i][i]; 
     } 
   xp=vector(1,npar);  } 
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);  void pstamp(FILE *fichier)
    {
   hstepm=1*YEARM; /* Every year of age */    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  }
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  /************ Frequencies ********************/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  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[])
     if (stepm >= YEARM) hstepm=1;  {  /* Some frequencies */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    
     gradg=matrix(1,npar,1,nlstate);    int i, m, jk, k1,i1, j1, bool, z1,j;
     gp=vector(1,nlstate);    int first;
     gm=vector(1,nlstate);    double ***freq; /* Frequencies */
     double *pp, **prop;
     for(theta=1; theta <=npar; theta++){    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       for(i=1; i<=npar; i++){ /* Computes gradient */    char fileresp[FILENAMELENGTH];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    
       }    pp=vector(1,nlstate);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    prop=matrix(1,nlstate,iagemin,iagemax+3);
       for(i=1;i<=nlstate;i++)    strcpy(fileresp,"p");
         gp[i] = prlim[i][i];    strcat(fileresp,fileres);
        if((ficresp=fopen(fileresp,"w"))==NULL) {
       for(i=1; i<=npar; i++) /* Computes gradient */      printf("Problem with prevalence resultfile: %s\n", fileresp);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      exit(0);
       for(i=1;i<=nlstate;i++)    }
         gm[i] = prlim[i][i];    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
       for(i=1;i<=nlstate;i++)    
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    j=cptcoveff;
     } /* End theta */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
     trgradg =matrix(1,nlstate,1,npar);    first=1;
   
     for(j=1; j<=nlstate;j++)    for(k1=1; k1<=j;k1++){
       for(theta=1; theta <=npar; theta++)      for(i1=1; i1<=ncodemax[k1];i1++){
         trgradg[j][theta]=gradg[theta][j];        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     for(i=1;i<=nlstate;i++)          scanf("%d", i);*/
       varpl[i][(int)age] =0.;        for (i=-5; i<=nlstate+ndeath; i++)  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            for(m=iagemin; m <= iagemax+3; m++)
     for(i=1;i<=nlstate;i++)              freq[i][jk][m]=0;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  
       for (i=1; i<=nlstate; i++)  
     fprintf(ficresvpl,"%.0f ",age );        for(m=iagemin; m <= iagemax+3; m++)
     for(i=1; i<=nlstate;i++)          prop[i][m]=0;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        
     fprintf(ficresvpl,"\n");        dateintsum=0;
     free_vector(gp,1,nlstate);        k2cpt=0;
     free_vector(gm,1,nlstate);        for (i=1; i<=imx; i++) {
     free_matrix(gradg,1,npar,1,nlstate);          bool=1;
     free_matrix(trgradg,1,nlstate,1,npar);          if  (cptcovn>0) {
   } /* End age */            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   free_vector(xp,1,npar);                bool=0;
   free_matrix(doldm,1,nlstate,1,npar);          }
   free_matrix(dnewm,1,nlstate,1,nlstate);          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
 }              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 /************ Variance of one-step probabilities  ******************/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 {                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   int i, j=0,  i1, k1, l1, t, tj;                if (m<lastpass) {
   int k2, l2, j1,  z1;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   int k=0,l, cptcode;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   int first=1, first1;                }
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;                
   double **dnewm,**doldm;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   double *xp;                  dateintsum=dateintsum+k2;
   double *gp, *gm;                  k2cpt++;
   double **gradg, **trgradg;                }
   double **mu;                /*}*/
   double age,agelim, cov[NCOVMAX];            }
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */          }
   int theta;        }
   char fileresprob[FILENAMELENGTH];         
   char fileresprobcov[FILENAMELENGTH];        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   char fileresprobcor[FILENAMELENGTH];        pstamp(ficresp);
         if  (cptcovn>0) {
   double ***varpij;          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcpy(fileresprob,"prob");          fprintf(ficresp, "**********\n#");
   strcat(fileresprob,fileres);        }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        for(i=1; i<=nlstate;i++) 
     printf("Problem with resultfile: %s\n", fileresprob);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);        fprintf(ficresp, "\n");
   }        
   strcpy(fileresprobcov,"probcov");        for(i=iagemin; i <= iagemax+3; i++){
   strcat(fileresprobcov,fileres);          if(i==iagemax+3){
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {            fprintf(ficlog,"Total");
     printf("Problem with resultfile: %s\n", fileresprobcov);          }else{
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);            if(first==1){
   }              first=0;
   strcpy(fileresprobcor,"probcor");              printf("See log file for details...\n");
   strcat(fileresprobcor,fileres);            }
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {            fprintf(ficlog,"Age %d", i);
     printf("Problem with resultfile: %s\n", fileresprobcor);          }
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);              pp[jk] += freq[jk][m][i]; 
   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);          for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);            for(m=-1, pos=0; m <=0 ; m++)
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);              pos += freq[jk][m][i];
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);            if(pp[jk]>=1.e-10){
                if(first==1){
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   fprintf(ficresprob,"# Age");              }
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   fprintf(ficresprobcov,"# Age");            }else{
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");              if(first==1)
   fprintf(ficresprobcov,"# Age");                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   for(i=1; i<=nlstate;i++)          }
     for(j=1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficresprobcov," p%1d-%1d ",i,j);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       fprintf(ficresprobcor," p%1d-%1d ",i,j);              pp[jk] += freq[jk][m][i];
     }            }       
   fprintf(ficresprob,"\n");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   fprintf(ficresprobcov,"\n");            pos += pp[jk];
   fprintf(ficresprobcor,"\n");            posprop += prop[jk][i];
   xp=vector(1,npar);          }
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          for(jk=1; jk <=nlstate ; jk++){
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));            if(pos>=1.e-5){
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);              if(first==1)
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   first=1;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            }else{
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);              if(first==1)
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     exit(0);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   }            }
   else{            if( i <= iagemax){
     fprintf(ficgp,"\n# Routine varprob");              if(pos>=1.e-5){
   }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {                /*probs[i][jk][j1]= pp[jk]/pos;*/
     printf("Problem with html file: %s\n", optionfilehtm);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);              }
     exit(0);              else
   }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   else{            }
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");          }
     fprintf(fichtm,"\n");          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");            for(m=-1; m <=nlstate+ndeath; m++)
     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(freq[jk][m][i] !=0 ) {
     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");              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
            if(i <= iagemax)
   cov[1]=1;            fprintf(ficresp,"\n");
   tj=cptcoveff;          if(first==1)
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}            printf("Others in log...\n");
   j1=0;          fprintf(ficlog,"\n");
   for(t=1; t<=tj;t++){        }
     for(i1=1; i1<=ncodemax[t];i1++){      }
       j1++;    }
          dateintmean=dateintsum/k2cpt; 
       if  (cptcovn>0) {   
         fprintf(ficresprob, "\n#********** Variable ");    fclose(ficresp);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         fprintf(ficresprob, "**********\n#");    free_vector(pp,1,nlstate);
         fprintf(ficresprobcov, "\n#********** Variable ");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /* End of Freq */
         fprintf(ficresprobcov, "**********\n#");  }
          
         fprintf(ficgp, "\n#********** Variable ");  /************ Prevalence ********************/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
         fprintf(ficgp, "**********\n#");  {  
            /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
               in each health status at the date of interview (if between dateprev1 and dateprev2).
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");       We still use firstpass and lastpass as another selection.
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    */
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");   
            int i, m, jk, k1, i1, j1, bool, z1,j;
         fprintf(ficresprobcor, "\n#********** Variable ");        double ***freq; /* Frequencies */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double *pp, **prop;
         fprintf(ficgp, "**********\n#");        double pos,posprop; 
       }    double  y2; /* in fractional years */
          int iagemin, iagemax;
       for (age=bage; age<=fage; age ++){  
         cov[2]=age;    iagemin= (int) agemin;
         for (k=1; k<=cptcovn;k++) {    iagemax= (int) agemax;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    /*pp=vector(1,nlstate);*/
         }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         for (k=1; k<=cptcovprod;k++)    j1=0;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    
            j=cptcoveff;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    
         gp=vector(1,(nlstate)*(nlstate+ndeath));    for(k1=1; k1<=j;k1++){
         gm=vector(1,(nlstate)*(nlstate+ndeath));      for(i1=1; i1<=ncodemax[k1];i1++){
            j1++;
         for(theta=1; theta <=npar; theta++){        
           for(i=1; i<=npar; i++)        for (i=1; i<=nlstate; i++)  
             xp[i] = x[i] + (i==theta ?delti[theta]:0);          for(m=iagemin; m <= iagemax+3; m++)
                      prop[i][m]=0.0;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);       
                  for (i=1; i<=imx; i++) { /* Each individual */
           k=0;          bool=1;
           for(i=1; i<= (nlstate); i++){          if  (cptcovn>0) {
             for(j=1; j<=(nlstate+ndeath);j++){            for (z1=1; z1<=cptcoveff; z1++) 
               k=k+1;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
               gp[k]=pmmij[i][j];                bool=0;
             }          } 
           }          if (bool==1) { 
                      for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           for(i=1; i<=npar; i++)              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                    if(agev[m][i]==0) agev[m][i]=iagemax+1;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           k=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(i=1; i<=(nlstate); i++){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
             for(j=1; j<=(nlstate+ndeath);j++){                  /*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]]);*/
               k=k+1;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
               gm[k]=pmmij[i][j];                  prop[s[m][i]][iagemax+3] += weight[i]; 
             }                } 
           }              }
                  } /* end selection of waves */
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)          }
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          }
         }        for(i=iagemin; i <= iagemax+3; i++){  
           
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           for(theta=1; theta <=npar; theta++)            posprop += prop[jk][i]; 
             trgradg[j][theta]=gradg[theta][j];          } 
          
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);          for(jk=1; jk <=nlstate ; jk++){     
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);            if( i <=  iagemax){ 
                      if(posprop>=1.e-5){ 
         pmij(pmmij,cov,ncovmodel,x,nlstate);                probs[i][jk][j1]= prop[jk][i]/posprop;
                      } else
         k=0;                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
         for(i=1; i<=(nlstate); i++){            } 
           for(j=1; j<=(nlstate+ndeath);j++){          }/* end jk */ 
             k=k+1;        }/* end i */ 
             mu[k][(int) age]=pmmij[i][j];      } /* end i1 */
           }    } /* end k1 */
         }    
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    /*free_vector(pp,1,nlstate);*/
             varpij[i][j][(int)age] = doldm[i][j];    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
         /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  /************* Waves Concatenation ***************/
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  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)
      }*/  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         fprintf(ficresprob,"\n%d ",(int)age);       Death is a valid wave (if date is known).
         fprintf(ficresprobcov,"\n%d ",(int)age);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         fprintf(ficresprobcor,"\n%d ",(int)age);       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 (i=1; i<=(nlstate)*(nlstate+ndeath);i++)       */
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));  
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    int i, mi, m;
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);       double sum=0., jmean=0.;*/
         }    int first;
         i=0;    int j, k=0,jk, ju, jl;
         for (k=1; k<=(nlstate);k++){    double sum=0.;
           for (l=1; l<=(nlstate+ndeath);l++){    first=0;
             i=i++;    jmin=1e+5;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    jmax=-1;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    jmean=0.;
             for (j=1; j<=i;j++){    for(i=1; i<=imx; i++){
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);      mi=0;
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));      m=firstpass;
             }      while(s[m][i] <= nlstate){
           }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         }/* end of loop for state */          mw[++mi][i]=m;
       } /* end of loop for age */        if(m >=lastpass)
           break;
       /* Confidence intervalle of pij  */        else
       /*          m++;
       fprintf(ficgp,"\nset noparametric;unset label");      }/* end while */
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");      if (s[m][i] > nlstate){
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        mi++;     /* Death is another wave */
       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);        /* if(mi==0)  never been interviewed correctly before death */
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);           /* Only death is a correct wave */
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);        mw[mi][i]=m;
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);      }
       */  
       wav[i]=mi;
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/      if(mi==0){
       first1=1;        nbwarn++;
       for (k1=1; k1<=(nlstate);k1++){        if(first==0){
         for (l1=1; l1<=(nlstate+ndeath);l1++){          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           if(l1==k1) continue;          first=1;
           i=(k1-1)*(nlstate+ndeath)+l1;        }
           for (k2=1; k2<=(nlstate);k2++){        if(first==1){
             for (l2=1; l2<=(nlstate+ndeath);l2++){          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
               if(l2==k2) continue;        }
               j=(k2-1)*(nlstate+ndeath)+l2;      } /* end mi==0 */
               if(j<=i) continue;    } /* End individuals */
               for (age=bage; age<=fage; age ++){  
                 if ((int)age %5==0){    for(i=1; i<=imx; i++){
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;      for(mi=1; mi<wav[i];mi++){
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;        if (stepm <=0)
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;          dh[mi][i]=1;
                   mu1=mu[i][(int) age]/stepm*YEARM ;        else{
                   mu2=mu[j][(int) age]/stepm*YEARM;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                   /* Computing eigen value of matrix of covariance */            if (agedc[i] < 2*AGESUP) {
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));              if(j==0) j=1;  /* Survives at least one month after exam */
                   if(first1==1){              else if(j<0){
                     first1=0;                nberr++;
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);                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(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);                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);
                   /* Eigen vectors */                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]);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));                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);
                   v21=sqrt(1.-v11*v11);              }
                   v12=-v21;              k=k+1;
                   v22=v11;              if (j >= jmax){
                   /*printf(fignu*/                jmax=j;
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */                ijmax=i;
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */              }
                   if(first==1){              if (j <= jmin){
                     first=0;                jmin=j;
                     fprintf(ficgp,"\nset parametric;set nolabel");                ijmin=i;
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);              }
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");              sum=sum+j;
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);            }
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);          }
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);          else{
                     /*              fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  /*        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]); */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  
                     */            k=k+1;
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\            if (j >= jmax) {
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \              jmax=j;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));              ijmax=i;
                   }else{            }
                     first=0;            else if (j <= jmin){
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);              jmin=j;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);              ijmin=i;
                     /*            }
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \            /*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]);*/
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);            if(j<0){
                     */              nberr++;
                     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("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]);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \              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]);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));            }
                   }/* if first */            sum=sum+j;
                 } /* age mod 5 */          }
               } /* end loop age */          jk= j/stepm;
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);          jl= j -jk*stepm;
               first=1;          ju= j -(jk+1)*stepm;
             } /*l12 */          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           } /* k12 */            if(jl==0){
         } /*l1 */              dh[mi][i]=jk;
       }/* k1 */              bh[mi][i]=0;
     } /* loop covariates */            }else{ /* We want a negative bias in order to only have interpolation ie
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);                    * to avoid the price of an extra matrix product in likelihood */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));              dh[mi][i]=jk+1;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));              bh[mi][i]=ju;
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);            }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          }else{
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            if(jl <= -ju){
   }              dh[mi][i]=jk;
   free_vector(xp,1,npar);              bh[mi][i]=jl;       /* bias is positive if real duration
   fclose(ficresprob);                                   * is higher than the multiple of stepm and negative otherwise.
   fclose(ficresprobcov);                                   */
   fclose(ficresprobcor);            }
   fclose(ficgp);            else{
   fclose(fichtm);              dh[mi][i]=jk+1;
 }              bh[mi][i]=ju;
             }
             if(dh[mi][i]==0){
 /******************* Printing html file ***********/              dh[mi][i]=1; /* At least one step */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \              bh[mi][i]=ju; /* At least one step */
                   int lastpass, int stepm, int weightopt, char model[],\              /*  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);*/
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\            }
                   int popforecast, int estepm ,\          } /* end if mle */
                   double jprev1, double mprev1,double anprev1, \        }
                   double jprev2, double mprev2,double anprev2){      } /* end wave */
   int jj1, k1, i1, cpt;    }
   /*char optionfilehtm[FILENAMELENGTH];*/    jmean=sum/k;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    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);
     printf("Problem with %s \n",optionfilehtm), exit(0);    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(ficlog,"Problem with %s \n",optionfilehtm), exit(0);   }
   }  
   /*********** Tricode ****************************/
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n  void tricode(int *Tvar, int **nbcode, int imx)
  - 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  {
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    /* Uses cptcovn+2*cptcovprod as the number of covariates */
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
  - Life expectancies by age and initial health status (estepm=%2d months):  
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    int modmaxcovj=0; /* Modality max of covariates j */
     cptcoveff=0; 
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
  m=cptcoveff;    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
  jj1=0;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
  for(k1=1; k1<=m;k1++){                                 modality of this covariate Vj*/ 
    for(i1=1; i1<=ncodemax[k1];i1++){        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
      jj1++;                                        modality of the nth covariate of individual i. */
      if (cptcovn > 0) {        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
        for (cpt=1; cpt<=cptcoveff;cpt++)        if (ij > modmaxcovj) modmaxcovj=ij; 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        /* getting the maximum value of the modality of the covariate
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
      }           female is 1, then modmaxcovj=1.*/
      /* Pij */      }
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>  
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*/
      /* Quasi-incidences */        if( Ndum[i] != 0 )
      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>          ncodemax[j]++; 
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        /* Number of modalities of the j th covariate. In fact
        /* Stable prevalence in each health state */           ncodemax[j]=2 (dichotom. variables only) but it could be more for
        for(cpt=1; cpt<nlstate;cpt++){           historical reasons */
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>      } /* Ndum[-1] number of undefined modalities */
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
      for(cpt=1; cpt<=nlstate;cpt++) {      ij=1; 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for (k=0; k<= maxncov; k++) { /* k=-1 ? NCOVMAX*/
      }          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
 health expectancies in states (1) and (2): e%s%d.png<br>                                       k is a modality. If we have model=V1+V1*sex 
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
    } /* end i1 */            ij++;
  }/* End k1 */          }
  fprintf(fichtm,"</ul>");          if (ij > ncodemax[j]) break; 
         }  
       } 
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    }  
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n   for (k=0; k< maxncov; k++) Ndum[k]=0;
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n  
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
  - 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);     Ndum[ij]++;
    }
  if(popforecast==1) fprintf(fichtm,"\n  
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n   ij=1;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n   for (i=1; i<= maxncov; i++) {
         <br>",fileres,fileres,fileres,fileres);     if((Ndum[i]!=0) && (i<=ncovcol)){
  else       Tvaraff[ij]=i; /*For printing */
    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);       ij++;
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");     }
    }
  m=cptcoveff;   ij--;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}   cptcoveff=ij; /*Number of simple covariates*/
   }
  jj1=0;  
  for(k1=1; k1<=m;k1++){  /*********** Health Expectancies ****************/
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
      if (cptcovn > 0) {  
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  {
        for (cpt=1; cpt<=cptcoveff;cpt++)    /* Health expectancies, no variances */
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    int nhstepma, nstepma; /* Decreasing with age */
      }    double age, agelim, hf;
      for(cpt=1; cpt<=nlstate;cpt++) {    double ***p3mat;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    double eip;
 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);      pstamp(ficreseij);
      }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
    } /* end i1 */    fprintf(ficreseij,"# Age");
  }/* End k1 */    for(i=1; i<=nlstate;i++){
  fprintf(fichtm,"</ul>");      for(j=1; j<=nlstate;j++){
 fclose(fichtm);        fprintf(ficreseij," e%1d%1d ",i,j);
 }      }
       fprintf(ficreseij," e%1d. ",i);
 /******************* Gnuplot file **************/    }
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    fprintf(ficreseij,"\n");
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    
   int ng;    if(estepm < stepm){
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      printf ("Problem %d lower than %d\n",estepm, stepm);
     printf("Problem with file %s",optionfilegnuplot);    }
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);    else  hstepm=estepm;   
   }    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
 #ifdef windows     * if stepm=24 months pijx are given only every 2 years and by summing them
     fprintf(ficgp,"cd \"%s\" \n",pathc);     * we are calculating an estimate of the Life Expectancy assuming a linear 
 #endif     * progression in between and thus overestimating or underestimating according
 m=pow(2,cptcoveff);     * to the curvature of the survival function. If, for the same date, we 
       * estimate the model with stepm=1 month, we can keep estepm to 24 months
  /* 1eme*/     * to compare the new estimate of Life expectancy with the same linear 
   for (cpt=1; cpt<= nlstate ; cpt ++) {     * hypothesis. A more precise result, taking into account a more precise
    for (k1=1; k1<= m ; k1 ++) {     * curvature will be obtained if estepm is as small as stepm. */
   
 #ifdef windows    /* For example we decided to compute the life expectancy with the smallest unit */
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      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);       nhstepm is the number of hstepm from age to agelim 
 #endif       nstepm is the number of stepm from age to agelin. 
 #ifdef unix       Look at hpijx to understand the reason of that which relies in memory size
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);       and note for a fixed period like estepm months */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 #endif       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
 for (i=1; i<= nlstate ; i ++) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       results. So we changed our mind and took the option of the best precision.
   else fprintf(ficgp," \%%*lf (\%%*lf)");    */
 }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     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 ++) {    agelim=AGESUP;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* If stepm=6 months */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      
      for (i=1; i<= nlstate ; i ++) {  /* nhstepm age range expressed in number of stepm */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 }      /* if (stepm >= YEARM) hstepm=1;*/
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 #ifdef unix    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");  
 #endif    for (age=bage; age<=fage; age ++){ 
    }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   /*2 eme*/      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      /* If stepm=6 months */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
             in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     for (i=1; i<= nlstate+1 ; i ++) {      
       k=2*i;      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      
       for (j=1; j<= nlstate+1 ; j ++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      
   else fprintf(ficgp," \%%*lf (\%%*lf)");      printf("%d|",(int)age);fflush(stdout);
 }        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      /* Computing expectancies */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(i=1; i<=nlstate;i++)
       for (j=1; j<= nlstate+1 ; j ++) {        for(j=1; j<=nlstate;j++)
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 }              
       fprintf(ficgp,"\" t\"\" w l 0,");            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {          }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficreseij,"%3.0f",age );
 }        for(i=1; i<=nlstate;i++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        eip=0;
       else fprintf(ficgp,"\" t\"\" w l 0,");        for(j=1; j<=nlstate;j++){
     }          eip +=eij[i][j][(int)age];
   }          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
          }
   /*3eme*/        fprintf(ficreseij,"%9.4f", eip );
       }
   for (k1=1; k1<= m ; k1 ++) {      fprintf(ficreseij,"\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {      
       k=2+nlstate*(2*cpt-2);    }
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    printf("\n");
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    fprintf(ficlog,"\n");
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  }
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  
   {
 */    /* Covariances of health expectancies eij and of total life expectancies according
       for (i=1; i< nlstate ; i ++) {     to initial status i, ei. .
         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);    */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
       }    int nhstepma, nstepma; /* Decreasing with age */
     }    double age, agelim, hf;
   }    double ***p3matp, ***p3matm, ***varhe;
      double **dnewm,**doldm;
   /* CV preval stat */    double *xp, *xm;
     for (k1=1; k1<= m ; k1 ++) {    double **gp, **gm;
     for (cpt=1; cpt<nlstate ; cpt ++) {    double ***gradg, ***trgradg;
       k=3;    int theta;
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    double eip, vip;
   
       for (i=1; i< nlstate ; i ++)    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         fprintf(ficgp,"+$%d",k+i+1);    xp=vector(1,npar);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    xm=vector(1,npar);
          dnewm=matrix(1,nlstate*nlstate,1,npar);
       l=3+(nlstate+ndeath)*cpt;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    
       for (i=1; i< nlstate ; i ++) {    pstamp(ficresstdeij);
         l=3+(nlstate+ndeath)*cpt;    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
         fprintf(ficgp,"+$%d",l+i+1);    fprintf(ficresstdeij,"# Age");
       }    for(i=1; i<=nlstate;i++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        for(j=1; j<=nlstate;j++)
     }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   }        fprintf(ficresstdeij," e%1d. ",i);
      }
   /* proba elementaires */    fprintf(ficresstdeij,"\n");
    for(i=1,jk=1; i <=nlstate; i++){  
     for(k=1; k <=(nlstate+ndeath); k++){    pstamp(ficrescveij);
       if (k != i) {    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
         for(j=1; j <=ncovmodel; j++){    fprintf(ficrescveij,"# Age");
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    for(i=1; i<=nlstate;i++)
           jk++;      for(j=1; j<=nlstate;j++){
           fprintf(ficgp,"\n");        cptj= (j-1)*nlstate+i;
         }        for(i2=1; i2<=nlstate;i2++)
       }          for(j2=1; j2<=nlstate;j2++){
     }            cptj2= (j2-1)*nlstate+i2;
    }            if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/          }
      for(jk=1; jk <=m; jk++) {      }
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    fprintf(ficrescveij,"\n");
        if (ng==2)    
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    if(estepm < stepm){
        else      printf ("Problem %d lower than %d\n",estepm, stepm);
          fprintf(ficgp,"\nset title \"Probability\"\n");    }
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    else  hstepm=estepm;   
        i=1;    /* We compute the life expectancy from trapezoids spaced every estepm months
        for(k2=1; k2<=nlstate; k2++) {     * This is mainly to measure the difference between two models: for example
          k3=i;     * if stepm=24 months pijx are given only every 2 years and by summing them
          for(k=1; k<=(nlstate+ndeath); k++) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
            if (k != k2){     * progression in between and thus overestimating or underestimating according
              if(ng==2)     * to the curvature of the survival function. If, for the same date, we 
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
              else     * to compare the new estimate of Life expectancy with the same linear 
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);     * hypothesis. A more precise result, taking into account a more precise
              ij=1;     * curvature will be obtained if estepm is as small as stepm. */
              for(j=3; j <=ncovmodel; j++) {  
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* For example we decided to compute the life expectancy with the smallest unit */
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                  ij++;       nhstepm is the number of hstepm from age to agelim 
                }       nstepm is the number of stepm from age to agelin. 
                else       Look at hpijx to understand the reason of that which relies in memory size
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       and note for a fixed period like estepm months */
              }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
              fprintf(ficgp,")/(1");       survival function given by stepm (the optimization length). Unfortunately it
                     means that if the survival funtion is printed only each two years of age and if
              for(k1=1; k1 <=nlstate; k1++){         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);       results. So we changed our mind and took the option of the best precision.
                ij=1;    */
                for(j=3; j <=ncovmodel; j++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /* If stepm=6 months */
                    ij++;    /* nhstepm age range expressed in number of stepm */
                  }    agelim=AGESUP;
                  else    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                }    /* if (stepm >= YEARM) hstepm=1;*/
                fprintf(ficgp,")");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
              }    
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              i=i+ncovmodel;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
            }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
          } /* end k */    gp=matrix(0,nhstepm,1,nlstate*nlstate);
        } /* end k2 */    gm=matrix(0,nhstepm,1,nlstate*nlstate);
      } /* end jk */  
    } /* end ng */    for (age=bage; age<=fage; age ++){ 
    fclose(ficgp);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
 }  /* end gnuplot */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
 /*************** Moving average **************/  
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
   int i, cpt, cptcod;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)      
       for (i=1; i<=nlstate;i++)      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  
           mobaverage[(int)agedeb][i][cptcod]=0.;      /* Computing  Variances of health expectancies */
          /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){         decrease memory allocation */
       for (i=1; i<=nlstate;i++){      for(theta=1; theta <=npar; theta++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(i=1; i<=npar; i++){ 
           for (cpt=0;cpt<=4;cpt++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          xm[i] = x[i] - (i==theta ?delti[theta]:0);
           }        }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         }        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       }    
     }        for(j=1; j<= nlstate; j++){
              for(i=1; i<=nlstate; i++){
 }            for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
 /************** Forecasting ******************/            }
 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){          }
          }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       
   int *popage;        for(ij=1; ij<= nlstate*nlstate; ij++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          for(h=0; h<=nhstepm-1; h++){
   double *popeffectif,*popcount;            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   double ***p3mat;          }
   char fileresf[FILENAMELENGTH];      }/* End theta */
       
  agelim=AGESUP;      
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
        
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);       for(ij=1;ij<=nlstate*nlstate;ij++)
   if((ficresf=fopen(fileresf,"w"))==NULL) {        for(ji=1;ji<=nlstate*nlstate;ji++)
     printf("Problem with forecast resultfile: %s\n", fileresf);          varhe[ij][ji][(int)age] =0.;
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);  
   }       printf("%d|",(int)age);fflush(stdout);
   printf("Computing forecasting: result on file '%s' \n", fileresf);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   if (mobilav==1) {          for(ij=1;ij<=nlstate*nlstate;ij++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(ji=1;ji<=nlstate*nlstate;ji++)
     movingaverage(agedeb, fage, ageminpar, mobaverage);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   }        }
       }
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;      /* Computing expectancies */
        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   agelim=AGESUP;      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
   hstepm=1;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   hstepm=hstepm/stepm;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   yp1=modf(dateintmean,&yp);            
   anprojmean=yp;            /* 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]);*/
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;          }
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;      fprintf(ficresstdeij,"%3.0f",age );
   if(jprojmean==0) jprojmean=1;      for(i=1; i<=nlstate;i++){
   if(mprojmean==0) jprojmean=1;        eip=0.;
          vip=0.;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        for(j=1; j<=nlstate;j++){
            eip += eij[i][j][(int)age];
   for(cptcov=1;cptcov<=i2;cptcov++){          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];
       k=k+1;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       fprintf(ficresf,"\n#******");        }
       for(j=1;j<=cptcoveff;j++) {        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }
       }      fprintf(ficresstdeij,"\n");
       fprintf(ficresf,"******\n");  
       fprintf(ficresf,"# StartingAge FinalAge");      fprintf(ficrescveij,"%3.0f",age );
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate;j++){
                cptj= (j-1)*nlstate+i;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          for(i2=1; i2<=nlstate;i2++)
         fprintf(ficresf,"\n");            for(j2=1; j2<=nlstate;j2++){
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            }
           nhstepm = nhstepm/hstepm;        }
                fprintf(ficrescveij,"\n");
           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);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
            free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           for (h=0; h<=nhstepm; h++){    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
             if (h==(int) (calagedate+YEARM*cpt)) {    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             }    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             for(j=1; j<=nlstate+ndeath;j++) {    printf("\n");
               kk1=0.;kk2=0;    fprintf(ficlog,"\n");
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)    free_vector(xm,1,npar);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    free_vector(xp,1,npar);
                 else {    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                 }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                  }
               }  
               if (h==(int)(calagedate+12*cpt)){  /************ Variance ******************/
                 fprintf(ficresf," %.3f", kk1);  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[])
                          {
               }    /* Variance of health expectancies */
             }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           }    /* double **newm;*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **dnewm,**doldm;
         }    double **dnewmp,**doldmp;
       }    int i, j, nhstepm, hstepm, h, nstepm ;
     }    int k, cptcode;
   }    double *xp;
            double **gp, **gm;  /* for var eij */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
   fclose(ficresf);    double *gpp, *gmp; /* for var p point j */
 }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 /************** Forecasting ******************/    double ***p3mat;
 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){    double age,agelim, hf;
      double ***mobaverage;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    int theta;
   int *popage;    char digit[4];
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    char digitp[25];
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;    char fileresprobmorprev[FILENAMELENGTH];
   char filerespop[FILENAMELENGTH];  
     if(popbased==1){
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if(mobilav!=0)
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        strcpy(digitp,"-populbased-mobilav-");
   agelim=AGESUP;      else strcpy(digitp,"-populbased-nomobil-");
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    }
      else 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      strcpy(digitp,"-stablbased-");
    
      if (mobilav!=0) {
   strcpy(filerespop,"pop");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(filerespop,fileres);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     printf("Problem with forecast resultfile: %s\n", filerespop);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);      }
   }    }
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
   if (mobilav==1) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(fileresprobmorprev,fileres);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    }
   if (stepm<=12) stepsize=1;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     
   agelim=AGESUP;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      pstamp(ficresprobmorprev);
   hstepm=1;    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   hstepm=hstepm/stepm;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   if (popforecast==1) {      fprintf(ficresprobmorprev," p.%-d SE",j);
     if((ficpop=fopen(popfile,"r"))==NULL) {      for(i=1; i<=nlstate;i++)
       printf("Problem with population file : %s\n",popfile);exit(0);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);    }  
     }    fprintf(ficresprobmorprev,"\n");
     popage=ivector(0,AGESUP);    fprintf(ficgp,"\n# Routine varevsij");
     popeffectif=vector(0,AGESUP);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     popcount=vector(0,AGESUP);    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);
     i=1;    /*   } */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        pstamp(ficresvij);
     imx=i;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    if(popbased==1)
   }      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
   for(cptcov=1;cptcov<=i2;cptcov++){      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficresvij,"# Age");
       k=k+1;    for(i=1; i<=nlstate;i++)
       fprintf(ficrespop,"\n#******");      for(j=1; j<=nlstate;j++)
       for(j=1;j<=cptcoveff;j++) {        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresvij,"\n");
       }  
       fprintf(ficrespop,"******\n");    xp=vector(1,npar);
       fprintf(ficrespop,"# Age");    dnewm=matrix(1,nlstate,1,npar);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    doldm=matrix(1,nlstate,1,nlstate);
       if (popforecast==1)  fprintf(ficrespop," [Population]");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
          doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for (cpt=0; cpt<=0;cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
            gpp=vector(nlstate+1,nlstate+ndeath);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    gmp=vector(nlstate+1,nlstate+ndeath);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           nhstepm = nhstepm/hstepm;    
              if(estepm < stepm){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf ("Problem %d lower than %d\n",estepm, stepm);
           oldm=oldms;savm=savms;    }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      else  hstepm=estepm;   
            /* For example we decided to compute the life expectancy with the smallest unit */
           for (h=0; h<=nhstepm; h++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             if (h==(int) (calagedate+YEARM*cpt)) {       nhstepm is the number of hstepm from age to agelim 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);       nstepm is the number of stepm from age to agelin. 
             }       Look at function hpijx to understand why (it is linked to memory size questions) */
             for(j=1; j<=nlstate+ndeath;j++) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               kk1=0.;kk2=0;       survival function given by stepm (the optimization length). Unfortunately it
               for(i=1; i<=nlstate;i++) {                     means that if the survival funtion is printed every two years of age and if
                 if (mobilav==1)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];       results. So we changed our mind and took the option of the best precision.
                 else {    */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                 }    agelim = AGESUP;
               }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
               if (h==(int)(calagedate+12*cpt)){      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   /*fprintf(ficrespop," %.3f", kk1);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
               }      gp=matrix(0,nhstepm,1,nlstate);
             }      gm=matrix(0,nhstepm,1,nlstate);
             for(i=1; i<=nlstate;i++){  
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){      for(theta=1; theta <=npar; theta++){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                 }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        }
             }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        if (popbased==1) {
           }          if(mobilav ==0){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(i=1; i<=nlstate;i++)
         }              prlim[i][i]=probs[(int)age][i][ij];
       }          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
   /******/              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(j=1; j<= nlstate; j++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for(h=0; h<=nhstepm; h++){
           nhstepm = nhstepm/hstepm;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                        gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           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);          /* This for computing probability of death (h=1 means
           for (h=0; h<=nhstepm; h++){           computed over hstepm matrices product = hstepm*stepm months) 
             if (h==(int) (calagedate+YEARM*cpt)) {           as a weighted average of prlim.
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        */
             }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             for(j=1; j<=nlstate+ndeath;j++) {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
               kk1=0.;kk2=0;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
               for(i=1; i<=nlstate;i++) {                      }    
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            /* end probability of death */
               }  
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
             }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         }   
       }        if (popbased==1) {
    }          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   if (popforecast==1) {              prlim[i][i]=mobaverage[(int)age][i][ij];
     free_ivector(popage,0,AGESUP);          }
     free_vector(popeffectif,0,AGESUP);        }
     free_vector(popcount,0,AGESUP);  
   }        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(h=0; h<=nhstepm; h++){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   fclose(ficrespop);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 }          }
         }
 /***********************************************/        /* This for computing probability of death (h=1 means
 /**************** Main Program *****************/           computed over hstepm matrices product = hstepm*stepm months) 
 /***********************************************/           as a weighted average of prlim.
         */
 int main(int argc, char *argv[])        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 {          for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        }    
   double agedeb, agefin,hf;        /* end probability of death */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
         for(j=1; j<= nlstate; j++) /* vareij */
   double fret;          for(h=0; h<=nhstepm; h++){
   double **xi,tmp,delta;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   double dum; /* Dummy variable */  
   double ***p3mat;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   int *indx;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   char line[MAXLINE], linepar[MAXLINE];        }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];  
   int firstobs=1, lastobs=10;      } /* End theta */
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      for(h=0; h<=nhstepm; h++) /* veij */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        for(j=1; j<=nlstate;j++)
   int mobilav=0,popforecast=0;          for(theta=1; theta <=npar; theta++)
   int hstepm, nhstepm;            trgradg[h][j][theta]=gradg[h][theta][j];
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   double bage, fage, age, agelim, agebase;        for(theta=1; theta <=npar; theta++)
   double ftolpl=FTOL;          trgradgp[j][theta]=gradgp[theta][j];
   double **prlim;    
   double *severity;  
   double ***param; /* Matrix of parameters */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   double  *p;      for(i=1;i<=nlstate;i++)
   double **matcov; /* Matrix of covariance */        for(j=1;j<=nlstate;j++)
   double ***delti3; /* Scale */          vareij[i][j][(int)age] =0.;
   double *delti; /* Scale */  
   double ***eij, ***vareij;      for(h=0;h<=nhstepm;h++){
   double **varpl; /* Variances of prevalence limits by age */        for(k=0;k<=nhstepm;k++){
   double *epj, vepp;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   double kk1, kk2;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   char *alph[]={"a","a","b","c","d","e"}, str[4];        }
       }
     
   char z[1]="c", occ;      /* pptj */
 #include <sys/time.h>      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
 #include <time.h>      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      for(j=nlstate+1;j<=nlstate+ndeath;j++)
          for(i=nlstate+1;i<=nlstate+ndeath;i++)
   /* long total_usecs;          varppt[j][i]=doldmp[j][i];
   struct timeval start_time, end_time;      /* end ppptj */
        /*  x centered again */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   getcwd(pathcd, size);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
   printf("\n%s",version);      if (popbased==1) {
   if(argc <=1){        if(mobilav ==0){
     printf("\nEnter the parameter file name: ");          for(i=1; i<=nlstate;i++)
     scanf("%s",pathtot);            prlim[i][i]=probs[(int)age][i][ij];
   }        }else{ /* mobilav */ 
   else{          for(i=1; i<=nlstate;i++)
     strcpy(pathtot,argv[1]);            prlim[i][i]=mobaverage[(int)age][i][ij];
   }        }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      }
   /*cygwin_split_path(pathtot,path,optionfile);               
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      /* This for computing probability of death (h=1 means
   /* cutv(path,optionfile,pathtot,'\\');*/         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   chdir(path);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   replace(pathc,path);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
 /*-------- arguments in the command line --------*/      /* end probability of death */
   
   /* Log file */      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   strcat(filelog, optionfilefiname);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   strcat(filelog,".log");    /* */        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   if((ficlog=fopen(filelog,"w"))==NULL)    {        for(i=1; i<=nlstate;i++){
     printf("Problem with logfile %s\n",filelog);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     goto end;        }
   }      } 
   fprintf(ficlog,"Log filename:%s\n",filelog);      fprintf(ficresprobmorprev,"\n");
   fprintf(ficlog,"\n%s",version);  
   fprintf(ficlog,"\nEnter the parameter file name: ");      fprintf(ficresvij,"%.0f ",age );
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      for(i=1; i<=nlstate;i++)
   fflush(ficlog);        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   /* */        }
   strcpy(fileres,"r");      fprintf(ficresvij,"\n");
   strcat(fileres, optionfilefiname);      free_matrix(gp,0,nhstepm,1,nlstate);
   strcat(fileres,".txt");    /* Other files have txt extension */      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   /*---------arguments file --------*/      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    } /* End age */
     printf("Problem with optionfile %s\n",optionfile);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     goto end;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
   strcpy(filereso,"o");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   strcat(filereso,fileres);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   if((ficparo=fopen(filereso,"w"))==NULL) {  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     printf("Problem with Output resultfile: %s\n", filereso);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     goto end;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   /* Reads comments: lines beginning with '#' */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   while((c=getc(ficpar))=='#' && c!= EOF){    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);
     ungetc(c,ficpar);    /*  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);
     fgets(line, MAXLINE, ficpar);  */
     puts(line);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fputs(line,ficparo);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   }  
   ungetc(c,ficpar);    free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
   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);    free_matrix(dnewm,1,nlstate,1,npar);
   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);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
 while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     ungetc(c,ficpar);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fgets(line, MAXLINE, ficpar);    fclose(ficresprobmorprev);
     puts(line);    fflush(ficgp);
     fputs(line,ficparo);    fflush(fichtm); 
   }  }  /* end varevsij */
   ungetc(c,ficpar);  
    /************ 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[])
   covar=matrix(0,NCOVMAX,1,n);  {
   cptcovn=0;    /* Variance of prevalence limit */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
   ncovmodel=2+cptcovn;    double **dnewm,**doldm;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    int i, j, nhstepm, hstepm;
      int k, cptcode;
   /* Read guess parameters */    double *xp;
   /* Reads comments: lines beginning with '#' */    double *gp, *gm;
   while((c=getc(ficpar))=='#' && c!= EOF){    double **gradg, **trgradg;
     ungetc(c,ficpar);    double age,agelim;
     fgets(line, MAXLINE, ficpar);    int theta;
     puts(line);    
     fputs(line,ficparo);    pstamp(ficresvpl);
   }    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   ungetc(c,ficpar);    fprintf(ficresvpl,"# Age");
      for(i=1; i<=nlstate;i++)
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        fprintf(ficresvpl," %1d-%1d",i,i);
     for(i=1; i <=nlstate; i++)    fprintf(ficresvpl,"\n");
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    xp=vector(1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);    dnewm=matrix(1,nlstate,1,npar);
       if(mle==1)    doldm=matrix(1,nlstate,1,nlstate);
         printf("%1d%1d",i,j);    
       fprintf(ficlog,"%1d%1d",i,j);    hstepm=1*YEARM; /* Every year of age */
       for(k=1; k<=ncovmodel;k++){    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         fscanf(ficpar," %lf",&param[i][j][k]);    agelim = AGESUP;
         if(mle==1){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           printf(" %lf",param[i][j][k]);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           fprintf(ficlog," %lf",param[i][j][k]);      if (stepm >= YEARM) hstepm=1;
         }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         else      gradg=matrix(1,npar,1,nlstate);
           fprintf(ficlog," %lf",param[i][j][k]);      gp=vector(1,nlstate);
         fprintf(ficparo," %lf",param[i][j][k]);      gm=vector(1,nlstate);
       }  
       fscanf(ficpar,"\n");      for(theta=1; theta <=npar; theta++){
       if(mle==1)        for(i=1; i<=npar; i++){ /* Computes gradient */
         printf("\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficlog,"\n");        }
       fprintf(ficparo,"\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }        for(i=1;i<=nlstate;i++)
            gp[i] = prlim[i][i];
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      
         for(i=1; i<=npar; i++) /* Computes gradient */
   p=param[1][1];          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /* Reads comments: lines beginning with '#' */        for(i=1;i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){          gm[i] = prlim[i][i];
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);        for(i=1;i<=nlstate;i++)
     puts(line);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     fputs(line,ficparo);      } /* End theta */
   }  
   ungetc(c,ficpar);      trgradg =matrix(1,nlstate,1,npar);
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(j=1; j<=nlstate;j++)
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        for(theta=1; theta <=npar; theta++)
   for(i=1; i <=nlstate; i++){          trgradg[j][theta]=gradg[theta][j];
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);      for(i=1;i<=nlstate;i++)
       printf("%1d%1d",i,j);        varpl[i][(int)age] =0.;
       fprintf(ficparo,"%1d%1d",i1,j1);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       for(k=1; k<=ncovmodel;k++){      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
         fscanf(ficpar,"%le",&delti3[i][j][k]);      for(i=1;i<=nlstate;i++)
         printf(" %le",delti3[i][j][k]);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }      fprintf(ficresvpl,"%.0f ",age );
       fscanf(ficpar,"\n");      for(i=1; i<=nlstate;i++)
       printf("\n");        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficparo,"\n");      fprintf(ficresvpl,"\n");
     }      free_vector(gp,1,nlstate);
   }      free_vector(gm,1,nlstate);
   delti=delti3[1][1];      free_matrix(gradg,1,npar,1,nlstate);
        free_matrix(trgradg,1,nlstate,1,npar);
   /* Reads comments: lines beginning with '#' */    } /* End age */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    free_vector(xp,1,npar);
     fgets(line, MAXLINE, ficpar);    free_matrix(doldm,1,nlstate,1,npar);
     puts(line);    free_matrix(dnewm,1,nlstate,1,nlstate);
     fputs(line,ficparo);  
   }  }
   ungetc(c,ficpar);  
    /************ Variance of one-step probabilities  ******************/
   matcov=matrix(1,npar,1,npar);  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[])
   for(i=1; i <=npar; i++){  {
     fscanf(ficpar,"%s",&str);    int i, j=0,  i1, k1, l1, t, tj;
     if(mle==1)    int k2, l2, j1,  z1;
       printf("%s",str);    int k=0,l, cptcode;
     fprintf(ficlog,"%s",str);    int first=1, first1;
     fprintf(ficparo,"%s",str);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     for(j=1; j <=i; j++){    double **dnewm,**doldm;
       fscanf(ficpar," %le",&matcov[i][j]);    double *xp;
       if(mle==1){    double *gp, *gm;
         printf(" %.5le",matcov[i][j]);    double **gradg, **trgradg;
         fprintf(ficlog," %.5le",matcov[i][j]);    double **mu;
       }    double age,agelim, cov[NCOVMAX];
       else    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         fprintf(ficlog," %.5le",matcov[i][j]);    int theta;
       fprintf(ficparo," %.5le",matcov[i][j]);    char fileresprob[FILENAMELENGTH];
     }    char fileresprobcov[FILENAMELENGTH];
     fscanf(ficpar,"\n");    char fileresprobcor[FILENAMELENGTH];
     if(mle==1)  
       printf("\n");    double ***varpij;
     fprintf(ficlog,"\n");  
     fprintf(ficparo,"\n");    strcpy(fileresprob,"prob"); 
   }    strcat(fileresprob,fileres);
   for(i=1; i <=npar; i++)    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     for(j=i+1;j<=npar;j++)      printf("Problem with resultfile: %s\n", fileresprob);
       matcov[i][j]=matcov[j][i];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
        }
   if(mle==1)    strcpy(fileresprobcov,"probcov"); 
     printf("\n");    strcat(fileresprobcov,fileres);
   fprintf(ficlog,"\n");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     /*-------- Rewriting paramater file ----------*/    }
      strcpy(rfileres,"r");    /* "Rparameterfile */    strcpy(fileresprobcor,"probcor"); 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    strcat(fileresprobcor,fileres);
      strcat(rfileres,".");    /* */    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      printf("Problem with resultfile: %s\n", fileresprobcor);
     if((ficres =fopen(rfileres,"w"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    }
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficres,"#%s\n",version);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
        fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     /*-------- data file ----------*/    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     if((fic=fopen(datafile,"r"))==NULL)    {    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       printf("Problem with datafile: %s\n", datafile);goto end;    pstamp(ficresprob);
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     }    fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     n= lastobs;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     severity = vector(1,maxwav);    fprintf(ficresprobcov,"# Age");
     outcome=imatrix(1,maxwav+1,1,n);    pstamp(ficresprobcor);
     num=ivector(1,n);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     moisnais=vector(1,n);    fprintf(ficresprobcor,"# Age");
     annais=vector(1,n);  
     moisdc=vector(1,n);  
     andc=vector(1,n);    for(i=1; i<=nlstate;i++)
     agedc=vector(1,n);      for(j=1; j<=(nlstate+ndeath);j++){
     cod=ivector(1,n);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     weight=vector(1,n);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     mint=matrix(1,maxwav,1,n);      }  
     anint=matrix(1,maxwav,1,n);   /* fprintf(ficresprob,"\n");
     s=imatrix(1,maxwav+1,1,n);    fprintf(ficresprobcov,"\n");
     adl=imatrix(1,maxwav+1,1,n);        fprintf(ficresprobcor,"\n");
     tab=ivector(1,NCOVMAX);   */
     ncodemax=ivector(1,8);    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     i=1;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     while (fgets(line, MAXLINE, fic) != NULL)    {    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       if ((i >= firstobs) && (i <=lastobs)) {    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
            first=1;
         for (j=maxwav;j>=1;j--){    fprintf(ficgp,"\n# Routine varprob");
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
           strcpy(line,stra);    fprintf(fichtm,"\n");
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
         }    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
            file %s<br>\n",optionfilehtmcov);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    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. \
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  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 \
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  standard deviations wide on each axis. <br>\
         for (j=ncovcol;j>=1;j--){   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);   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");
         num[i]=atol(stra);  
            cov[1]=1;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    tj=cptcoveff;
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
         i=i+1;    for(t=1; t<=tj;t++){
       }      for(i1=1; i1<=ncodemax[t];i1++){ 
     }        j1++;
     /* printf("ii=%d", ij);        if  (cptcovn>0) {
        scanf("%d",i);*/          fprintf(ficresprob, "\n#********** Variable "); 
   imx=i-1; /* Number of individuals */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
   /* for (i=1; i<=imx; i++){          fprintf(ficresprobcov, "\n#********** Variable "); 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          fprintf(ficresprobcov, "**********\n#\n");
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          
     }*/          fprintf(ficgp, "\n#********** Variable "); 
    /*  for (i=1; i<=imx; i++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      if (s[4][i]==9)  s[4][i]=-1;          fprintf(ficgp, "**********\n#\n");
      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]));}*/          
            
            fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   /* Calculation of the number of parameter from char model*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   Tprod=ivector(1,15);          
   Tvaraff=ivector(1,15);          fprintf(ficresprobcor, "\n#********** Variable ");    
   Tvard=imatrix(1,15,1,2);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   Tage=ivector(1,15);                fprintf(ficresprobcor, "**********\n#");    
            }
   if (strlen(model) >1){        
     j=0, j1=0, k1=1, k2=1;        for (age=bage; age<=fage; age ++){ 
     j=nbocc(model,'+');          cov[2]=age;
     j1=nbocc(model,'*');          for (k=1; k<=cptcovn;k++) {
     cptcovn=j+1;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     cptcovprod=j1;          }
              for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     strcpy(modelsav,model);          for (k=1; k<=cptcovprod;k++)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       printf("Error. Non available option model=%s ",model);          
       fprintf(ficlog,"Error. Non available option model=%s ",model);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       goto end;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     }          gp=vector(1,(nlstate)*(nlstate+ndeath));
              gm=vector(1,(nlstate)*(nlstate+ndeath));
     for(i=(j+1); i>=1;i--){      
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */          for(theta=1; theta <=npar; theta++){
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */            for(i=1; i<=npar; i++)
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       /*scanf("%d",i);*/            
       if (strchr(strb,'*')) {  /* Model includes a product */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/            
         if (strcmp(strc,"age")==0) { /* Vn*age */            k=0;
           cptcovprod--;            for(i=1; i<= (nlstate); i++){
           cutv(strb,stre,strd,'V');              for(j=1; j<=(nlstate+ndeath);j++){
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/                k=k+1;
           cptcovage++;                gp[k]=pmmij[i][j];
             Tage[cptcovage]=i;              }
             /*printf("stre=%s ", stre);*/            }
         }            
         else if (strcmp(strd,"age")==0) { /* or age*Vn */            for(i=1; i<=npar; i++)
           cptcovprod--;              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
           cutv(strb,stre,strc,'V');      
           Tvar[i]=atoi(stre);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           cptcovage++;            k=0;
           Tage[cptcovage]=i;            for(i=1; i<=(nlstate); i++){
         }              for(j=1; j<=(nlstate+ndeath);j++){
         else {  /* Age is not in the model */                k=k+1;
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/                gm[k]=pmmij[i][j];
           Tvar[i]=ncovcol+k1;              }
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */            }
           Tprod[k1]=i;       
           Tvard[k1][1]=atoi(strc); /* m*/            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
           Tvard[k1][2]=atoi(stre); /* n */              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           Tvar[cptcovn+k2]=Tvard[k1][1];          }
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            for(theta=1; theta <=npar; theta++)
           k1++;              trgradg[j][theta]=gradg[theta][j];
           k2=k2+2;          
         }          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       }          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       else { /* no more sum */          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
        /*  scanf("%d",i);*/          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       cutv(strd,strc,strb,'V');          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       Tvar[i]=atoi(strc);  
       }          pmij(pmmij,cov,ncovmodel,x,nlstate);
       strcpy(modelsav,stra);            
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          k=0;
         scanf("%d",i);*/          for(i=1; i<=(nlstate); i++){
     } /* end of loop + */            for(j=1; j<=(nlstate+ndeath);j++){
   } /* end model */              k=k+1;
                mu[k][(int) age]=pmmij[i][j];
   /* 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);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   scanf("%d ",i);*/            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     fclose(fic);              varpij[i][j][(int)age] = doldm[i][j];
   
     /*  if(mle==1){*/          /*printf("\n%d ",(int)age);
     if (weightopt != 1) { /* Maximisation without weights*/            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       for(i=1;i<=n;i++) weight[i]=1.0;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     /*-calculation of age at interview from date of interview and age at death -*/            }*/
     agev=matrix(1,maxwav,1,imx);  
           fprintf(ficresprob,"\n%d ",(int)age);
     for (i=1; i<=imx; i++) {          fprintf(ficresprobcov,"\n%d ",(int)age);
       for(m=2; (m<= maxwav); m++) {          fprintf(ficresprobcor,"\n%d ",(int)age);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
          s[m][i]=-1;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
        }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     }          }
           i=0;
     for (i=1; i<=imx; i++)  {          for (k=1; k<=(nlstate);k++){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            for (l=1; l<=(nlstate+ndeath);l++){ 
       for(m=1; (m<= maxwav); m++){              i=i++;
         if(s[m][i] >0){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
           if (s[m][i] >= nlstate+1) {              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
             if(agedc[i]>0)              for (j=1; j<=i;j++){
               if(moisdc[i]!=99 && andc[i]!=9999)                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 agev[m][i]=agedc[i];                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/              }
            else {            }
               if (andc[i]!=9999){          }/* end of loop for state */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        } /* end of loop for age */
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;        /* Confidence intervalle of pij  */
               }        /*
             }          fprintf(ficgp,"\nunset parametric;unset label");
           }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           else if(s[m][i] !=9){ /* Should no more exist */          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          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);
             if(mint[m][i]==99 || anint[m][i]==9999)          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
               agev[m][i]=1;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
             else if(agev[m][i] <agemin){          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
               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);*/  
             }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
             else if(agev[m][i] >agemax){        first1=1;
               agemax=agev[m][i];        for (k2=1; k2<=(nlstate);k2++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             }            if(l2==k2) continue;
             /*agev[m][i]=anint[m][i]-annais[i];*/            j=(k2-1)*(nlstate+ndeath)+l2;
             /*   agev[m][i] = age[i]+2*m;*/            for (k1=1; k1<=(nlstate);k1++){
           }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
           else { /* =9 */                if(l1==k1) continue;
             agev[m][i]=1;                i=(k1-1)*(nlstate+ndeath)+l1;
             s[m][i]=-1;                if(i<=j) continue;
           }                for (age=bage; age<=fage; age ++){ 
         }                  if ((int)age %5==0){
         else /*= 0 Unknown */                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
           agev[m][i]=1;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                        mu1=mu[i][(int) age]/stepm*YEARM ;
     }                    mu2=mu[j][(int) age]/stepm*YEARM;
     for (i=1; i<=imx; i++)  {                    c12=cv12/sqrt(v1*v2);
       for(m=1; (m<= maxwav); m++){                    /* Computing eigen value of matrix of covariance */
         if (s[m][i] > (nlstate+ndeath)) {                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           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);                      lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           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);                      if ((lc2 <0) || (lc1 <0) ){
           goto end;                      printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
         }                      fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
       }                      lc1=fabs(lc1);
     }                      lc2=fabs(lc2);
                     }
 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);                    /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     free_vector(severity,1,maxwav);                    /*v21=sqrt(1.-v11*v11); *//* error */
     free_imatrix(outcome,1,maxwav+1,1,n);                    v21=(lc1-v1)/cv12*v11;
     free_vector(moisnais,1,n);                    v12=-v21;
     free_vector(annais,1,n);                    v22=v11;
     /* free_matrix(mint,1,maxwav,1,n);                    tnalp=v21/v11;
        free_matrix(anint,1,maxwav,1,n);*/                    if(first1==1){
     free_vector(moisdc,1,n);                      first1=0;
     free_vector(andc,1,n);                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                        fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     wav=ivector(1,imx);                    /*printf(fignu*/
     dh=imatrix(1,lastpass-firstpass+1,1,imx);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                        if(first==1){
     /* Concatenates waves */                      first=0;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);                      fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       Tcode=ivector(1,100);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
       ncodemax[1]=1;  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                                    subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
    codtab=imatrix(1,100,1,10);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
    h=0;                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
    m=pow(2,cptcoveff);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                        fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
    for(k=1;k<=cptcoveff; k++){                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
      for(i=1; i <=(m/pow(2,k));i++){                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
        for(j=1; j <= ncodemax[k]; j++){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
            h++;                    }else{
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;                      first=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(fichtmcov," %d (%.3f),",(int) age, c12);
          }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
        }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
      }                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
    }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       codtab[1][2]=1;codtab[2][2]=2; */                    }/* if first */
    /* for(i=1; i <=m ;i++){                  } /* age mod 5 */
       for(k=1; k <=cptcovn; k++){                } /* end loop age */
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       }                first=1;
       printf("\n");              } /*l12 */
       }            } /* k12 */
       scanf("%d",i);*/          } /*l1 */
            }/* k1 */
    /* Calculates basic frequencies. Computes observed prevalence at single age      } /* loop covariates */
        and prints on file fileres'p'. */    }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
        free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
        free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_vector(xp,1,npar);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficresprob);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficresprobcov);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fclose(ficresprobcor);
          fflush(ficgp);
     /* For Powell, parameters are in a vector p[] starting at p[1]    fflush(fichtmcov);
        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) */  
   
     if(mle==1){  /******************* Printing html file ***********/
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     }                    int lastpass, int stepm, int weightopt, char model[],\
                        int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     /*--------- results files --------------*/                    int popforecast, int estepm ,\
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);                    double jprev1, double mprev1,double anprev1, \
                      double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
    jk=1;  
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  </ul>");
    for(i=1,jk=1; i <=nlstate; i++){     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
      for(k=1; k <=(nlstate+ndeath); k++){   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
        if (k != i)             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
          {     fprintf(fichtm,"\
            printf("%d%d ",i,k);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            fprintf(ficlog,"%d%d ",i,k);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
            fprintf(ficres,"%1d%1d ",i,k);     fprintf(fichtm,"\
            for(j=1; j <=ncovmodel; j++){   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              printf("%f ",p[jk]);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
              fprintf(ficlog,"%f ",p[jk]);     fprintf(fichtm,"\
              fprintf(ficres,"%f ",p[jk]);   - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
              jk++;     <a href=\"%s\">%s</a> <br>\n",
            }             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
            printf("\n");     fprintf(fichtm,"\
            fprintf(ficlog,"\n");   - Population projections by age and states: \
            fprintf(ficres,"\n");     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
          }  
      }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    }  
    if(mle==1){   m=cptcoveff;
      /* Computing hessian and covariance matrix */   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
      ftolhess=ftol; /* Usually correct */  
      hesscov(matcov, p, npar, delti, ftolhess, func);   jj1=0;
    }   for(k1=1; k1<=m;k1++){
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");     for(i1=1; i1<=ncodemax[k1];i1++){
    printf("# Scales (for hessian or gradient estimation)\n");       jj1++;
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");       if (cptcovn > 0) {
    for(i=1,jk=1; i <=nlstate; i++){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
      for(j=1; j <=nlstate+ndeath; j++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
        if (j!=i) {           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(ficres,"%1d%1d",i,j);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
          printf("%1d%1d",i,j);       }
          fprintf(ficlog,"%1d%1d",i,j);       /* Pij */
          for(k=1; k<=ncovmodel;k++){       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> \
            printf(" %.5e",delti[jk]);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
            fprintf(ficlog," %.5e",delti[jk]);       /* Quasi-incidences */
            fprintf(ficres," %.5e",delti[jk]);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
            jk++;   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
          }  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          printf("\n");         /* Period (stable) prevalence in each health state */
          fprintf(ficlog,"\n");         for(cpt=1; cpt<nlstate;cpt++){
          fprintf(ficres,"\n");           fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
        }  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
      }         }
    }       for(cpt=1; cpt<=nlstate;cpt++) {
              fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
    k=1;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
    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)     } /* end i1 */
      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");   }/* End k1 */
    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");   fprintf(fichtm,"</ul>");
    for(i=1;i<=npar;i++){  
      /*  if (k>nlstate) k=1;  
          i1=(i-1)/(ncovmodel*nlstate)+1;   fprintf(fichtm,"\
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
          printf("%s%d%d",alph[k],i1,tab[i]);*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
      fprintf(ficres,"%3d",i);  
      if(mle==1)   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
        printf("%3d",i);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
      fprintf(ficlog,"%3d",i);   fprintf(fichtm,"\
      for(j=1; j<=i;j++){   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
        fprintf(ficres," %.5e",matcov[i][j]);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
        if(mle==1)  
          printf(" %.5e",matcov[i][j]);   fprintf(fichtm,"\
        fprintf(ficlog," %.5e",matcov[i][j]);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
      }           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
      fprintf(ficres,"\n");   fprintf(fichtm,"\
      if(mle==1)   - 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): \
        printf("\n");     <a href=\"%s\">%s</a> <br>\n</li>",
      fprintf(ficlog,"\n");             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
      k++;   fprintf(fichtm,"\
    }   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
         <a href=\"%s\">%s</a> <br>\n</li>",
    while((c=getc(ficpar))=='#' && c!= EOF){             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
      ungetc(c,ficpar);   fprintf(fichtm,"\
      fgets(line, MAXLINE, ficpar);   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
      puts(line);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
      fputs(line,ficparo);   fprintf(fichtm,"\
    }   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
    ungetc(c,ficpar);           estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    estepm=0;   fprintf(fichtm,"\
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
    if (estepm==0 || estepm < stepm) estepm=stepm;           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
    if (fage <= 2) {  
      bage = ageminpar;  /*  if(popforecast==1) fprintf(fichtm,"\n */
      fage = agemaxpar;  /*  - 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); */
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");  /*  else  */
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);   fflush(fichtm);
       fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
    while((c=getc(ficpar))=='#' && c!= EOF){  
      ungetc(c,ficpar);   m=cptcoveff;
      fgets(line, MAXLINE, ficpar);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
      puts(line);  
      fputs(line,ficparo);   jj1=0;
    }   for(k1=1; k1<=m;k1++){
    ungetc(c,ficpar);     for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);       if (cptcovn > 0) {
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         for (cpt=1; cpt<=cptcoveff;cpt++) 
               fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
    while((c=getc(ficpar))=='#' && c!= EOF){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      ungetc(c,ficpar);       }
      fgets(line, MAXLINE, ficpar);       for(cpt=1; cpt<=nlstate;cpt++) {
      puts(line);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
      fputs(line,ficparo);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
    }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
    ungetc(c,ficpar);       }
         fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  true period expectancies (those weighted with period prevalences are also\
    dateprev2=anprev2+mprev2/12.+jprev2/365.;   drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   fscanf(ficpar,"pop_based=%d\n",&popbased);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   fprintf(ficparo,"pop_based=%d\n",popbased);       } /* end i1 */
   fprintf(ficres,"pop_based=%d\n",popbased);     }/* End k1 */
     fprintf(fichtm,"</ul>");
   while((c=getc(ficpar))=='#' && c!= EOF){   fflush(fichtm);
     ungetc(c,ficpar);  }
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /******************* Gnuplot file **************/
     fputs(line,ficparo);  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   }  
   ungetc(c,ficpar);    char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   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);    int ng=0;
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 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);  /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    /*#ifdef windows */
     fgets(line, MAXLINE, ficpar);    fprintf(ficgp,"cd \"%s\" \n",pathc);
     puts(line);      /*#endif */
     fputs(line,ficparo);    m=pow(2,cptcoveff);
   }  
   ungetc(c,ficpar);    strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);   /* 1eme*/
   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 (cpt=1; cpt<= nlstate ; cpt ++) {
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);     for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
 /*------------ gnuplot -------------*/  set ylabel \"Probability\" \n\
   strcpy(optionfilegnuplot,optionfilefiname);  set ter png small\n\
   strcat(optionfilegnuplot,".gp");  set size 0.65,0.65\n\
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
     printf("Problem with file %s",optionfilegnuplot);  
   }       for (i=1; i<= nlstate ; i ++) {
   fclose(ficgp);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);         else        fprintf(ficgp," \%%*lf (\%%*lf)");
 /*--------- index.htm --------*/       }
        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);
   strcpy(optionfilehtm,optionfile);       for (i=1; i<= nlstate ; i ++) {
   strcat(optionfilehtm,".htm");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {         else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("Problem with %s \n",optionfilehtm), exit(0);       } 
   }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n         else fprintf(ficgp," \%%*lf (\%%*lf)");
 \n       }  
 Total number of observations=%d <br>\n       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n     }
 <hr  size=\"2\" color=\"#EC5E5E\">    }
  <ul><li><h4>Parameter files</h4>\n    /*2 eme*/
  - 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    for (k1=1; k1<= m ; k1 ++) { 
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   fclose(fichtm);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);      for (i=1; i<= nlstate+1 ; i ++) {
          k=2*i;
 /*------------ free_vector  -------------*/        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
  chdir(path);        for (j=1; j<= nlstate+1 ; j ++) {
            if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  free_ivector(wav,1,imx);          else fprintf(ficgp," \%%*lf (\%%*lf)");
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        }   
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
  free_ivector(num,1,n);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
  free_vector(agedc,1,n);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        for (j=1; j<= nlstate+1 ; j ++) {
  fclose(ficparo);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  fclose(ficres);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
   /*--------------- Prevalence limit --------------*/        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
          for (j=1; j<= nlstate+1 ; j ++) {
   strcpy(filerespl,"pl");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   strcat(filerespl,fileres);          else fprintf(ficgp," \%%*lf (\%%*lf)");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        }   
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;        else fprintf(ficgp,"\" t\"\" w l 0,");
   }      }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    }
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);    
   fprintf(ficrespl,"#Prevalence limit\n");    /*3eme*/
   fprintf(ficrespl,"#Age ");    
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for (k1=1; k1<= m ; k1 ++) { 
   fprintf(ficrespl,"\n");      for (cpt=1; cpt<= nlstate ; cpt ++) {
          /*       k=2+nlstate*(2*cpt-2); */
   prlim=matrix(1,nlstate,1,nlstate);        k=2+(nlstate+1)*(cpt-1);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficgp,"set ter png small\n\
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  set size 0.65,0.65\n\
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   k=0;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   agebase=ageminpar;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   agelim=agemaxpar;          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   ftolpl=1.e-10;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   i1=cptcoveff;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   if (cptcovn < 1){i1=1;}          
         */
   for(cptcov=1;cptcov<=i1;cptcov++){        for (i=1; i< nlstate ; i ++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          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);
         k=k+1;          /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          
         fprintf(ficrespl,"\n#******");        } 
         printf("\n#******");        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
         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]]);    /* CV preval stable (period) */
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (k1=1; k1<= m ; k1 ++) { 
         }      for (cpt=1; cpt<=nlstate ; cpt ++) {
         fprintf(ficrespl,"******\n");        k=3;
         printf("******\n");        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficlog,"******\n");        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
          set ter png small\nset size 0.65,0.65\n\
         for (age=agebase; age<=agelim; age++){  unset log y\n\
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
           fprintf(ficrespl,"%.0f",age );        
           for(i=1; i<=nlstate;i++)        for (i=1; i< nlstate ; i ++)
           fprintf(ficrespl," %.5f", prlim[i][i]);          fprintf(ficgp,"+$%d",k+i+1);
           fprintf(ficrespl,"\n");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         }        
       }        l=3+(nlstate+ndeath)*cpt;
     }        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   fclose(ficrespl);        for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
   /*------------- h Pij x at various ages ------------*/          fprintf(ficgp,"+$%d",l+i+1);
          }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   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;    
   }    /* proba elementaires */
   printf("Computing pij: result on file '%s' \n", filerespij);    for(i=1,jk=1; i <=nlstate; i++){
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);      for(k=1; k <=(nlstate+ndeath); k++){
          if (k != i) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(j=1; j <=ncovmodel; j++){
   /*if (stepm<=24) stepsize=2;*/            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
   agelim=AGESUP;            fprintf(ficgp,"\n");
   hstepm=stepsize*YEARM; /* Every year of age */          }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        }
       }
   /* hstepm=1;   aff par mois*/     }
   
   k=0;     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   for(cptcov=1;cptcov<=i1;cptcov++){       for(jk=1; jk <=m; jk++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
       k=k+1;         if (ng==2)
         fprintf(ficrespij,"\n#****** ");           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
         for(j=1;j<=cptcoveff;j++)         else
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           fprintf(ficgp,"\nset title \"Probability\"\n");
         fprintf(ficrespij,"******\n");         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
                 i=1;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */         for(k2=1; k2<=nlstate; k2++) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */           k3=i;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */           for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
           /*      nhstepm=nhstepm*YEARM; aff par mois*/               if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);               else
           oldm=oldms;savm=savms;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                 ij=1;
           fprintf(ficrespij,"# Age");               for(j=3; j <=ncovmodel; j++) {
           for(i=1; i<=nlstate;i++)                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
             for(j=1; j<=nlstate+ndeath;j++)                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
               fprintf(ficrespij," %1d-%1d",i,j);                   ij++;
           fprintf(ficrespij,"\n");                 }
            for (h=0; h<=nhstepm; h++){                 else
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
             for(i=1; i<=nlstate;i++)               }
               for(j=1; j<=nlstate+ndeath;j++)               fprintf(ficgp,")/(1");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);               
             fprintf(ficrespij,"\n");               for(k1=1; k1 <=nlstate; k1++){   
              }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                 ij=1;
           fprintf(ficrespij,"\n");                 for(j=3; j <=ncovmodel; j++){
         }                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     }                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   }                     ij++;
                    }
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);                   else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   fclose(ficrespij);                 }
                  fprintf(ficgp,")");
                }
   /*---------- Forecasting ------------------*/               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   if((stepm == 1) && (strcmp(model,".")==0)){               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);               i=i+ncovmodel;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);             }
   }           } /* end k */
   else{         } /* end k2 */
     erreur=108;       } /* end jk */
     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);     } /* end ng */
     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);     fflush(ficgp); 
   }  }  /* end gnuplot */
    
   
   /*---------- Health expectancies and variances ------------*/  /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   strcpy(filerest,"t");  
   strcat(filerest,fileres);    int i, cpt, cptcod;
   if((ficrest=fopen(filerest,"w"))==NULL) {    int modcovmax =1;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    int mobilavrange, mob;
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;    double age;
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);                             a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   strcpy(filerese,"e");    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   strcat(filerese,fileres);      if(mobilav==1) mobilavrange=5; /* default */
   if((ficreseij=fopen(filerese,"w"))==NULL) {      else mobilavrange=mobilav;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      for (age=bage; age<=fage; age++)
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        for (i=1; i<=nlstate;i++)
   }          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);      /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   strcpy(fileresv,"v");         we use a 5 terms etc. until the borders are no more concerned. 
   strcat(fileresv,fileres);      */ 
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      for (mob=3;mob <=mobilavrange;mob=mob+2){
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);          for (i=1; i<=nlstate;i++){
   }            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   calagedate=-1;                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
   k=0;              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   for(cptcov=1;cptcov<=i1;cptcov++){            }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          }
       k=k+1;        }/* end age */
       fprintf(ficrest,"\n#****** ");      }/* end mob */
       for(j=1;j<=cptcoveff;j++)    }else return -1;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    return 0;
       fprintf(ficrest,"******\n");  }/* End movingaverage */
   
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)  /************** Forecasting ******************/
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
       fprintf(ficreseij,"******\n");    /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
       fprintf(ficresvij,"\n#****** ");       dateprev1 dateprev2 range of dates during which prevalence is computed
       for(j=1;j<=cptcoveff;j++)       anproj2 year of en of projection (same day and month as proj1).
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    */
       fprintf(ficresvij,"******\n");    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double agec; /* generic age */
       oldm=oldms;savm=savms;    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      double *popeffectif,*popcount;
      double ***p3mat;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double ***mobaverage;
       oldm=oldms;savm=savms;    char fileresf[FILENAMELENGTH];
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);  
       if(popbased==1){    agelim=AGESUP;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
        }   
     strcpy(fileresf,"f"); 
      strcat(fileresf,fileres);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    if((ficresf=fopen(fileresf,"w"))==NULL) {
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficrest,"\n");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
       epj=vector(1,nlstate+1);    printf("Computing forecasting: result on file '%s' \n", fileresf);
       for(age=bage; age <=fage ;age++){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==1) {    if (cptcoveff==0) ncodemax[cptcoveff]=1;
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][k];    if (mobilav!=0) {
         }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
              if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficrest," %4.0f",age);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           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]);*/  
           }    stepsize=(int) (stepm+YEARM-1)/YEARM;
           epj[nlstate+1] +=epj[j];    if (stepm<=12) stepsize=1;
         }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
         for(i=1, vepp=0.;i <=nlstate;i++)    }
           for(j=1;j <=nlstate;j++)    else  hstepm=estepm;   
             vepp += vareij[i][j][(int)age];  
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    hstepm=hstepm/stepm; 
         for(j=1;j <=nlstate;j++){    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                                 fractional in yp1 */
         }    anprojmean=yp;
         fprintf(ficrest,"\n");    yp2=modf((yp1*12),&yp);
       }    mprojmean=yp;
     }    yp1=modf((yp2*30.5),&yp);
   }    jprojmean=yp;
 free_matrix(mint,1,maxwav,1,n);    if(jprojmean==0) jprojmean=1;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    if(mprojmean==0) jprojmean=1;
     free_vector(weight,1,n);  
   fclose(ficreseij);    i1=cptcoveff;
   fclose(ficresvij);    if (cptcovn < 1){i1=1;}
   fclose(ficrest);    
   fclose(ficpar);    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   free_vector(epj,1,nlstate+1);    
      fprintf(ficresf,"#****** Routine prevforecast **\n");
   /*------- Variance limit prevalence------*/    
   /*            if (h==(int)(YEARM*yearp)){ */
   strcpy(fileresvpl,"vpl");    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   strcat(fileresvpl,fileres);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        k=k+1;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        fprintf(ficresf,"\n#******");
     exit(0);        for(j=1;j<=cptcoveff;j++) {
   }          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        }
         fprintf(ficresf,"******\n");
   k=0;        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   for(cptcov=1;cptcov<=i1;cptcov++){        for(j=1; j<=nlstate+ndeath;j++){ 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for(i=1; i<=nlstate;i++)              
       k=k+1;            fprintf(ficresf," p%d%d",i,j);
       fprintf(ficresvpl,"\n#****** ");          fprintf(ficresf," p.%d",j);
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
       fprintf(ficresvpl,"******\n");          fprintf(ficresf,"\n");
                fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;          for (agec=fage; agec>=(ageminpar-1); agec--){ 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
     }            nhstepm = nhstepm/hstepm; 
  }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
   fclose(ficresvpl);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
   /*---------- End : free ----------------*/            for (h=0; h<=nhstepm; h++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);              if (h*hstepm/YEARM*stepm ==yearp) {
                  fprintf(ficresf,"\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                for(j=1;j<=cptcoveff;j++) 
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                  fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
                } 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);              for(j=1; j<=nlstate+ndeath;j++) {
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                ppij=0.;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                for(i=1; i<=nlstate;i++) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                  if (mobilav==1) 
                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   free_matrix(matcov,1,npar,1,npar);                  else {
   free_vector(delti,1,npar);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   free_matrix(agev,1,maxwav,1,imx);                  }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                  if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
   fprintf(fichtm,"\n</body>");                  }
   fclose(fichtm);                } /* end i */
   fclose(ficgp);                if (h*hstepm/YEARM*stepm==yearp) {
                    fprintf(ficresf," %.3f", ppij);
                 }
   if(erreur >0){              }/* end j */
     printf("End of Imach with error or warning %d\n",erreur);            } /* end h */
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }else{          } /* end agec */
    printf("End of Imach\n");        } /* end yearp */
    fprintf(ficlog,"End of Imach\n");      } /* end cptcod */
   }    } /* end  cptcov */
   printf("See log file on %s\n",filelog);         
   fclose(ficlog);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
      fclose(ficresf);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  }
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/  /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
  end:    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
 #ifdef windows    int *popage;
   /* chdir(pathcd);*/    double calagedatem, agelim, kk1, kk2;
 #endif    double *popeffectif,*popcount;
  /*system("wgnuplot graph.plt");*/    double ***p3mat,***tabpop,***tabpopprev;
  /*system("../gp37mgw/wgnuplot graph.plt");*/    double ***mobaverage;
  /*system("cd ../gp37mgw");*/    char filerespop[FILENAMELENGTH];
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  strcat(plotcmd," ");    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  strcat(plotcmd,optionfilegnuplot);    agelim=AGESUP;
  system(plotcmd);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
 #ifdef windows    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   while (z[0] != 'q') {    
     /* chdir(path); */    
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    strcpy(filerespop,"pop"); 
     scanf("%s",z);    strcat(filerespop,fileres);
     if (z[0] == 'c') system("./imach");    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     else if (z[0] == 'e') system(optionfilehtm);      printf("Problem with forecast resultfile: %s\n", filerespop);
     else if (z[0] == 'g') system(plotcmd);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     else if (z[0] == 'q') exit(0);    }
   }    printf("Computing forecasting: result on file '%s' \n", filerespop);
 #endif    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
 }  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%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);
           fprintf(ficlog,"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);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   
   int decodemodel ( char model[], int lastobs)
   {
     int i, j, k;
     int i1, j1, k1, k2;
     char modelsav[80];
      char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     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; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3 
                     but the covariates which are product must be computed and stored. */
       cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
       
       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);fflush(ficlog);
         return 1;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*    modelsav=V3*age+V2+V1+V4 strb=V3*age stra=V2+V1+V4 
           i=1 Tvar[1]=3 Tage[1]=1  
           i=2 Tvar[2]=2
           i=3 Tvar[3]=1
           i=4 Tvar[4]= 4
           i=5 Tvar[5]
         for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        */
       for(k=1; k<=(j+1);k++){
         cutv(strb,stra,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav=V3*age+V2+V1+V4 strb=V3*age stra=V2+V1+V4 
                                       */ 
         /* if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);*/ /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V3*age+V2+V1+V4 strb=V3*age */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V'); /* stre="V3" */
             Tvar[k]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3, and Tvar[3]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] =2 */
             /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           }
           else {  /* Age is not in the model V1+V3*V2+V2  strb=V3*V2*/
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1;  /* find 'n' in Vn and stores in Tvar. 
                                     If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]  */
             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 (i=1; i<=lastobs;i++) /* Computes the new covariate which is a product of covar[n][i]* covar[m][i]
                                        and is stored at ncovol+k1 */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             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);  /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0);
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" 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);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (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 plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       cptcovn=nbocc(model,'+')+1;
     /* ncovprod */
     ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read 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++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. 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(decodemodel(model, lastobs) == 1)
       goto end;
   
       /*  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);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     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++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) {
               h=1;
               codtab[h][k]=j;
               codtab[h][Tvar[k]]=j;
             }
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ 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); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         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;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           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);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       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 */
    endfree:
     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_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   
Removed from v.1.50  
changed lines
  Added in v.1.136

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