Diff for /imach/src/imach.c between versions 1.52 and 1.139

version 1.52, 2002/07/19 18:49:30 version 1.139, 2010/06/14 07:50:17
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.139  2010/06/14 07:50:17  brouard
      After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   This program computes Healthy Life Expectancies from    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.138  2010/04/30 18:19:40  brouard
   interviewed on their health status or degree of disability (in the    *** empty log message ***
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.137  2010/04/29 18:11:38  brouard
   (if any) in individual health status.  Health expectancies are    (Module): Checking covariates for more complex models
   computed from the time spent in each health state according to a    than V1+V2. A lot of change to be done. Unstable.
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.136  2010/04/26 20:30:53  brouard
   simplest model is the multinomial logistic model where pij is the    (Module): merging some libgsl code. Fixing computation
   probability to be observed in state j at the second wave    of likelione (using inter/intrapolation if mle = 0) in order to
   conditional to be observed in state i at the first wave. Therefore    get same likelihood as if mle=1.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Some cleaning of code and comments added.
   '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    Revision 1.135  2009/10/29 15:33:14  brouard
   where the markup *Covariates have to be included here again* invites    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.134  2009/10/29 13:18:53  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.133  2009/07/06 10:21:25  brouard
   identical for each individual. Also, if a individual missed an    just nforces
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
   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 1.131  2009/06/20 16:22:47  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Some dimensions resccaled
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.130  2009/05/26 06:44:34  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Max Covariate is now set to 20 instead of 8. A
   and the contribution of each individual to the likelihood is simply    lot of cleaning with variables initialized to 0. Trying to make
   hPijx.    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.129  2007/08/31 13:49:27  lievre
   of the life expectancies. It also computes the prevalence limits.    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.128  2006/06/30 13:02:05  brouard
            Institut national d'études démographiques, Paris.    (Module): Clarifications on computing e.j
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.127  2006/04/28 18:11:50  brouard
   It is copyrighted identically to a GNU software product, ie programme and    (Module): Yes the sum of survivors was wrong since
   software can be distributed freely for non commercial use. Latest version    imach-114 because nhstepm was no more computed in the age
   can be accessed at http://euroreves.ined.fr/imach .    loop. Now we define nhstepma in the age loop.
   **********************************************************************/    (Module): In order to speed up (in case of numerous covariates) we
      compute health expectancies (without variances) in a first step
 #include <math.h>    and then all the health expectancies with variances or standard
 #include <stdio.h>    deviation (needs data from the Hessian matrices) which slows the
 #include <stdlib.h>    computation.
 #include <unistd.h>    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "gnuplot"    Revision 1.126  2006/04/28 17:23:28  brouard
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    (Module): Yes the sum of survivors was wrong since
 #define FILENAMELENGTH 80    imach-114 because nhstepm was no more computed in the age
 /*#define DEBUG*/    loop. Now we define nhstepma in the age loop.
 #define windows    Version 0.98h
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Forecasting file added.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.124  2006/03/22 17:13:53  lievre
 #define NINTERVMAX 8    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    The log-likelihood is printed in the log file
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.123  2006/03/20 10:52:43  brouard
 #define MAXN 20000    * imach.c (Module): <title> changed, corresponds to .htm file
 #define YEARM 12. /* Number of months per year */    name. <head> headers where missing.
 #define AGESUP 130  
 #define AGEBASE 40    * imach.c (Module): Weights can have a decimal point as for
 #ifdef windows    English (a comma might work with a correct LC_NUMERIC environment,
 #define DIRSEPARATOR '\\'    otherwise the weight is truncated).
 #define ODIRSEPARATOR '/'    Modification of warning when the covariates values are not 0 or
 #else    1.
 #define DIRSEPARATOR '/'    Version 0.98g
 #define ODIRSEPARATOR '\\'  
 #endif    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    English (a comma might work with a correct LC_NUMERIC environment,
 int erreur; /* Error number */    otherwise the weight is truncated).
 int nvar;    Modification of warning when the covariates values are not 0 or
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    1.
 int npar=NPARMAX;    Version 0.98g
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.121  2006/03/16 17:45:01  lievre
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    * imach.c (Module): Comments concerning covariates added
 int popbased=0;  
     * imach.c (Module): refinements in the computation of lli if
 int *wav; /* Number of waves for this individuual 0 is possible */    status=-2 in order to have more reliable computation if stepm is
 int maxwav; /* Maxim number of waves */    not 1 month. Version 0.98f
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.120  2006/03/16 15:10:38  lievre
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): refinements in the computation of lli if
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    status=-2 in order to have more reliable computation if stepm is
 double jmean; /* Mean space between 2 waves */    not 1 month. Version 0.98f
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.119  2006/03/15 17:42:26  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Module): Bug if status = -2, the loglikelihood was
 FILE *ficlog;    computed as likelihood omitting the logarithm. Version O.98e
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficresprobmorprev;    Revision 1.118  2006/03/14 18:20:07  brouard
 FILE *fichtm; /* Html File */    (Module): varevsij Comments added explaining the second
 FILE *ficreseij;    table of variances if popbased=1 .
 char filerese[FILENAMELENGTH];    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 FILE  *ficresvij;    (Module): Function pstamp added
 char fileresv[FILENAMELENGTH];    (Module): Version 0.98d
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    Revision 1.117  2006/03/14 17:16:22  brouard
 char title[MAXLINE];    (Module): varevsij Comments added explaining the second
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    table of variances if popbased=1 .
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    (Module): Version 0.98d
 char filelog[FILENAMELENGTH]; /* Log file */  
 char filerest[FILENAMELENGTH];    Revision 1.116  2006/03/06 10:29:27  brouard
 char fileregp[FILENAMELENGTH];    (Module): Variance-covariance wrong links and
 char popfile[FILENAMELENGTH];    varian-covariance of ej. is needed (Saito).
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.114  2006/02/26 12:57:58  brouard
 #define FTOL 1.0e-10    (Module): Some improvements in processing parameter
     filename with strsep.
 #define NRANSI  
 #define ITMAX 200    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 #define TOL 2.0e-4    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.112  2006/01/30 09:55:26  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
 #define GOLD 1.618034    Revision 1.111  2006/01/25 20:38:18  brouard
 #define GLIMIT 100.0    (Module): Lots of cleaning and bugs added (Gompertz)
 #define TINY 1.0e-20    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.110  2006/01/25 00:51:50  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Lots of cleaning and bugs added (Gompertz)
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.109  2006/01/24 19:37:15  brouard
 #define rint(a) floor(a+0.5)    (Module): Comments (lines starting with a #) are allowed in data.
   
 static double sqrarg;    Revision 1.108  2006/01/19 18:05:42  lievre
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Gnuplot problem appeared...
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    To be fixed
   
 int imx;    Revision 1.107  2006/01/19 16:20:37  brouard
 int stepm;    Test existence of gnuplot in imach path
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.106  2006/01/19 13:24:36  brouard
 int estepm;    Some cleaning and links added in html output
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Revision 1.105  2006/01/05 20:23:19  lievre
 int m,nb;    *** empty log message ***
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.104  2005/09/30 16:11:43  lievre
 double **pmmij, ***probs, ***mobaverage;    (Module): sump fixed, loop imx fixed, and simplifications.
 double dateintmean=0;    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
 double *weight;    (instead of missing=-1 in earlier versions) and his/her
 int **s; /* Status */    contributions to the likelihood is 1 - Prob of dying from last
 double *agedc, **covar, idx;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    the healthy state at last known wave). Version is 0.98
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.103  2005/09/30 15:54:49  lievre
 double ftolhess; /* Tolerance for computing hessian */    (Module): sump fixed, loop imx fixed, and simplifications.
   
 /**************** split *************************/    Revision 1.102  2004/09/15 17:31:30  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Add the possibility to read data file including tab characters.
 {  
    char *s;                             /* pointer */    Revision 1.101  2004/09/15 10:38:38  brouard
    int  l1, l2;                         /* length counters */    Fix on curr_time
   
    l1 = strlen( path );                 /* length of path */    Revision 1.100  2004/07/12 18:29:06  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Add version for Mac OS X. Just define UNIX in Makefile
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.99  2004/06/05 08:57:40  brouard
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    *** empty log message ***
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.98  2004/05/16 15:05:56  brouard
       extern char       *getwd( );    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
       if ( getwd( dirc ) == NULL ) {    state at each age, but using a Gompertz model: log u =a + b*age .
 #else    This is the basic analysis of mortality and should be done before any
       extern char       *getcwd( );    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    from other sources like vital statistic data.
 #endif  
          return( GLOCK_ERROR_GETCWD );    The same imach parameter file can be used but the option for mle should be -3.
       }  
       strcpy( name, path );             /* we've got it */    Agnès, who wrote this part of the code, tried to keep most of the
    } else {                             /* strip direcotry from path */    former routines in order to include the new code within the former code.
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    The output is very simple: only an estimate of the intercept and of
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    the slope with 95% confident intervals.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Current limitations:
       dirc[l1-l2] = 0;                  /* add zero */    A) Even if you enter covariates, i.e. with the
    }    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    l1 = strlen( dirc );                 /* length of directory */    B) There is no computation of Life Expectancy nor Life Table.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.97  2004/02/20 13:25:42  lievre
 #else    Version 0.96d. Population forecasting command line is (temporarily)
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    suppressed.
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.96  2003/07/15 15:38:55  brouard
    s++;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
    strcpy(ext,s);                       /* save extension */    rewritten within the same printf. Workaround: many printfs.
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.95  2003/07/08 07:54:34  brouard
    strncpy( finame, name, l1-l2);    * imach.c (Repository):
    finame[l1-l2]= 0;    (Repository): Using imachwizard code to output a more meaningful covariance
    return( 0 );                         /* we're done */    matrix (cov(a12,c31) instead of numbers.
 }  
     Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 /******************************************/  
     Revision 1.93  2003/06/25 16:33:55  brouard
 void replace(char *s, char*t)    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   int i;    (Module): Version 0.96b
   int lg=20;  
   i=0;    Revision 1.92  2003/06/25 16:30:45  brouard
   lg=strlen(t);    (Module): On windows (cygwin) function asctime_r doesn't
   for(i=0; i<= lg; i++) {    exist so I changed back to asctime which exists.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    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
     helps to forecast when convergence will be reached. Elapsed time
 int nbocc(char *s, char occ)    is stamped in powell.  We created a new html file for the graphs
 {    concerning matrix of covariance. It has extension -cov.htm.
   int i,j=0;  
   int lg=20;    Revision 1.90  2003/06/24 12:34:15  brouard
   i=0;    (Module): Some bugs corrected for windows. Also, when
   lg=strlen(s);    mle=-1 a template is output in file "or"mypar.txt with the design
   for(i=0; i<= lg; i++) {    of the covariance matrix to be input.
   if  (s[i] == occ ) j++;  
   }    Revision 1.89  2003/06/24 12:30:52  brouard
   return j;    (Module): Some bugs corrected for windows. Also, when
 }    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.88  2003/06/23 17:54:56  brouard
   /* cuts string t into u and v where u is ended by char occ excluding it    * 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.
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  
      gives u="abcedf" and v="ghi2j" */    Revision 1.87  2003/06/18 12:26:01  brouard
   int i,lg,j,p=0;    Version 0.96
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.86  2003/06/17 20:04:08  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Module): Change position of html and gnuplot routines and added
   }    routine fileappend.
   
   lg=strlen(t);    Revision 1.85  2003/06/17 13:12:43  brouard
   for(j=0; j<p; j++) {    * imach.c (Repository): Check when date of death was earlier that
     (u[j] = t[j]);    current date of interview. It may happen when the death was just
   }    prior to the death. In this case, dh was negative and likelihood
      u[p]='\0';    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
    for(j=0; j<= lg; j++) {    interview.
     if (j>=(p+1))(v[j-p-1] = t[j]);    (Repository): Because some people have very long ID (first column)
   }    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)
 /********************** nrerror ********************/    (Repository): No more line truncation errors.
   
 void nrerror(char error_text[])    Revision 1.84  2003/06/13 21:44:43  brouard
 {    * imach.c (Repository): Replace "freqsummary" at a correct
   fprintf(stderr,"ERREUR ...\n");    place. It differs from routine "prevalence" which may be called
   fprintf(stderr,"%s\n",error_text);    many times. Probs is memory consuming and must be used with
   exit(1);    parcimony.
 }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /*********************** vector *******************/  
 double *vector(int nl, int nh)    Revision 1.83  2003/06/10 13:39:11  lievre
 {    *** empty log message ***
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.82  2003/06/05 15:57:20  brouard
   if (!v) nrerror("allocation failure in vector");    Add log in  imach.c and  fullversion number is now printed.
   return v-nl+NR_END;  
 }  */
   /*
 /************************ free vector ******************/     Interpolated Markov Chain
 void free_vector(double*v, int nl, int nh)  
 {    Short summary of the programme:
   free((FREE_ARG)(v+nl-NR_END));    
 }    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 /************************ivector *******************************/    first survey ("cross") where individuals from different ages are
 int *ivector(long nl,long nh)    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
   int *v;    second wave of interviews ("longitudinal") which measure each change
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (if any) in individual health status.  Health expectancies are
   if (!v) nrerror("allocation failure in ivector");    computed from the time spent in each health state according to a
   return v-nl+NR_END;    model. More health states you consider, more time is necessary to reach the
 }    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 /******************free ivector **************************/    probability to be observed in state j at the second wave
 void free_ivector(int *v, long nl, long nh)    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
   free((FREE_ARG)(v+nl-NR_END));    '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
     where the markup *Covariates have to be included here again* invites
 /******************* imatrix *******************************/    you to do it.  More covariates you add, slower the
 int **imatrix(long nrl, long nrh, long ncl, long nch)    convergence.
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    The advantage of this computer programme, compared to a simple
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    multinomial logistic model, is clear when the delay between waves is not
   int **m;    identical for each individual. Also, if a individual missed an
      intermediate interview, the information is lost, but taken into
   /* allocate pointers to rows */    account using an interpolation or extrapolation.  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    hPijx is the probability to be observed in state i at age x+h
   m += NR_END;    conditional to the observed state i at age x. The delay 'h' can be
   m -= nrl;    split into an exact number (nh*stepm) of unobserved intermediate
      states. This elementary transition (by month, quarter,
      semester or year) is modelled as a multinomial logistic.  The hPx
   /* allocate rows and set pointers to them */    matrix is simply the matrix product of nh*stepm elementary matrices
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    and the contribution of each individual to the likelihood is simply
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    hPijx.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Also this programme outputs the covariance matrix of the parameters but also
      of the life expectancies. It also computes the period (stable) prevalence. 
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   /* return pointer to array of pointers to rows */             Institut national d'études démographiques, Paris.
   return m;    This software have been partly granted by Euro-REVES, a concerted action
 }    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 /****************** free_imatrix *************************/    software can be distributed freely for non commercial use. Latest version
 void free_imatrix(m,nrl,nrh,ncl,nch)    can be accessed at http://euroreves.ined.fr/imach .
       int **m;  
       long nch,ncl,nrh,nrl;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
      /* free an int matrix allocated by imatrix() */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 {    
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    **********************************************************************/
   free((FREE_ARG) (m+nrl-NR_END));  /*
 }    main
     read parameterfile
 /******************* matrix *******************************/    read datafile
 double **matrix(long nrl, long nrh, long ncl, long nch)    concatwav
 {    freqsummary
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    if (mle >= 1)
   double **m;      mlikeli
     print results files
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if mle==1 
   if (!m) nrerror("allocation failure 1 in matrix()");       computes hessian
   m += NR_END;    read end of parameter file: agemin, agemax, bage, fage, estepm
   m -= nrl;        begin-prev-date,...
     open gnuplot file
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    open html file
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    period (stable) prevalence
   m[nrl] += NR_END;     for age prevalim()
   m[nrl] -= ncl;    h Pij x
     variance of p varprob
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    forecasting if prevfcast==1 prevforecast call prevalence()
   return m;    health expectancies
 }    Variance-covariance of DFLE
     prevalence()
 /*************************free matrix ************************/     movingaverage()
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    varevsij() 
 {    if popbased==1 varevsij(,popbased)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    total life expectancies
   free((FREE_ARG)(m+nrl-NR_END));    Variance of period (stable) prevalence
 }   end
   */
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;   
   double ***m;  #include <math.h>
   #include <stdio.h>
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #include <stdlib.h>
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <string.h>
   m += NR_END;  #include <unistd.h>
   m -= nrl;  
   #include <limits.h>
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <sys/types.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <sys/stat.h>
   m[nrl] += NR_END;  #include <errno.h>
   m[nrl] -= ncl;  extern int errno;
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /* #include <sys/time.h> */
   #include <time.h>
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #include "timeval.h"
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  #ifdef GSL
   m[nrl][ncl] -= nll;  #include <gsl/gsl_errno.h>
   for (j=ncl+1; j<=nch; j++)  #include <gsl/gsl_multimin.h>
     m[nrl][j]=m[nrl][j-1]+nlay;  #endif
    
   for (i=nrl+1; i<=nrh; i++) {  /* #include <libintl.h> */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /* #define _(String) gettext (String) */
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  #define MAXLINE 256
   }  
   return m;  #define GNUPLOTPROGRAM "gnuplot"
 }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
   free((FREE_ARG)(m+nrl-NR_END));  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 }  
   #define NINTERVMAX 8
 /***************** f1dim *************************/  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 extern int ncom;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 extern double *pcom,*xicom;  #define NCOVMAX 20 /* Maximum number of covariates */
 extern double (*nrfunc)(double []);  #define MAXN 20000
    #define YEARM 12. /* Number of months per year */
 double f1dim(double x)  #define AGESUP 130
 {  #define AGEBASE 40
   int j;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   double f;  #ifdef UNIX
   double *xt;  #define DIRSEPARATOR '/'
    #define CHARSEPARATOR "/"
   xt=vector(1,ncom);  #define ODIRSEPARATOR '\\'
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #else
   f=(*nrfunc)(xt);  #define DIRSEPARATOR '\\'
   free_vector(xt,1,ncom);  #define CHARSEPARATOR "\\"
   return f;  #define ODIRSEPARATOR '/'
 }  #endif
   
 /*****************brent *************************/  /* $Id$ */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /* $State$ */
 {  
   int iter;  char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
   double a,b,d,etemp;  char fullversion[]="$Revision$ $Date$"; 
   double fu,fv,fw,fx;  char strstart[80];
   double ftemp;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double e=0.0;  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' */
   a=(ax < cx ? ax : cx);  int npar=NPARMAX;
   b=(ax > cx ? ax : cx);  int nlstate=2; /* Number of live states */
   x=w=v=bx;  int ndeath=1; /* Number of dead states */
   fw=fv=fx=(*f)(x);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   for (iter=1;iter<=ITMAX;iter++) {  int popbased=0;
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int *wav; /* Number of waves for this individuual 0 is possible */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int maxwav=0; /* Maxim number of waves */
     printf(".");fflush(stdout);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     fprintf(ficlog,".");fflush(ficlog);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
 #ifdef DEBUG  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     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);                     to the likelihood and the sum of weights (done by funcone)*/
     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 mle=1, weightopt=0;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #endif  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       *xmin=x;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       return fx;  double jmean=1; /* Mean space between 2 waves */
     }  double **oldm, **newm, **savm; /* Working pointers to matrices */
     ftemp=fu;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     if (fabs(e) > tol1) {  /*FILE *fic ; */ /* Used in readdata only */
       r=(x-w)*(fx-fv);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       q=(x-v)*(fx-fw);  FILE *ficlog, *ficrespow;
       p=(x-v)*q-(x-w)*r;  int globpr=0; /* Global variable for printing or not */
       q=2.0*(q-r);  double fretone; /* Only one call to likelihood */
       if (q > 0.0) p = -p;  long ipmx=0; /* Number of contributions */
       q=fabs(q);  double sw; /* Sum of weights */
       etemp=e;  char filerespow[FILENAMELENGTH];
       e=d;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  FILE *ficresilk;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       else {  FILE *ficresprobmorprev;
         d=p/q;  FILE *fichtm, *fichtmcov; /* Html File */
         u=x+d;  FILE *ficreseij;
         if (u-a < tol2 || b-u < tol2)  char filerese[FILENAMELENGTH];
           d=SIGN(tol1,xm-x);  FILE *ficresstdeij;
       }  char fileresstde[FILENAMELENGTH];
     } else {  FILE *ficrescveij;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  char filerescve[FILENAMELENGTH];
     }  FILE  *ficresvij;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  char fileresv[FILENAMELENGTH];
     fu=(*f)(u);  FILE  *ficresvpl;
     if (fu <= fx) {  char fileresvpl[FILENAMELENGTH];
       if (u >= x) a=x; else b=x;  char title[MAXLINE];
       SHFT(v,w,x,u)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
         SHFT(fv,fw,fx,fu)  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         } else {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
           if (u < x) a=u; else b=u;  char command[FILENAMELENGTH];
           if (fu <= fw || w == x) {  int  outcmd=0;
             v=w;  
             w=u;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
             fv=fw;  
             fw=fu;  char filelog[FILENAMELENGTH]; /* Log file */
           } else if (fu <= fv || v == x || v == w) {  char filerest[FILENAMELENGTH];
             v=u;  char fileregp[FILENAMELENGTH];
             fv=fu;  char popfile[FILENAMELENGTH];
           }  
         }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   }  
   nrerror("Too many iterations in brent");  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   *xmin=x;  struct timezone tzp;
   return fx;  extern int gettimeofday();
 }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
 /****************** mnbrak ***********************/  extern long time();
   char strcurr[80], strfor[80];
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  char *endptr;
 {  long lval;
   double ulim,u,r,q, dum;  double dval;
   double fu;  
    #define NR_END 1
   *fa=(*func)(*ax);  #define FREE_ARG char*
   *fb=(*func)(*bx);  #define FTOL 1.0e-10
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)  #define NRANSI 
       SHFT(dum,*fb,*fa,dum)  #define ITMAX 200 
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  #define TOL 2.0e-4 
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  #define CGOLD 0.3819660 
     r=(*bx-*ax)*(*fb-*fc);  #define ZEPS 1.0e-10 
     q=(*bx-*cx)*(*fb-*fa);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define GOLD 1.618034 
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define GLIMIT 100.0 
     if ((*bx-u)*(u-*cx) > 0.0) {  #define TINY 1.0e-20 
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {  static double maxarg1,maxarg2;
       fu=(*func)(u);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       if (fu < *fc) {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    
           SHFT(*fb,*fc,fu,(*func)(u))  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
           }  #define rint(a) floor(a+0.5)
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  static double sqrarg;
       fu=(*func)(u);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     } else {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       u=(*cx)+GOLD*(*cx-*bx);  int agegomp= AGEGOMP;
       fu=(*func)(u);  
     }  int imx; 
     SHFT(*ax,*bx,*cx,u)  int stepm=1;
       SHFT(*fa,*fb,*fc,fu)  /* Stepm, step in month: minimum step interpolation*/
       }  
 }  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 /*************** linmin ************************/  
   int m,nb;
 int ncom;  long *num;
 double *pcom,*xicom;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 double (*nrfunc)(double []);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    double **pmmij, ***probs;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  double *ageexmed,*agecens;
 {  double dateintmean=0;
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  double *weight;
   double f1dim(double x);  int **s; /* Status */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double *agedc, **covar, idx;
               double *fc, double (*func)(double));  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   int j;  double *lsurv, *lpop, *tpop;
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
    double ftolhess; /* Tolerance for computing hessian */
   ncom=n;  
   pcom=vector(1,n);  /**************** split *************************/
   xicom=vector(1,n);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   nrfunc=func;  {
   for (j=1;j<=n;j++) {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     pcom[j]=p[j];       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     xicom[j]=xi[j];    */ 
   }    char  *ss;                            /* pointer */
   ax=0.0;    int   l1, l2;                         /* length counters */
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    l1 = strlen(path );                   /* length of path */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 #ifdef DEBUG    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      strcpy( name, path );               /* we got the fullname name because no directory */
 #endif      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   for (j=1;j<=n;j++) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     xi[j] *= xmin;      /* get current working directory */
     p[j] += xi[j];      /*    extern  char* getcwd ( char *buf , int len);*/
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   free_vector(xicom,1,n);        return( GLOCK_ERROR_GETCWD );
   free_vector(pcom,1,n);      }
 }      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
 /*************** powell ************************/    } else {                              /* strip direcotry from path */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      ss++;                               /* after this, the filename */
             double (*func)(double []))      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   void linmin(double p[], double xi[], int n, double *fret,      strcpy( name, ss );         /* save file name */
               double (*func)(double []));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   int i,ibig,j;      dirc[l1-l2] = 0;                    /* add zero */
   double del,t,*pt,*ptt,*xit;      printf(" DIRC2 = %s \n",dirc);
   double fp,fptt;    }
   double *xits;    /* We add a separator at the end of dirc if not exists */
   pt=vector(1,n);    l1 = strlen( dirc );                  /* length of directory */
   ptt=vector(1,n);    if( dirc[l1-1] != DIRSEPARATOR ){
   xit=vector(1,n);      dirc[l1] =  DIRSEPARATOR;
   xits=vector(1,n);      dirc[l1+1] = 0; 
   *fret=(*func)(p);      printf(" DIRC3 = %s \n",dirc);
   for (j=1;j<=n;j++) pt[j]=p[j];    }
   for (*iter=1;;++(*iter)) {    ss = strrchr( name, '.' );            /* find last / */
     fp=(*fret);    if (ss >0){
     ibig=0;      ss++;
     del=0.0;      strcpy(ext,ss);                     /* save extension */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      l1= strlen( name);
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      l2= strlen(ss)+1;
     for (i=1;i<=n;i++)      strncpy( finame, name, l1-l2);
       printf(" %d %.12f",i, p[i]);      finame[l1-l2]= 0;
     fprintf(ficlog," %d %.12f",i, p[i]);    }
     printf("\n");  
     fprintf(ficlog,"\n");    return( 0 );                          /* we're done */
     for (i=1;i<=n;i++) {  }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  
 #ifdef DEBUG  /******************************************/
       printf("fret=%lf \n",*fret);  
       fprintf(ficlog,"fret=%lf \n",*fret);  void replace_back_to_slash(char *s, char*t)
 #endif  {
       printf("%d",i);fflush(stdout);    int i;
       fprintf(ficlog,"%d",i);fflush(ficlog);    int lg=0;
       linmin(p,xit,n,fret,func);    i=0;
       if (fabs(fptt-(*fret)) > del) {    lg=strlen(t);
         del=fabs(fptt-(*fret));    for(i=0; i<= lg; i++) {
         ibig=i;      (s[i] = t[i]);
       }      if (t[i]== '\\') s[i]='/';
 #ifdef DEBUG    }
       printf("%d %.12e",i,(*fret));  }
       fprintf(ficlog,"%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  char *trimbb(char *out, char *in)
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
         printf(" x(%d)=%.12e",j,xit[j]);    char *s;
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);    s=out;
       }    while (*in != '\0'){
       for(j=1;j<=n;j++) {      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         printf(" p=%.12e",p[j]);        in++;
         fprintf(ficlog," p=%.12e",p[j]);      }
       }      *out++ = *in++;
       printf("\n");    }
       fprintf(ficlog,"\n");    *out='\0';
 #endif    return s;
     }  }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  char *cutv(char *blocc, char *alocc, char *in, char occ)
       int k[2],l;  {
       k[0]=1;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       k[1]=-1;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       printf("Max: %.12e",(*func)(p));       gives blocc="abcdef2ghi" and alocc="j".
       fprintf(ficlog,"Max: %.12e",(*func)(p));       If occ is not found blocc is null and alocc is equal to in. Returns alocc
       for (j=1;j<=n;j++) {    */
         printf(" %.12e",p[j]);    char *s, *t;
         fprintf(ficlog," %.12e",p[j]);    t=in;s=in;
       }    while (*in != '\0'){
       printf("\n");      while( *in == occ){
       fprintf(ficlog,"\n");        *blocc++ = *in++;
       for(l=0;l<=1;l++) {        s=in;
         for (j=1;j<=n;j++) {      }
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      *blocc++ = *in++;
           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]);    if (s == t) /* occ not found */
         }      *(blocc-(in-s))='\0';
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    else
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      *(blocc-(in-s)-1)='\0';
       }    in=s;
 #endif    while ( *in != '\0'){
       *alocc++ = *in++;
     }
       free_vector(xit,1,n);  
       free_vector(xits,1,n);    *alocc='\0';
       free_vector(ptt,1,n);    return s;
       free_vector(pt,1,n);  }
       return;  
     }  int nbocc(char *s, char occ)
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  {
     for (j=1;j<=n;j++) {    int i,j=0;
       ptt[j]=2.0*p[j]-pt[j];    int lg=20;
       xit[j]=p[j]-pt[j];    i=0;
       pt[j]=p[j];    lg=strlen(s);
     }    for(i=0; i<= lg; i++) {
     fptt=(*func)(ptt);    if  (s[i] == occ ) j++;
     if (fptt < fp) {    }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    return j;
       if (t < 0.0) {  }
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  /* void cutv(char *u,char *v, char*t, char occ) */
           xi[j][ibig]=xi[j][n];  /* { */
           xi[j][n]=xit[j];  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
         }  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
 #ifdef DEBUG  /*      gives u="abcdef2ghi" and v="j" *\/ */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /*   int i,lg,j,p=0; */
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /*   i=0; */
         for(j=1;j<=n;j++){  /*   lg=strlen(t); */
           printf(" %.12e",xit[j]);  /*   for(j=0; j<=lg-1; j++) { */
           fprintf(ficlog," %.12e",xit[j]);  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
         }  /*   } */
         printf("\n");  
         fprintf(ficlog,"\n");  /*   for(j=0; j<p; j++) { */
 #endif  /*     (u[j] = t[j]); */
       }  /*   } */
     }  /*      u[p]='\0'; */
   }  
 }  /*    for(j=0; j<= lg; j++) { */
   /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
 /**** Prevalence limit ****************/  /*   } */
   /* } */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {  /********************** nrerror ********************/
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  void nrerror(char error_text[])
   {
   int i, ii,j,k;    fprintf(stderr,"ERREUR ...\n");
   double min, max, maxmin, maxmax,sumnew=0.;    fprintf(stderr,"%s\n",error_text);
   double **matprod2();    exit(EXIT_FAILURE);
   double **out, cov[NCOVMAX], **pmij();  }
   double **newm;  /*********************** vector *******************/
   double agefin, delaymax=50 ; /* Max number of years to converge */  double *vector(int nl, int nh)
   {
   for (ii=1;ii<=nlstate+ndeath;ii++)    double *v;
     for (j=1;j<=nlstate+ndeath;j++){    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    if (!v) nrerror("allocation failure in vector");
     }    return v-nl+NR_END;
   }
    cov[1]=1.;  
    /************************ free vector ******************/
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  void free_vector(double*v, int nl, int nh)
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  {
     newm=savm;    free((FREE_ARG)(v+nl-NR_END));
     /* Covariates have to be included here again */  }
      cov[2]=agefin;  
    /************************ivector *******************************/
       for (k=1; k<=cptcovn;k++) {  int *ivector(long nl,long nh)
         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]]);*/    int *v;
       }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    if (!v) nrerror("allocation failure in ivector");
       for (k=1; k<=cptcovprod;k++)    return v-nl+NR_END;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  }
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  /******************free ivector **************************/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  void free_ivector(int *v, long nl, long nh)
       /*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);    free((FREE_ARG)(v+nl-NR_END));
   }
     savm=oldm;  
     oldm=newm;  /************************lvector *******************************/
     maxmax=0.;  long *lvector(long nl,long nh)
     for(j=1;j<=nlstate;j++){  {
       min=1.;    long *v;
       max=0.;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       for(i=1; i<=nlstate; i++) {    if (!v) nrerror("allocation failure in ivector");
         sumnew=0;    return v-nl+NR_END;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  }
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  /******************free lvector **************************/
         min=FMIN(min,prlim[i][j]);  void free_lvector(long *v, long nl, long nh)
       }  {
       maxmin=max-min;    free((FREE_ARG)(v+nl-NR_END));
       maxmax=FMAX(maxmax,maxmin);  }
     }  
     if(maxmax < ftolpl){  /******************* imatrix *******************************/
       return prlim;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   }  { 
 }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
 /*************** transition probabilities ***************/    
     /* allocate pointers to rows */ 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 {    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double s1, s2;    m += NR_END; 
   /*double t34;*/    m -= nrl; 
   int i,j,j1, nc, ii, jj;    
     
     for(i=1; i<= nlstate; i++){    /* allocate rows and set pointers to them */ 
     for(j=1; j<i;j++){    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         /*s2 += param[i][j][nc]*cov[nc];*/    m[nrl] += NR_END; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    m[nrl] -= ncl; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    
       }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       ps[i][j]=s2;    
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    /* return pointer to array of pointers to rows */ 
     }    return m; 
     for(j=i+1; j<=nlstate+ndeath;j++){  } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /****************** free_imatrix *************************/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  void free_imatrix(m,nrl,nrh,ncl,nch)
       }        int **m;
       ps[i][j]=s2;        long nch,ncl,nrh,nrl; 
     }       /* free an int matrix allocated by imatrix() */ 
   }  { 
     /*ps[3][2]=1;*/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
   for(i=1; i<= nlstate; i++){  } 
      s1=0;  
     for(j=1; j<i; j++)  /******************* matrix *******************************/
       s1+=exp(ps[i][j]);  double **matrix(long nrl, long nrh, long ncl, long nch)
     for(j=i+1; j<=nlstate+ndeath; j++)  {
       s1+=exp(ps[i][j]);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     ps[i][i]=1./(s1+1.);    double **m;
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for(j=i+1; j<=nlstate+ndeath; j++)    if (!m) nrerror("allocation failure 1 in matrix()");
       ps[i][j]= exp(ps[i][j])*ps[i][i];    m += NR_END;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    m -= nrl;
   } /* end i */  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for(jj=1; jj<= nlstate+ndeath; jj++){    m[nrl] += NR_END;
       ps[ii][jj]=0;    m[nrl] -= ncl;
       ps[ii][ii]=1;  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   }    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
      */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  /*************************free matrix ************************/
    }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     printf("\n ");  {
     }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     printf("\n ");printf("%lf ",cov[2]);*/    free((FREE_ARG)(m+nrl-NR_END));
 /*  }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  
   goto end;*/  /******************* ma3x *******************************/
     return ps;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 }  {
     long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 /**************** Product of 2 matrices ******************/    double ***m;
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    m += NR_END;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    m -= nrl;
   /* in, b, out are matrice of pointers which should have been initialized  
      before: only the contents of out is modified. The function returns    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      a pointer to pointers identical to out */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   long i, j, k;    m[nrl] += NR_END;
   for(i=nrl; i<= nrh; i++)    m[nrl] -= ncl;
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         out[i][k] +=in[i][j]*b[j][k];  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   return out;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 }    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
 /************* Higher Matrix Product ***************/      m[nrl][j]=m[nrl][j-1]+nlay;
     
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    for (i=nrl+1; i<=nrh; i++) {
 {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      for (j=ncl+1; j<=nch; j++) 
      duration (i.e. until        m[i][j]=m[i][j-1]+nlay;
      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    return m; 
      (typically every 2 years instead of every month which is too big).    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
      Model is determined by parameters x and covariates have to be             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
      included manually here.    */
   }
      */  
   /*************************free ma3x ************************/
   int i, j, d, h, k;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   double **out, cov[NCOVMAX];  {
   double **newm;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
   /* Hstepm could be zero and should return the unit matrix */    free((FREE_ARG)(m+nrl-NR_END));
   for (i=1;i<=nlstate+ndeath;i++)  }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  /*************** function subdirf ***********/
       po[i][j][0]=(i==j ? 1.0 : 0.0);  char *subdirf(char fileres[])
     }  {
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* Caution optionfilefiname is hidden */
   for(h=1; h <=nhstepm; h++){    strcpy(tmpout,optionfilefiname);
     for(d=1; d <=hstepm; d++){    strcat(tmpout,"/"); /* Add to the right */
       newm=savm;    strcat(tmpout,fileres);
       /* Covariates have to be included here again */    return tmpout;
       cov[1]=1.;  }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /*************** function subdirf2 ***********/
       for (k=1; k<=cptcovage;k++)  char *subdirf2(char fileres[], char *preop)
         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]]];    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    strcat(tmpout,preop);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    strcat(tmpout,fileres);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    return tmpout;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  }
       savm=oldm;  
       oldm=newm;  /*************** function subdirf3 ***********/
     }  char *subdirf3(char fileres[], char *preop, char *preop2)
     for(i=1; i<=nlstate+ndeath; i++)  {
       for(j=1;j<=nlstate+ndeath;j++) {    
         po[i][j][h]=newm[i][j];    /* Caution optionfilefiname is hidden */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    strcpy(tmpout,optionfilefiname);
          */    strcat(tmpout,"/");
       }    strcat(tmpout,preop);
   } /* end h */    strcat(tmpout,preop2);
   return po;    strcat(tmpout,fileres);
 }    return tmpout;
   }
   
 /*************** log-likelihood *************/  /***************** f1dim *************************/
 double func( double *x)  extern int ncom; 
 {  extern double *pcom,*xicom;
   int i, ii, j, k, mi, d, kk;  extern double (*nrfunc)(double []); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];   
   double **out;  double f1dim(double x) 
   double sw; /* Sum of weights */  { 
   double lli; /* Individual log likelihood */    int j; 
   long ipmx;    double f;
   /*extern weight */    double *xt; 
   /* We are differentiating ll according to initial status */   
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    xt=vector(1,ncom); 
   /*for(i=1;i<imx;i++)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     printf(" %d\n",s[4][i]);    f=(*nrfunc)(xt); 
   */    free_vector(xt,1,ncom); 
   cov[1]=1.;    return f; 
   } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  /*****************brent *************************/
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     for(mi=1; mi<= wav[i]-1; mi++){  { 
       for (ii=1;ii<=nlstate+ndeath;ii++)    int iter; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    double a,b,d,etemp;
       for(d=0; d<dh[mi][i]; d++){    double fu,fv,fw,fx;
         newm=savm;    double ftemp;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         for (kk=1; kk<=cptcovage;kk++) {    double e=0.0; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];   
         }    a=(ax < cx ? ax : cx); 
            b=(ax > cx ? ax : cx); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    x=w=v=bx; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    fw=fv=fx=(*f)(x); 
         savm=oldm;    for (iter=1;iter<=ITMAX;iter++) { 
         oldm=newm;      xm=0.5*(a+b); 
              tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
              /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       } /* end mult */      printf(".");fflush(stdout);
            fprintf(ficlog,".");fflush(ficlog);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  #ifdef DEBUG
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       ipmx +=1;      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);
       sw += weight[i];      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  #endif
     } /* end of wave */      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   } /* end of individual */        *xmin=x; 
         return fx; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      } 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      ftemp=fu;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      if (fabs(e) > tol1) { 
   return -l;        r=(x-w)*(fx-fv); 
 }        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
 /*********** Maximum Likelihood Estimation ***************/        if (q > 0.0) p = -p; 
         q=fabs(q); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        etemp=e; 
 {        e=d; 
   int i,j, iter;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double **xi,*delti;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double fret;        else { 
   xi=matrix(1,npar,1,npar);          d=p/q; 
   for (i=1;i<=npar;i++)          u=x+d; 
     for (j=1;j<=npar;j++)          if (u-a < tol2 || b-u < tol2) 
       xi[i][j]=(i==j ? 1.0 : 0.0);            d=SIGN(tol1,xm-x); 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");        } 
   powell(p,xi,npar,ftol,&iter,&fret,func);      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      } 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      fu=(*f)(u); 
       if (fu <= fx) { 
 }        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
 /**** Computes Hessian and covariance matrix ***/          SHFT(fv,fw,fx,fu) 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          } else { 
 {            if (u < x) a=u; else b=u; 
   double  **a,**y,*x,pd;            if (fu <= fw || w == x) { 
   double **hess;              v=w; 
   int i, j,jk;              w=u; 
   int *indx;              fv=fw; 
               fw=fu; 
   double hessii(double p[], double delta, int theta, double delti[]);            } else if (fu <= fv || v == x || v == w) { 
   double hessij(double p[], double delti[], int i, int j);              v=u; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;              fv=fu; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;            } 
           } 
   hess=matrix(1,npar,1,npar);    } 
     nrerror("Too many iterations in brent"); 
   printf("\nCalculation of the hessian matrix. Wait...\n");    *xmin=x; 
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    return fx; 
   for (i=1;i<=npar;i++){  } 
     printf("%d",i);fflush(stdout);  
     fprintf(ficlog,"%d",i);fflush(ficlog);  /****************** mnbrak ***********************/
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     /*printf(" %lf ",hess[i][i]);*/              double (*func)(double)) 
   }  { 
      double ulim,u,r,q, dum;
   for (i=1;i<=npar;i++) {    double fu; 
     for (j=1;j<=npar;j++)  {   
       if (j>i) {    *fa=(*func)(*ax); 
         printf(".%d%d",i,j);fflush(stdout);    *fb=(*func)(*bx); 
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    if (*fb > *fa) { 
         hess[i][j]=hessij(p,delti,i,j);      SHFT(dum,*ax,*bx,dum) 
         hess[j][i]=hess[i][j];            SHFT(dum,*fb,*fa,dum) 
         /*printf(" %lf ",hess[i][j]);*/        } 
       }    *cx=(*bx)+GOLD*(*bx-*ax); 
     }    *fc=(*func)(*cx); 
   }    while (*fb > *fc) { 
   printf("\n");      r=(*bx-*ax)*(*fb-*fc); 
   fprintf(ficlog,"\n");      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");      ulim=(*bx)+GLIMIT*(*cx-*bx); 
        if ((*bx-u)*(u-*cx) > 0.0) { 
   a=matrix(1,npar,1,npar);        fu=(*func)(u); 
   y=matrix(1,npar,1,npar);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   x=vector(1,npar);        fu=(*func)(u); 
   indx=ivector(1,npar);        if (fu < *fc) { 
   for (i=1;i<=npar;i++)          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];            SHFT(*fb,*fc,fu,(*func)(u)) 
   ludcmp(a,npar,indx,&pd);            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   for (j=1;j<=npar;j++) {        u=ulim; 
     for (i=1;i<=npar;i++) x[i]=0;        fu=(*func)(u); 
     x[j]=1;      } else { 
     lubksb(a,npar,indx,x);        u=(*cx)+GOLD*(*cx-*bx); 
     for (i=1;i<=npar;i++){        fu=(*func)(u); 
       matcov[i][j]=x[i];      } 
     }      SHFT(*ax,*bx,*cx,u) 
   }        SHFT(*fa,*fb,*fc,fu) 
         } 
   printf("\n#Hessian matrix#\n");  } 
   fprintf(ficlog,"\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {  /*************** linmin ************************/
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  int ncom; 
       fprintf(ficlog,"%.3e ",hess[i][j]);  double *pcom,*xicom;
     }  double (*nrfunc)(double []); 
     printf("\n");   
     fprintf(ficlog,"\n");  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   }  { 
     double brent(double ax, double bx, double cx, 
   /* Recompute Inverse */                 double (*f)(double), double tol, double *xmin); 
   for (i=1;i<=npar;i++)    double f1dim(double x); 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   ludcmp(a,npar,indx,&pd);                double *fc, double (*func)(double)); 
     int j; 
   /*  printf("\n#Hessian matrix recomputed#\n");    double xx,xmin,bx,ax; 
     double fx,fb,fa;
   for (j=1;j<=npar;j++) {   
     for (i=1;i<=npar;i++) x[i]=0;    ncom=n; 
     x[j]=1;    pcom=vector(1,n); 
     lubksb(a,npar,indx,x);    xicom=vector(1,n); 
     for (i=1;i<=npar;i++){    nrfunc=func; 
       y[i][j]=x[i];    for (j=1;j<=n;j++) { 
       printf("%.3e ",y[i][j]);      pcom[j]=p[j]; 
       fprintf(ficlog,"%.3e ",y[i][j]);      xicom[j]=xi[j]; 
     }    } 
     printf("\n");    ax=0.0; 
     fprintf(ficlog,"\n");    xx=1.0; 
   }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   */    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
   free_matrix(a,1,npar,1,npar);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   free_matrix(y,1,npar,1,npar);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   free_vector(x,1,npar);  #endif
   free_ivector(indx,1,npar);    for (j=1;j<=n;j++) { 
   free_matrix(hess,1,npar,1,npar);      xi[j] *= xmin; 
       p[j] += xi[j]; 
     } 
 }    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
 /*************** hessian matrix ****************/  } 
 double hessii( double x[], double delta, int theta, double delti[])  
 {  char *asc_diff_time(long time_sec, char ascdiff[])
   int i;  {
   int l=1, lmax=20;    long sec_left, days, hours, minutes;
   double k1,k2;    days = (time_sec) / (60*60*24);
   double p2[NPARMAX+1];    sec_left = (time_sec) % (60*60*24);
   double res;    hours = (sec_left) / (60*60) ;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    sec_left = (sec_left) %(60*60);
   double fx;    minutes = (sec_left) /60;
   int k=0,kmax=10;    sec_left = (sec_left) % (60);
   double l1;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   fx=func(x);  }
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){  /*************** powell ************************/
     l1=pow(10,l);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     delts=delt;              double (*func)(double [])) 
     for(k=1 ; k <kmax; k=k+1){  { 
       delt = delta*(l1*k);    void linmin(double p[], double xi[], int n, double *fret, 
       p2[theta]=x[theta] +delt;                double (*func)(double [])); 
       k1=func(p2)-fx;    int i,ibig,j; 
       p2[theta]=x[theta]-delt;    double del,t,*pt,*ptt,*xit;
       k2=func(p2)-fx;    double fp,fptt;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double *xits;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    int niterf, itmp;
        
 #ifdef DEBUG    pt=vector(1,n); 
       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);    ptt=vector(1,n); 
       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);    xit=vector(1,n); 
 #endif    xits=vector(1,n); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    *fret=(*func)(p); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    for (j=1;j<=n;j++) pt[j]=p[j]; 
         k=kmax;    for (*iter=1;;++(*iter)) { 
       }      fp=(*fret); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      ibig=0; 
         k=kmax; l=lmax*10.;      del=0.0; 
       }      last_time=curr_time;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      (void) gettimeofday(&curr_time,&tzp);
         delts=delt;      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);
       }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
     }  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
   }     for (i=1;i<=n;i++) {
   delti[theta]=delts;        printf(" %d %.12f",i, p[i]);
   return res;        fprintf(ficlog," %d %.12lf",i, p[i]);
          fprintf(ficrespow," %.12lf", p[i]);
 }      }
       printf("\n");
 double hessij( double x[], double delti[], int thetai,int thetaj)      fprintf(ficlog,"\n");
 {      fprintf(ficrespow,"\n");fflush(ficrespow);
   int i;      if(*iter <=3){
   int l=1, l1, lmax=20;        tm = *localtime(&curr_time.tv_sec);
   double k1,k2,k3,k4,res,fx;        strcpy(strcurr,asctime(&tm));
   double p2[NPARMAX+1];  /*       asctime_r(&tm,strcurr); */
   int k;        forecast_time=curr_time; 
         itmp = strlen(strcurr);
   fx=func(x);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   for (k=1; k<=2; k++) {          strcurr[itmp-1]='\0';
     for (i=1;i<=npar;i++) p2[i]=x[i];        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     p2[thetai]=x[thetai]+delti[thetai]/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[thetaj]=x[thetaj]+delti[thetaj]/k;        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);
            tmf = *localtime(&forecast_time.tv_sec);
     p2[thetai]=x[thetai]+delti[thetai]/k;  /*      asctime_r(&tmf,strfor); */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          strcpy(strfor,asctime(&tmf));
     k2=func(p2)-fx;          itmp = strlen(strfor);
            if(strfor[itmp-1]=='\n')
     p2[thetai]=x[thetai]-delti[thetai]/k;          strfor[itmp-1]='\0';
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          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);
     k3=func(p2)-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);
          }
     p2[thetai]=x[thetai]-delti[thetai]/k;      }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      for (i=1;i<=n;i++) { 
     k4=func(p2)-fx;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        fptt=(*fret); 
 #ifdef DEBUG  #ifdef DEBUG
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        printf("fret=%lf \n",*fret);
     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);        fprintf(ficlog,"fret=%lf \n",*fret);
 #endif  #endif
   }        printf("%d",i);fflush(stdout);
   return res;        fprintf(ficlog,"%d",i);fflush(ficlog);
 }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
 /************** Inverse of matrix **************/          del=fabs(fptt-(*fret)); 
 void ludcmp(double **a, int n, int *indx, double *d)          ibig=i; 
 {        } 
   int i,imax,j,k;  #ifdef DEBUG
   double big,dum,sum,temp;        printf("%d %.12e",i,(*fret));
   double *vv;        fprintf(ficlog,"%d %.12e",i,(*fret));
          for (j=1;j<=n;j++) {
   vv=vector(1,n);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   *d=1.0;          printf(" x(%d)=%.12e",j,xit[j]);
   for (i=1;i<=n;i++) {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     big=0.0;        }
     for (j=1;j<=n;j++)        for(j=1;j<=n;j++) {
       if ((temp=fabs(a[i][j])) > big) big=temp;          printf(" p=%.12e",p[j]);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          fprintf(ficlog," p=%.12e",p[j]);
     vv[i]=1.0/big;        }
   }        printf("\n");
   for (j=1;j<=n;j++) {        fprintf(ficlog,"\n");
     for (i=1;i<j;i++) {  #endif
       sum=a[i][j];      } 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       a[i][j]=sum;  #ifdef DEBUG
     }        int k[2],l;
     big=0.0;        k[0]=1;
     for (i=j;i<=n;i++) {        k[1]=-1;
       sum=a[i][j];        printf("Max: %.12e",(*func)(p));
       for (k=1;k<j;k++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
         sum -= a[i][k]*a[k][j];        for (j=1;j<=n;j++) {
       a[i][j]=sum;          printf(" %.12e",p[j]);
       if ( (dum=vv[i]*fabs(sum)) >= big) {          fprintf(ficlog," %.12e",p[j]);
         big=dum;        }
         imax=i;        printf("\n");
       }        fprintf(ficlog,"\n");
     }        for(l=0;l<=1;l++) {
     if (j != imax) {          for (j=1;j<=n;j++) {
       for (k=1;k<=n;k++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         dum=a[imax][k];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         a[imax][k]=a[j][k];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         a[j][k]=dum;          }
       }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       *d = -(*d);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       vv[imax]=vv[j];        }
     }  #endif
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {        free_vector(xit,1,n); 
       dum=1.0/(a[j][j]);        free_vector(xits,1,n); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
   }        return; 
   free_vector(vv,1,n);  /* Doesn't work */      } 
 ;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 }      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
 void lubksb(double **a, int n, int *indx, double b[])        xit[j]=p[j]-pt[j]; 
 {        pt[j]=p[j]; 
   int i,ii=0,ip,j;      } 
   double sum;      fptt=(*func)(ptt); 
        if (fptt < fp) { 
   for (i=1;i<=n;i++) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     ip=indx[i];        if (t < 0.0) { 
     sum=b[ip];          linmin(p,xit,n,fret,func); 
     b[ip]=b[i];          for (j=1;j<=n;j++) { 
     if (ii)            xi[j][ibig]=xi[j][n]; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            xi[j][n]=xit[j]; 
     else if (sum) ii=i;          }
     b[i]=sum;  #ifdef DEBUG
   }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (i=n;i>=1;i--) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     sum=b[i];          for(j=1;j<=n;j++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            printf(" %.12e",xit[j]);
     b[i]=sum/a[i][i];            fprintf(ficlog," %.12e",xit[j]);
   }          }
 }          printf("\n");
           fprintf(ficlog,"\n");
 /************ Frequencies ********************/  #endif
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        }
 {  /* Some frequencies */      } 
      } 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  } 
   int first;  
   double ***freq; /* Frequencies */  /**** Prevalence limit (stable or period prevalence)  ****************/
   double *pp;  
   double pos, k2, dateintsum=0,k2cpt=0;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   FILE *ficresp;  {
   char fileresp[FILENAMELENGTH];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         matrix by transitions matrix until convergence is reached */
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i, ii,j,k;
   strcpy(fileresp,"p");    double min, max, maxmin, maxmax,sumnew=0.;
   strcat(fileresp,fileres);    double **matprod2();
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double **out, cov[NCOVMAX+1], **pmij();
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double **newm;
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);    double agefin, delaymax=50 ; /* Max number of years to converge */
     exit(0);  
   }    for (ii=1;ii<=nlstate+ndeath;ii++)
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for (j=1;j<=nlstate+ndeath;j++){
   j1=0;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        }
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}     cov[1]=1.;
    
   first=1;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for(k1=1; k1<=j;k1++){      newm=savm;
     for(i1=1; i1<=ncodemax[k1];i1++){      /* Covariates have to be included here again */
       j1++;      cov[2]=agefin;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      
         scanf("%d", i);*/      for (k=1; k<=cptcovn;k++) {
       for (i=-1; i<=nlstate+ndeath; i++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (jk=-1; jk<=nlstate+ndeath; jk++)          /*        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]]);*/
           for(m=agemin; m <= agemax+3; m++)      }
             freq[i][jk][m]=0;      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
            for (k=1; k<=cptcovprod;k++)
       dateintsum=0;        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       k2cpt=0;      
       for (i=1; i<=imx; i++) {      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         bool=1;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         if  (cptcovn>0) {      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
           for (z1=1; z1<=cptcoveff; z1++)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      
               bool=0;      savm=oldm;
         }      oldm=newm;
         if (bool==1) {      maxmax=0.;
           for(m=firstpass; m<=lastpass; m++){      for(j=1;j<=nlstate;j++){
             k2=anint[m][i]+(mint[m][i]/12.);        min=1.;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        max=0.;
               if(agev[m][i]==0) agev[m][i]=agemax+1;        for(i=1; i<=nlstate; i++) {
               if(agev[m][i]==1) agev[m][i]=agemax+2;          sumnew=0;
               if (m<lastpass) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          prlim[i][j]= newm[i][j]/(1-sumnew);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          max=FMAX(max,prlim[i][j]);
               }          min=FMIN(min,prlim[i][j]);
                      }
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        maxmin=max-min;
                 dateintsum=dateintsum+k2;        maxmax=FMAX(maxmax,maxmin);
                 k2cpt++;      }
               }      if(maxmax < ftolpl){
             }        return prlim;
           }      }
         }    }
       }  }
          
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  /*************** transition probabilities ***************/ 
   
       if  (cptcovn>0) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         fprintf(ficresp, "\n#********** Variable ");  {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /* According to parameters values stored in x and the covariate's values stored in cov,
         fprintf(ficresp, "**********\n#");       computes the probability to be observed in state j being in state i by appying the
       }       model to the ncovmodel covariates (including constant and age).
       for(i=1; i<=nlstate;i++)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
       fprintf(ficresp, "\n");       ncth covariate in the global vector x is given by the formula:
             j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
       for(i=(int)agemin; i <= (int)agemax+3; i++){       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
         if(i==(int)agemax+3){       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
           fprintf(ficlog,"Total");       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
         }else{       Outputs ps[i][j] the probability to be observed in j being in j according to
           if(first==1){       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
             first=0;    */
             printf("See log file for details...\n");    double s1, lnpijopii;
           }    /*double t34;*/
           fprintf(ficlog,"Age %d", i);    int i,j,j1, nc, ii, jj;
         }  
         for(jk=1; jk <=nlstate ; jk++){      for(i=1; i<= nlstate; i++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for(j=1; j<i;j++){
             pp[jk] += freq[jk][m][i];          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         }            /*lnpijopii += param[i][j][nc]*cov[nc];*/
         for(jk=1; jk <=nlstate ; jk++){            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           for(m=-1, pos=0; m <=0 ; m++)  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
             pos += freq[jk][m][i];          }
           if(pp[jk]>=1.e-10){          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
             if(first==1){  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        }
             }        for(j=i+1; j<=nlstate+ndeath;j++){
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           }else{            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
             if(first==1)            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          }
           }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }        }
       }
         for(jk=1; jk <=nlstate ; jk++){      
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      for(i=1; i<= nlstate; i++){
             pp[jk] += freq[jk][m][i];        s1=0;
         }        for(j=1; j<i; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         for(jk=1,pos=0; jk <=nlstate ; jk++)          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           pos += pp[jk];        }
         for(jk=1; jk <=nlstate ; jk++){        for(j=i+1; j<=nlstate+ndeath; j++){
           if(pos>=1.e-5){          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
             if(first==1)          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        }
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
           }else{        ps[i][i]=1./(s1+1.);
             if(first==1)        /* Computing other pijs */
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        for(j=1; j<i; j++)
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          ps[i][j]= exp(ps[i][j])*ps[i][i];
           }        for(j=i+1; j<=nlstate+ndeath; j++)
           if( i <= (int) agemax){          ps[i][j]= exp(ps[i][j])*ps[i][i];
             if(pos>=1.e-5){        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      } /* end i */
               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]);*/      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
             }        for(jj=1; jj<= nlstate+ndeath; jj++){
             else          ps[ii][jj]=0;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          ps[ii][ii]=1;
           }        }
         }      }
              
         for(jk=-1; jk <=nlstate+ndeath; jk++)  
           for(m=-1; m <=nlstate+ndeath; m++)  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
             if(freq[jk][m][i] !=0 ) {  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
             if(first==1)  /*         printf("ddd %lf ",ps[ii][jj]); */
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  /*       } */
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);  /*       printf("\n "); */
             }  /*        } */
         if(i <= (int) agemax)  /*        printf("\n ");printf("%lf ",cov[2]); */
           fprintf(ficresp,"\n");         /*
         if(first==1)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           printf("Others in log...\n");        goto end;*/
         fprintf(ficlog,"\n");      return ps;
       }  }
     }  
   }  /**************** Product of 2 matrices ******************/
   dateintmean=dateintsum/k2cpt;  
    double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   fclose(ficresp);  {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   free_vector(pp,1,nlstate);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      /* in, b, out are matrice of pointers which should have been initialized 
   /* End of Freq */       before: only the contents of out is modified. The function returns
 }       a pointer to pointers identical to out */
     long i, j, k;
 /************ Prevalence ********************/    for(i=nrl; i<= nrh; i++)
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      for(k=ncolol; k<=ncoloh; k++)
 {  /* Some frequencies */        for(j=ncl,out[i][k]=0.; j<=nch; j++)
            out[i][k] +=in[i][j]*b[j][k];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */    return out;
   double *pp;  }
   double pos, k2;  
   
   pp=vector(1,nlstate);  /************* Higher Matrix Product ***************/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
    double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  {
   j1=0;    /* Computes the transition matrix starting at age 'age' over 
         'nhstepm*hstepm*stepm' months (i.e. until
   j=cptcoveff;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}       nhstepm*hstepm matrices. 
         Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   for(k1=1; k1<=j;k1++){       (typically every 2 years instead of every month which is too big 
     for(i1=1; i1<=ncodemax[k1];i1++){       for the memory).
       j1++;       Model is determined by parameters x and covariates have to be 
             included manually here. 
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)         */
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;    int i, j, d, h, k;
          double **out, cov[NCOVMAX+1];
       for (i=1; i<=imx; i++) {    double **newm;
         bool=1;  
         if  (cptcovn>0) {    /* Hstepm could be zero and should return the unit matrix */
           for (z1=1; z1<=cptcoveff; z1++)    for (i=1;i<=nlstate+ndeath;i++)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for (j=1;j<=nlstate+ndeath;j++){
               bool=0;        oldm[i][j]=(i==j ? 1.0 : 0.0);
         }        po[i][j][0]=(i==j ? 1.0 : 0.0);
         if (bool==1) {      }
           for(m=firstpass; m<=lastpass; m++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
             k2=anint[m][i]+(mint[m][i]/12.);    for(h=1; h <=nhstepm; h++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      for(d=1; d <=hstepm; d++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;        newm=savm;
               if(agev[m][i]==1) agev[m][i]=agemax+2;        /* Covariates have to be included here again */
               if (m<lastpass) {        cov[1]=1.;
                 if (calagedate>0)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        for (k=1; k<=cptcovn;k++) 
                 else          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for (k=1; k<=cptcovage;k++)
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          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]]];
           }  
         }  
       }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       for(i=(int)agemin; i <= (int)agemax+3; i++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         for(jk=1; jk <=nlstate ; jk++){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
             pp[jk] += freq[jk][m][i];        savm=oldm;
         }        oldm=newm;
         for(jk=1; jk <=nlstate ; jk++){      }
           for(m=-1, pos=0; m <=0 ; m++)      for(i=1; i<=nlstate+ndeath; i++)
             pos += freq[jk][m][i];        for(j=1;j<=nlstate+ndeath;j++) {
         }          po[i][j][h]=newm[i][j];
                  /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         for(jk=1; jk <=nlstate ; jk++){        }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      /*printf("h=%d ",h);*/
             pp[jk] += freq[jk][m][i];    } /* end h */
         }  /*     printf("\n H=%d \n",h); */
            return po;
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  }
          
         for(jk=1; jk <=nlstate ; jk++){      
           if( i <= (int) agemax){  /*************** log-likelihood *************/
             if(pos>=1.e-5){  double func( double *x)
               probs[i][jk][j1]= pp[jk]/pos;  {
             }    int i, ii, j, k, mi, d, kk;
           }    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         }/* end jk */    double **out;
       }/* end i */    double sw; /* Sum of weights */
     } /* end i1 */    double lli; /* Individual log likelihood */
   } /* end k1 */    int s1, s2;
     double bbh, survp;
      long ipmx;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /*extern weight */
   free_vector(pp,1,nlstate);    /* We are differentiating ll according to initial status */
      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 }  /* End of Freq */    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
 /************* Waves Concatenation ***************/    */
     cov[1]=1.;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {    for(k=1; k<=nlstate; k++) ll[k]=0.;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  
      Death is a valid wave (if date is known).    if(mle==1){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        /* Computes the values of the ncovmodel covariates of the model
      and mw[mi+1][i]. dh depends on stepm.           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
      */           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
            to be observed in j being in i according to the model.
   int i, mi, m;         */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      double sum=0., jmean=0.;*/        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   int first;           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
   int j, k=0,jk, ju, jl;           has been calculated etc */
   double sum=0.;        for(mi=1; mi<= wav[i]-1; mi++){
   first=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
   jmin=1e+5;            for (j=1;j<=nlstate+ndeath;j++){
   jmax=-1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   jmean=0.;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<=imx; i++){            }
     mi=0;          for(d=0; d<dh[mi][i]; d++){
     m=firstpass;            newm=savm;
     while(s[m][i] <= nlstate){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if(s[m][i]>=1)            for (kk=1; kk<=cptcovage;kk++) {
         mw[++mi][i]=m;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
       if(m >=lastpass)            }
         break;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         m++;            savm=oldm;
     }/* end while */            oldm=newm;
     if (s[m][i] > nlstate){          } /* end mult */
       mi++;     /* Death is another wave */        
       /* if(mi==0)  never been interviewed correctly before death */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
          /* Only death is a correct wave */          /* But now since version 0.9 we anticipate for bias at large stepm.
       mw[mi][i]=m;           * 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
     wav[i]=mi;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     if(mi==0){           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       if(first==0){           * probability in order to take into account the bias as a fraction of the way
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         first=1;           * -stepm/2 to stepm/2 .
       }           * For stepm=1 the results are the same as for previous versions of Imach.
       if(first==1){           * For stepm > 1 the results are less biased than in previous versions. 
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);           */
       }          s1=s[mw[mi][i]][i];
     } /* end mi==0 */          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias bh is positive if real duration
   for(i=1; i<=imx; i++){           * is higher than the multiple of stepm and negative otherwise.
     for(mi=1; mi<wav[i];mi++){           */
       if (stepm <=0)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         dh[mi][i]=1;          if( s2 > nlstate){ 
       else{            /* i.e. if s2 is a death state and if the date of death is known 
         if (s[mw[mi+1][i]][i] > nlstate) {               then the contribution to the likelihood is the probability to 
           if (agedc[i] < 2*AGESUP) {               die between last step unit time and current  step unit time, 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);               which is also equal to probability to die before dh 
           if(j==0) j=1;  /* Survives at least one month after exam */               minus probability to die before dh-stepm . 
           k=k+1;               In version up to 0.92 likelihood was computed
           if (j >= jmax) jmax=j;          as if date of death was unknown. Death was treated as any other
           if (j <= jmin) jmin=j;          health state: the date of the interview describes the actual state
           sum=sum+j;          and not the date of a change in health state. The former idea was
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          to consider that at each interview the state was recorded
           }          (healthy, disable or death) and IMaCh was corrected; but when we
         }          introduced the exact date of death then we should have modified
         else{          the contribution of an exact death to the likelihood. This new
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          contribution is smaller and very dependent of the step unit
           k=k+1;          stepm. It is no more the probability to die between last interview
           if (j >= jmax) jmax=j;          and month of death but the probability to survive from last
           else if (j <= jmin)jmin=j;          interview up to one month before death multiplied by the
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          probability to die within a month. Thanks to Chris
           sum=sum+j;          Jackson for correcting this bug.  Former versions increased
         }          mortality artificially. The bad side is that we add another loop
         jk= j/stepm;          which slows down the processing. The difference can be up to 10%
         jl= j -jk*stepm;          lower mortality.
         ju= j -(jk+1)*stepm;            */
         if(jl <= -ju)            lli=log(out[s1][s2] - savm[s1][s2]);
           dh[mi][i]=jk;  
         else  
           dh[mi][i]=jk+1;          } else if  (s2==-2) {
         if(dh[mi][i]==0)            for (j=1,survp=0. ; j<=nlstate; j++) 
           dh[mi][i]=1; /* At least one step */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            /*survp += out[s1][j]; */
     }            lli= log(survp);
   }          }
   jmean=sum/k;          
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          else if  (s2==-4) { 
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            for (j=3,survp=0. ; j<=nlstate; j++)  
  }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
 /*********** Tricode ****************************/          } 
 void tricode(int *Tvar, int **nbcode, int imx)  
 {          else if  (s2==-5) { 
   int Ndum[20],ij=1, k, j, i;            for (j=1,survp=0. ; j<=2; j++)  
   int cptcode=0;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   cptcoveff=0;            lli= log(survp); 
            } 
   for (k=0; k<19; k++) Ndum[k]=0;          
   for (k=1; k<=7; k++) ncodemax[k]=0;          else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for (j=1; j<=(cptcovn+2*cptcovprod); 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 */
     for (i=1; i<=imx; i++) {          } 
       ij=(int)(covar[Tvar[j]][i]);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       Ndum[ij]++;          /*if(lli ==000.0)*/
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          /*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); */
       if (ij > cptcode) cptcode=ij;          ipmx +=1;
     }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=0; i<=cptcode; i++) {        } /* end of wave */
       if(Ndum[i]!=0) ncodemax[j]++;      } /* end of individual */
     }    }  else if(mle==2){
     ij=1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1; i<=ncodemax[j]; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (k=0; k<=19; k++) {            for (j=1;j<=nlstate+ndeath;j++){
         if (Ndum[k] != 0) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           nbcode[Tvar[j]][ij]=k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                      }
           ij++;          for(d=0; d<=dh[mi][i]; d++){
         }            newm=savm;
         if (ij > ncodemax[j]) break;            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 (k=0; k<19; k++) Ndum[k]=0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
  for (i=1; i<=ncovmodel-2; i++) {            oldm=newm;
    ij=Tvar[i];          } /* end mult */
    Ndum[ij]++;        
  }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
  ij=1;          bbh=(double)bh[mi][i]/(double)stepm; 
  for (i=1; i<=10; i++) {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
    if((Ndum[i]!=0) && (i<=ncovcol)){          ipmx +=1;
      Tvaraff[ij]=i;          sw += weight[i];
      ij++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    }        } /* end of wave */
  }      } /* end of individual */
      }  else if(mle==3){  /* exponential inter-extrapolation */
  cptcoveff=ij-1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 /*********** Health Expectancies ****************/          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 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 )              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {            }
   /* Health expectancies */          for(d=0; d<dh[mi][i]; d++){
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;            newm=savm;
   double age, agelim, hf;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***p3mat,***varhe;            for (kk=1; kk<=cptcovage;kk++) {
   double **dnewm,**doldm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *xp;            }
   double **gp, **gm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***gradg, ***trgradg;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int theta;            savm=oldm;
             oldm=newm;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          } /* end mult */
   xp=vector(1,npar);        
   dnewm=matrix(1,nlstate*2,1,npar);          s1=s[mw[mi][i]][i];
   doldm=matrix(1,nlstate*2,1,nlstate*2);          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficreseij,"# Health expectancies\n");          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   fprintf(ficreseij,"# Age");          ipmx +=1;
   for(i=1; i<=nlstate;i++)          sw += weight[i];
     for(j=1; j<=nlstate;j++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        } /* end of wave */
   fprintf(ficreseij,"\n");      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
   if(estepm < stepm){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     printf ("Problem %d lower than %d\n",estepm, stepm);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   else  hstepm=estepm;            for (ii=1;ii<=nlstate+ndeath;ii++)
   /* We compute the life expectancy from trapezoids spaced every estepm months            for (j=1;j<=nlstate+ndeath;j++){
    * This is mainly to measure the difference between two models: for example              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    * if stepm=24 months pijx are given only every 2 years and by summing them              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    * we are calculating an estimate of the Life Expectancy assuming a linear            }
    * progression inbetween and thus overestimating or underestimating according          for(d=0; d<dh[mi][i]; d++){
    * to the curvature of the survival function. If, for the same date, we            newm=savm;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
    * to compare the new estimate of Life expectancy with the same linear            for (kk=1; kk<=cptcovage;kk++) {
    * hypothesis. A more precise result, taking into account a more precise              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
    * curvature will be obtained if estepm is as small as stepm. */            }
           
   /* For example we decided to compute the life expectancy with the smallest unit */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      nhstepm is the number of hstepm from age to agelim            savm=oldm;
      nstepm is the number of stepm from age to agelin.            oldm=newm;
      Look at hpijx to understand the reason of that which relies in memory size          } /* end mult */
      and note for a fixed period like estepm months */        
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          s1=s[mw[mi][i]][i];
      survival function given by stepm (the optimization length). Unfortunately it          s2=s[mw[mi+1][i]][i];
      means that if the survival funtion is printed only each two years of age and if          if( s2 > nlstate){ 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            lli=log(out[s1][s2] - savm[s1][s2]);
      results. So we changed our mind and took the option of the best precision.          }else{
   */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          }
           ipmx +=1;
   agelim=AGESUP;          sw += weight[i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     /* nhstepm age range expressed in number of stepm */  /*      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]); */
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        } /* end of wave */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      } /* end of individual */
     /* if (stepm >= YEARM) hstepm=1;*/    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        for(mi=1; mi<= wav[i]-1; mi++){
     gp=matrix(0,nhstepm,1,nlstate*2);          for (ii=1;ii<=nlstate+ndeath;ii++)
     gm=matrix(0,nhstepm,1,nlstate*2);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              savm[ii][j]=(ii==j ? 1.0 : 0.0);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            for(d=0; d<dh[mi][i]; d++){
              newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     /* Computing Variances of health expectancies */            }
           
      for(theta=1; theta <=npar; theta++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1; i<=npar; i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            savm=oldm;
       }            oldm=newm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            } /* end mult */
          
       cptj=0;          s1=s[mw[mi][i]][i];
       for(j=1; j<= nlstate; j++){          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 */
           cptj=cptj+1;          ipmx +=1;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          sw += weight[i];
             gp[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]);*/
         }        } /* end of wave */
       }      } /* end of individual */
          } /* End of if */
          for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for(i=1; i<=npar; i++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      return -l;
        }
       cptj=0;  
       for(j=1; j<= nlstate; j++){  /*************** log-likelihood *************/
         for(i=1;i<=nlstate;i++){  double funcone( double *x)
           cptj=cptj+1;  {
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    /* Same as likeli but slower because of a lot of printf and if */
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    int i, ii, j, k, mi, d, kk;
           }    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         }    double **out;
       }    double lli; /* Individual log likelihood */
       for(j=1; j<= nlstate*2; j++)    double llt;
         for(h=0; h<=nhstepm-1; h++){    int s1, s2;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double bbh, survp;
         }    /*extern weight */
      }    /* We are differentiating ll according to initial status */
        /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 /* End theta */    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    */
     cov[1]=1.;
      for(h=0; h<=nhstepm-1; h++)  
       for(j=1; j<=nlstate*2;j++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
            for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
      for(i=1;i<=nlstate*2;i++)        for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1;j<=nlstate*2;j++)          for (j=1;j<=nlstate+ndeath;j++){
         varhe[i][j][(int)age] =0.;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
      printf("%d|",(int)age);fflush(stdout);          }
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);        for(d=0; d<dh[mi][i]; d++){
      for(h=0;h<=nhstepm-1;h++){          newm=savm;
       for(k=0;k<=nhstepm-1;k++){          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);          for (kk=1; kk<=cptcovage;kk++) {
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(i=1;i<=nlstate*2;i++)          }
           for(j=1;j<=nlstate*2;j++)          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }          savm=oldm;
     }          oldm=newm;
     /* Computing expectancies */        } /* end mult */
     for(i=1; i<=nlstate;i++)        
       for(j=1; j<=nlstate;j++)        s1=s[mw[mi][i]][i];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        s2=s[mw[mi+1][i]][i];
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        bbh=(double)bh[mi][i]/(double)stepm; 
                  /* bias is positive if real duration
 /* 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]);*/         * is higher than the multiple of stepm and negative otherwise.
          */
         }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
     fprintf(ficreseij,"%3.0f",age );        } else if  (s2==-2) {
     cptj=0;          for (j=1,survp=0. ; j<=nlstate; j++) 
     for(i=1; i<=nlstate;i++)            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(j=1; j<=nlstate;j++){          lli= log(survp);
         cptj++;        }else if (mle==1){
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }        } else if(mle==2){
     fprintf(ficreseij,"\n");          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 */
     free_matrix(gm,0,nhstepm,1,nlstate*2);          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 */
     free_matrix(gp,0,nhstepm,1,nlstate*2);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          lli=log(out[s1][s2]); /* Original formula */
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        } else{  /* mle=0 back to 1 */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   }          /*lli=log(out[s1][s2]); */ /* Original formula */
   printf("\n");        } /* End of if */
   fprintf(ficlog,"\n");        ipmx +=1;
         sw += weight[i];
   free_vector(xp,1,npar);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_matrix(dnewm,1,nlstate*2,1,npar);        /*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]); */
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        if(globpr){
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
 }   %11.6f %11.6f %11.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
 /************ Variance ******************/                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 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)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
 {            llt +=ll[k]*gipmx/gsw;
   /* Variance of health expectancies */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          }
   /* double **newm;*/          fprintf(ficresilk," %10.6f\n", -llt);
   double **dnewm,**doldm;        }
   double **dnewmp,**doldmp;      } /* end of wave */
   int i, j, nhstepm, hstepm, h, nstepm ;    } /* end of individual */
   int k, cptcode;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double *xp;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double **gp, **gm;  /* for var eij */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double ***gradg, ***trgradg; /*for var eij */    if(globpr==0){ /* First time we count the contributions and weights */
   double **gradgp, **trgradgp; /* for var p point j */      gipmx=ipmx;
   double *gpp, *gmp; /* for var p point j */      gsw=sw;
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */    }
   double ***p3mat;    return -l;
   double age,agelim, hf;  }
   int theta;  
   char digit[4];  
   char digitp[16];  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   char fileresprobmorprev[FILENAMELENGTH];  {
     /* This routine should help understanding what is done with 
   if(popbased==1)       the selection of individuals/waves and
     strcpy(digitp,"-populbased-");       to check the exact contribution to the likelihood.
   else       Plotting could be done.
     strcpy(digitp,"-stablbased-");     */
     int k;
   strcpy(fileresprobmorprev,"prmorprev");  
   sprintf(digit,"%-d",ij);    if(*globpri !=0){ /* Just counts and sums, no printings */
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/      strcpy(fileresilk,"ilk"); 
   strcat(fileresprobmorprev,digit); /* Tvar to be done */      strcat(fileresilk,fileres);
   strcat(fileresprobmorprev,digitp); /* Popbased or not */      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   strcat(fileresprobmorprev,fileres);        printf("Problem with resultfile: %s\n", fileresilk);
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     printf("Problem with resultfile: %s\n", fileresprobmorprev);      }
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);      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 ");
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      for(k=1; k<=nlstate; k++) 
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    }
     fprintf(ficresprobmorprev," p.%-d SE",j);  
     for(i=1; i<=nlstate;i++)    *fretone=(*funcone)(p);
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);    if(*globpri !=0){
   }        fclose(ficresilk);
   fprintf(ficresprobmorprev,"\n");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      fflush(fichtm); 
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    } 
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    return;
     exit(0);  }
   }  
   else{  
     fprintf(ficgp,"\n# Routine varevsij");  /*********** Maximum Likelihood Estimation ***************/
   }  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     printf("Problem with html file: %s\n", optionfilehtm);  {
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    int i,j, iter;
     exit(0);    double **xi;
   }    double fret;
   else{    double fretone; /* Only one call to likelihood */
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");    /*  char filerespow[FILENAMELENGTH];*/
   }    xi=matrix(1,npar,1,npar);
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
   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");        xi[i][j]=(i==j ? 1.0 : 0.0);
   fprintf(ficresvij,"# Age");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   for(i=1; i<=nlstate;i++)    strcpy(filerespow,"pow"); 
     for(j=1; j<=nlstate;j++)    strcat(filerespow,fileres);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   fprintf(ficresvij,"\n");      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   xp=vector(1,npar);    }
   dnewm=matrix(1,nlstate,1,npar);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   doldm=matrix(1,nlstate,1,nlstate);    for (i=1;i<=nlstate;i++)
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);      for(j=1;j<=nlstate+ndeath;j++)
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);  
   gpp=vector(nlstate+1,nlstate+ndeath);    powell(p,xi,npar,ftol,&iter,&fret,func);
   gmp=vector(nlstate+1,nlstate+ndeath);  
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    free_matrix(xi,1,npar,1,npar);
      fclose(ficrespow);
   if(estepm < stepm){    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     printf ("Problem %d lower than %d\n",estepm, stepm);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   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.  
      nhstepm is the number of hstepm from age to agelim  /**** Computes Hessian and covariance matrix ***/
      nstepm is the number of stepm from age to agelin.  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
      Look at hpijx to understand the reason of that which relies in memory size  {
      and note for a fixed period like k years */    double  **a,**y,*x,pd;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    double **hess;
      survival function given by stepm (the optimization length). Unfortunately it    int i, j,jk;
      means that if the survival funtion is printed only each two years of age and if    int *indx;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   */    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    void lubksb(double **a, int npar, int *indx, double b[]) ;
   agelim = AGESUP;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double gompertz(double p[]);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    hess=matrix(1,npar,1,npar);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("\nCalculation of the hessian matrix. Wait...\n");
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     gp=matrix(0,nhstepm,1,nlstate);    for (i=1;i<=npar;i++){
     gm=matrix(0,nhstepm,1,nlstate);      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
      
     for(theta=1; theta <=npar; theta++){       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       for(i=1; i<=npar; i++){ /* Computes gradient */      
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      /*  printf(" %f ",p[i]);
       }          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    
     for (i=1;i<=npar;i++) {
       if (popbased==1) {      for (j=1;j<=npar;j++)  {
         for(i=1; i<=nlstate;i++)        if (j>i) { 
           prlim[i][i]=probs[(int)age][i][ij];          printf(".%d%d",i,j);fflush(stdout);
       }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
            hess[i][j]=hessij(p,delti,i,j,func,npar);
       for(j=1; j<= nlstate; j++){          
         for(h=0; h<=nhstepm; h++){          hess[j][i]=hess[i][j];    
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          /*printf(" %lf ",hess[i][j]);*/
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        }
         }      }
       }    }
       /* This for computing forces of mortality (h=1)as a weighted average */    printf("\n");
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    fprintf(ficlog,"\n");
         for(i=1; i<= nlstate; i++)  
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       }        fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       /* end force of mortality */    
     a=matrix(1,npar,1,npar);
       for(i=1; i<=npar; i++) /* Computes gradient */    y=matrix(1,npar,1,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    x=vector(1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      indx=ivector(1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       if (popbased==1) {    ludcmp(a,npar,indx,&pd);
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    for (j=1;j<=npar;j++) {
       }      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
       for(j=1; j<= nlstate; j++){      lubksb(a,npar,indx,x);
         for(h=0; h<=nhstepm; h++){      for (i=1;i<=npar;i++){ 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        matcov[i][j]=x[i];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      }
         }    }
       }  
       /* This for computing force of mortality (h=1)as a weighted average */    printf("\n#Hessian matrix#\n");
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    fprintf(ficlog,"\n#Hessian matrix#\n");
         for(i=1; i<= nlstate; i++)    for (i=1;i<=npar;i++) { 
           gmp[j] += prlim[i][i]*p3mat[i][j][1];      for (j=1;j<=npar;j++) { 
       }            printf("%.3e ",hess[i][j]);
       /* end force of mortality */        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
       for(j=1; j<= nlstate; j++) /* vareij */      printf("\n");
         for(h=0; h<=nhstepm; h++){      fprintf(ficlog,"\n");
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    }
         }  
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */    /* Recompute Inverse */
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];    for (i=1;i<=npar;i++)
       }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
     } /* End theta */  
     /*  printf("\n#Hessian matrix recomputed#\n");
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */  
     for (j=1;j<=npar;j++) {
     for(h=0; h<=nhstepm; h++) /* veij */      for (i=1;i<=npar;i++) x[i]=0;
       for(j=1; j<=nlstate;j++)      x[j]=1;
         for(theta=1; theta <=npar; theta++)      lubksb(a,npar,indx,x);
           trgradg[h][j][theta]=gradg[h][theta][j];      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */        printf("%.3e ",y[i][j]);
       for(theta=1; theta <=npar; theta++)        fprintf(ficlog,"%.3e ",y[i][j]);
         trgradgp[j][theta]=gradgp[theta][j];      }
       printf("\n");
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      fprintf(ficlog,"\n");
     for(i=1;i<=nlstate;i++)    }
       for(j=1;j<=nlstate;j++)    */
         vareij[i][j][(int)age] =0.;  
     free_matrix(a,1,npar,1,npar);
     for(h=0;h<=nhstepm;h++){    free_matrix(y,1,npar,1,npar);
       for(k=0;k<=nhstepm;k++){    free_vector(x,1,npar);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    free_ivector(indx,1,npar);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    free_matrix(hess,1,npar,1,npar);
         for(i=1;i<=nlstate;i++)  
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  }
       }  
     }  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     /* pptj */  {
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);    int i;
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);    int l=1, lmax=20;
     for(j=nlstate+1;j<=nlstate+ndeath;j++)    double k1,k2;
       for(i=nlstate+1;i<=nlstate+ndeath;i++)    double p2[MAXPARM+1]; /* identical to x */
         varppt[j][i]=doldmp[j][i];    double res;
     /* end ppptj */    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);      double fx;
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    int k=0,kmax=10;
      double l1;
     if (popbased==1) {  
       for(i=1; i<=nlstate;i++)    fx=func(x);
         prlim[i][i]=probs[(int)age][i][ij];    for (i=1;i<=npar;i++) p2[i]=x[i];
     }    for(l=0 ; l <=lmax; l++){
          l1=pow(10,l);
     /* This for computing force of mortality (h=1)as a weighted average */      delts=delt;
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){      for(k=1 ; k <kmax; k=k+1){
       for(i=1; i<= nlstate; i++)        delt = delta*(l1*k);
         gmp[j] += prlim[i][i]*p3mat[i][j][1];        p2[theta]=x[theta] +delt;
     }            k1=func(p2)-fx;
     /* end force of mortality */        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));        
       for(i=1; i<=nlstate;i++){  #ifdef DEBUGHESS
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     }  #endif
     fprintf(ficresprobmorprev,"\n");        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     fprintf(ficresvij,"%.0f ",age );          k=kmax;
     for(i=1; i<=nlstate;i++)        }
       for(j=1; j<=nlstate;j++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          k=kmax; l=lmax*10.;
       }        }
     fprintf(ficresvij,"\n");        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     free_matrix(gp,0,nhstepm,1,nlstate);          delts=delt;
     free_matrix(gm,0,nhstepm,1,nlstate);        }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    delti[theta]=delts;
   } /* End age */    return res; 
   free_vector(gpp,nlstate+1,nlstate+ndeath);    
   free_vector(gmp,nlstate+1,nlstate+ndeath);  }
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);  
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");  {
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    int i;
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");    int l=1, l1, lmax=20;
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);    double k1,k2,k3,k4,res,fx;
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);    double p2[MAXPARM+1];
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);    int k;
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);  
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);    fx=func(x);
   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);    for (k=1; k<=2; k++) {
 */      for (i=1;i<=npar;i++) p2[i]=x[i];
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   free_vector(xp,1,npar);      k1=func(p2)-fx;
   free_matrix(doldm,1,nlstate,1,nlstate);    
   free_matrix(dnewm,1,nlstate,1,npar);      p2[thetai]=x[thetai]+delti[thetai]/k;
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);      k2=func(p2)-fx;
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    
   fclose(ficresprobmorprev);      p2[thetai]=x[thetai]-delti[thetai]/k;
   fclose(ficgp);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   fclose(fichtm);      k3=func(p2)-fx;
     
 }      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 /************ Variance of prevlim ******************/      k4=func(p2)-fx;
 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)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 {  #ifdef DEBUG
   /* Variance of prevalence limit */      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   double **newm;  #endif
   double **dnewm,**doldm;    }
   int i, j, nhstepm, hstepm;    return res;
   int k, cptcode;  }
   double *xp;  
   double *gp, *gm;  /************** Inverse of matrix **************/
   double **gradg, **trgradg;  void ludcmp(double **a, int n, int *indx, double *d) 
   double age,agelim;  { 
   int theta;    int i,imax,j,k; 
        double big,dum,sum,temp; 
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    double *vv; 
   fprintf(ficresvpl,"# Age");   
   for(i=1; i<=nlstate;i++)    vv=vector(1,n); 
       fprintf(ficresvpl," %1d-%1d",i,i);    *d=1.0; 
   fprintf(ficresvpl,"\n");    for (i=1;i<=n;i++) { 
       big=0.0; 
   xp=vector(1,npar);      for (j=1;j<=n;j++) 
   dnewm=matrix(1,nlstate,1,npar);        if ((temp=fabs(a[i][j])) > big) big=temp; 
   doldm=matrix(1,nlstate,1,nlstate);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
        vv[i]=1.0/big; 
   hstepm=1*YEARM; /* Every year of age */    } 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for (j=1;j<=n;j++) { 
   agelim = AGESUP;      for (i=1;i<j;i++) { 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        sum=a[i][j]; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     if (stepm >= YEARM) hstepm=1;        a[i][j]=sum; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      } 
     gradg=matrix(1,npar,1,nlstate);      big=0.0; 
     gp=vector(1,nlstate);      for (i=j;i<=n;i++) { 
     gm=vector(1,nlstate);        sum=a[i][j]; 
         for (k=1;k<j;k++) 
     for(theta=1; theta <=npar; theta++){          sum -= a[i][k]*a[k][j]; 
       for(i=1; i<=npar; i++){ /* Computes gradient */        a[i][j]=sum; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       }          big=dum; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          imax=i; 
       for(i=1;i<=nlstate;i++)        } 
         gp[i] = prlim[i][i];      } 
          if (j != imax) { 
       for(i=1; i<=npar; i++) /* Computes gradient */        for (k=1;k<=n;k++) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          dum=a[imax][k]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          a[imax][k]=a[j][k]; 
       for(i=1;i<=nlstate;i++)          a[j][k]=dum; 
         gm[i] = prlim[i][i];        } 
         *d = -(*d); 
       for(i=1;i<=nlstate;i++)        vv[imax]=vv[j]; 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      } 
     } /* End theta */      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
     trgradg =matrix(1,nlstate,1,npar);      if (j != n) { 
         dum=1.0/(a[j][j]); 
     for(j=1; j<=nlstate;j++)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       for(theta=1; theta <=npar; theta++)      } 
         trgradg[j][theta]=gradg[theta][j];    } 
     free_vector(vv,1,n);  /* Doesn't work */
     for(i=1;i<=nlstate;i++)  ;
       varpl[i][(int)age] =0.;  } 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  void lubksb(double **a, int n, int *indx, double b[]) 
     for(i=1;i<=nlstate;i++)  { 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    int i,ii=0,ip,j; 
     double sum; 
     fprintf(ficresvpl,"%.0f ",age );   
     for(i=1; i<=nlstate;i++)    for (i=1;i<=n;i++) { 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      ip=indx[i]; 
     fprintf(ficresvpl,"\n");      sum=b[ip]; 
     free_vector(gp,1,nlstate);      b[ip]=b[i]; 
     free_vector(gm,1,nlstate);      if (ii) 
     free_matrix(gradg,1,npar,1,nlstate);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     free_matrix(trgradg,1,nlstate,1,npar);      else if (sum) ii=i; 
   } /* End age */      b[i]=sum; 
     } 
   free_vector(xp,1,npar);    for (i=n;i>=1;i--) { 
   free_matrix(doldm,1,nlstate,1,npar);      sum=b[i]; 
   free_matrix(dnewm,1,nlstate,1,nlstate);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
 }    } 
   } 
 /************ Variance of one-step probabilities  ******************/  
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)  void pstamp(FILE *fichier)
 {  {
   int i, j=0,  i1, k1, l1, t, tj;    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   int k2, l2, j1,  z1;  }
   int k=0,l, cptcode;  
   int first=1, first1;  /************ Frequencies ********************/
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;  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[])
   double **dnewm,**doldm;  {  /* Some frequencies */
   double *xp;    
   double *gp, *gm;    int i, m, jk, k1,i1, j1, bool, z1,j;
   double **gradg, **trgradg;    int first;
   double **mu;    double ***freq; /* Frequencies */
   double age,agelim, cov[NCOVMAX];    double *pp, **prop;
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   int theta;    char fileresp[FILENAMELENGTH];
   char fileresprob[FILENAMELENGTH];    
   char fileresprobcov[FILENAMELENGTH];    pp=vector(1,nlstate);
   char fileresprobcor[FILENAMELENGTH];    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
   double ***varpij;    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
   strcpy(fileresprob,"prob");      printf("Problem with prevalence resultfile: %s\n", fileresp);
   strcat(fileresprob,fileres);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      exit(0);
     printf("Problem with resultfile: %s\n", fileresprob);    }
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   }    j1=0;
   strcpy(fileresprobcov,"probcov");    
   strcat(fileresprobcov,fileres);    j=cptcoveff;
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     printf("Problem with resultfile: %s\n", fileresprobcov);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    first=1;
   }  
   strcpy(fileresprobcor,"probcor");    for(k1=1; k1<=j;k1++){
   strcat(fileresprobcor,fileres);      for(i1=1; i1<=ncodemax[k1];i1++){
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {        j1++;
     printf("Problem with resultfile: %s\n", fileresprobcor);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);          scanf("%d", i);*/
   }        for (i=-5; i<=nlstate+ndeath; i++)  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);            for(m=iagemin; m <= iagemax+3; m++)
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);              freq[i][jk][m]=0;
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);      for (i=1; i<=nlstate; i++)  
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);        for(m=iagemin; m <= iagemax+3; m++)
            prop[i][m]=0;
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");        
   fprintf(ficresprob,"# Age");        dateintsum=0;
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");        k2cpt=0;
   fprintf(ficresprobcov,"# Age");        for (i=1; i<=imx; i++) {
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");          bool=1;
   fprintf(ficresprobcov,"# Age");          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   for(i=1; i<=nlstate;i++)                bool=0;
     for(j=1; j<=(nlstate+ndeath);j++){          }
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);          if (bool==1){
       fprintf(ficresprobcov," p%1d-%1d ",i,j);            for(m=firstpass; m<=lastpass; m++){
       fprintf(ficresprobcor," p%1d-%1d ",i,j);              k2=anint[m][i]+(mint[m][i]/12.);
     }                /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   fprintf(ficresprob,"\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fprintf(ficresprobcov,"\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   fprintf(ficresprobcor,"\n");                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   xp=vector(1,npar);                if (m<lastpass) {
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);                }
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);                
   first=1;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {                  dateintsum=dateintsum+k2;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);                  k2cpt++;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);                }
     exit(0);                /*}*/
   }            }
   else{          }
     fprintf(ficgp,"\n# Routine varprob");        }
   }         
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     printf("Problem with html file: %s\n", optionfilehtm);        pstamp(ficresp);
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);        if  (cptcovn>0) {
     exit(0);          fprintf(ficresp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   else{          fprintf(ficresp, "**********\n#");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");        }
     fprintf(fichtm,"\n");        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");        fprintf(ficresp, "\n");
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");        
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
   }            fprintf(ficlog,"Total");
           }else{
              if(first==1){
   cov[1]=1;              first=0;
   tj=cptcoveff;              printf("See log file for details...\n");
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}            }
   j1=0;            fprintf(ficlog,"Age %d", i);
   for(t=1; t<=tj;t++){          }
     for(i1=1; i1<=ncodemax[t];i1++){          for(jk=1; jk <=nlstate ; jk++){
       j1++;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                    pp[jk] += freq[jk][m][i]; 
       if  (cptcovn>0) {          }
         fprintf(ficresprob, "\n#********** Variable ");          for(jk=1; jk <=nlstate ; jk++){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            for(m=-1, pos=0; m <=0 ; m++)
         fprintf(ficresprob, "**********\n#");              pos += freq[jk][m][i];
         fprintf(ficresprobcov, "\n#********** Variable ");            if(pp[jk]>=1.e-10){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              if(first==1){
         fprintf(ficresprobcov, "**********\n#");                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                      }
         fprintf(ficgp, "\n#********** Variable ");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            }else{
         fprintf(ficgp, "**********\n#");              if(first==1)
                        printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                      fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");            }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          }
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");  
                  for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficresprobcor, "\n#********** Variable ");                for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              pp[jk] += freq[jk][m][i];
         fprintf(ficgp, "**********\n#");              }       
       }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                  pos += pp[jk];
       for (age=bage; age<=fage; age ++){            posprop += prop[jk][i];
         cov[2]=age;          }
         for (k=1; k<=cptcovn;k++) {          for(jk=1; jk <=nlstate ; jk++){
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];            if(pos>=1.e-5){
         }              if(first==1)
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         for (k=1; k<=cptcovprod;k++)              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            }else{
                      if(first==1)
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         gp=vector(1,(nlstate)*(nlstate+ndeath));            }
         gm=vector(1,(nlstate)*(nlstate+ndeath));            if( i <= iagemax){
                  if(pos>=1.e-5){
         for(theta=1; theta <=npar; theta++){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           for(i=1; i<=npar; i++)                /*probs[i][jk][j1]= pp[jk]/pos;*/
             xp[i] = x[i] + (i==theta ?delti[theta]:0);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                        }
           pmij(pmmij,cov,ncovmodel,xp,nlstate);              else
                          fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
           k=0;            }
           for(i=1; i<= (nlstate); i++){          }
             for(j=1; j<=(nlstate+ndeath);j++){          
               k=k+1;          for(jk=-1; jk <=nlstate+ndeath; jk++)
               gp[k]=pmmij[i][j];            for(m=-1; m <=nlstate+ndeath; m++)
             }              if(freq[jk][m][i] !=0 ) {
           }              if(first==1)
                          printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           for(i=1; i<=npar; i++)                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
             xp[i] = x[i] - (i==theta ?delti[theta]:0);              }
              if(i <= iagemax)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            fprintf(ficresp,"\n");
           k=0;          if(first==1)
           for(i=1; i<=(nlstate); i++){            printf("Others in log...\n");
             for(j=1; j<=(nlstate+ndeath);j++){          fprintf(ficlog,"\n");
               k=k+1;        }
               gm[k]=pmmij[i][j];      }
             }    }
           }    dateintmean=dateintsum/k2cpt; 
         
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    fclose(ficresp);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         }    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)    /* End of Freq */
           for(theta=1; theta <=npar; theta++)  }
             trgradg[j][theta]=gradg[theta][j];  
          /************ Prevalence ********************/
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);  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)
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  {  
            /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         pmij(pmmij,cov,ncovmodel,x,nlstate);       in each health status at the date of interview (if between dateprev1 and dateprev2).
               We still use firstpass and lastpass as another selection.
         k=0;    */
         for(i=1; i<=(nlstate); i++){   
           for(j=1; j<=(nlstate+ndeath);j++){    int i, m, jk, k1, i1, j1, bool, z1,j;
             k=k+1;    double ***freq; /* Frequencies */
             mu[k][(int) age]=pmmij[i][j];    double *pp, **prop;
           }    double pos,posprop; 
         }    double  y2; /* in fractional years */
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    int iagemin, iagemax;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)  
             varpij[i][j][(int)age] = doldm[i][j];    iagemin= (int) agemin;
     iagemax= (int) agemax;
         /*printf("\n%d ",(int)age);    /*pp=vector(1,nlstate);*/
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    prop=matrix(1,nlstate,iagemin,iagemax+3); 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    j1=0;
      }*/    
     j=cptcoveff;
         fprintf(ficresprob,"\n%d ",(int)age);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         fprintf(ficresprobcov,"\n%d ",(int)age);    
         fprintf(ficresprobcor,"\n%d ",(int)age);    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)        j1++;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));        
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){        for (i=1; i<=nlstate; i++)  
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);          for(m=iagemin; m <= iagemax+3; m++)
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);            prop[i][m]=0.0;
         }       
         i=0;        for (i=1; i<=imx; i++) { /* Each individual */
         for (k=1; k<=(nlstate);k++){          bool=1;
           for (l=1; l<=(nlstate+ndeath);l++){          if  (cptcovn>0) {
             i=i++;            for (z1=1; z1<=cptcoveff; z1++) 
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);                bool=0;
             for (j=1; j<=i;j++){          } 
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);          if (bool==1) { 
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
             }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         }/* end of loop for state */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       } /* end of loop for age */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       /* Confidence intervalle of pij  */                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       /*                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       fprintf(ficgp,"\nset noparametric;unset label");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");                  prop[s[m][i]][iagemax+3] += weight[i]; 
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");                } 
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);              }
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);            } /* end selection of waves */
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);          }
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);        }
       */        for(i=iagemin; i <= iagemax+3; i++){  
           
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       first1=1;            posprop += prop[jk][i]; 
       for (k2=1; k2<=(nlstate);k2++){          } 
         for (l2=1; l2<=(nlstate+ndeath);l2++){  
           if(l2==k2) continue;          for(jk=1; jk <=nlstate ; jk++){     
           j=(k2-1)*(nlstate+ndeath)+l2;            if( i <=  iagemax){ 
           for (k1=1; k1<=(nlstate);k1++){              if(posprop>=1.e-5){ 
             for (l1=1; l1<=(nlstate+ndeath);l1++){                probs[i][jk][j1]= prop[jk][i]/posprop;
               if(l1==k1) continue;              } else
               i=(k1-1)*(nlstate+ndeath)+l1;                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
               if(i<=j) continue;            } 
               for (age=bage; age<=fage; age ++){          }/* end jk */ 
                 if ((int)age %5==0){        }/* end i */ 
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;      } /* end i1 */
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    } /* end k1 */
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    
                   mu1=mu[i][(int) age]/stepm*YEARM ;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                   mu2=mu[j][(int) age]/stepm*YEARM;    /*free_vector(pp,1,nlstate);*/
                   c12=cv12/sqrt(v1*v2);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
                   /* Computing eigen value of matrix of covariance */  }  /* End of prevalence */
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;  
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;  /************* Waves Concatenation ***************/
                   /* Eigen vectors */  
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));  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)
                   /*v21=sqrt(1.-v11*v11); *//* error */  {
                   v21=(lc1-v1)/cv12*v11;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
                   v12=-v21;       Death is a valid wave (if date is known).
                   v22=v11;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
                   tnalp=v21/v11;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                   if(first1==1){       and mw[mi+1][i]. dh depends on stepm.
                     first1=0;       */
                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);  
                   }    int i, mi, m;
                   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);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
                   /*printf(fignu*/       double sum=0., jmean=0.;*/
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    int first;
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */    int j, k=0,jk, ju, jl;
                   if(first==1){    double sum=0.;
                     first=0;    first=0;
                     fprintf(ficgp,"\nset parametric;unset label");    jmin=1e+5;
                     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);    jmax=-1;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    jmean=0.;
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);    for(i=1; i<=imx; i++){
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);      mi=0;
                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);      m=firstpass;
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);      while(s[m][i] <= nlstate){
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);          mw[++mi][i]=m;
                     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(m >=lastpass)
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\          break;
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));        else
                   }else{          m++;
                     first=0;      }/* end while */
                     fprintf(fichtm," %d (%.3f),",(int) age, c12);      if (s[m][i] > nlstate){
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);        mi++;     /* Death is another wave */
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);        /* if(mi==0)  never been interviewed correctly before death */
                     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",\           /* Only death is a correct wave */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\        mw[mi][i]=m;
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));      }
                   }/* if first */  
                 } /* age mod 5 */      wav[i]=mi;
               } /* end loop age */      if(mi==0){
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);        nbwarn++;
               first=1;        if(first==0){
             } /*l12 */          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           } /* k12 */          first=1;
         } /*l1 */        }
       }/* k1 */        if(first==1){
     } /* loop covariates */          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);        }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      } /* end mi==0 */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    } /* End individuals */
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for(i=1; i<=imx; i++){
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for(mi=1; mi<wav[i];mi++){
   }        if (stepm <=0)
   free_vector(xp,1,npar);          dh[mi][i]=1;
   fclose(ficresprob);        else{
   fclose(ficresprobcov);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   fclose(ficresprobcor);            if (agedc[i] < 2*AGESUP) {
   fclose(ficgp);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   fclose(fichtm);              if(j==0) j=1;  /* Survives at least one month after exam */
 }              else if(j<0){
                 nberr++;
                 printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 /******************* Printing html file ***********/                j=1; /* Temporary Dangerous patch */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \                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);
                   int lastpass, int stepm, int weightopt, char model[],\                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]);
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                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);
                   int popforecast, int estepm ,\              }
                   double jprev1, double mprev1,double anprev1, \              k=k+1;
                   double jprev2, double mprev2,double anprev2){              if (j >= jmax){
   int jj1, k1, i1, cpt;                jmax=j;
   /*char optionfilehtm[FILENAMELENGTH];*/                ijmax=i;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {              }
     printf("Problem with %s \n",optionfilehtm), exit(0);              if (j <= jmin){
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);                jmin=j;
   }                ijmin=i;
               }
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n              sum=sum+j;
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n            }
  - Life expectancies by age and initial health status (estepm=%2d months):          }
    <a href=\"e%s\">e%s</a> <br>\n</li>", \          else{
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  
             k=k+1;
  m=cptcoveff;            if (j >= jmax) {
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              jmax=j;
               ijmax=i;
  jj1=0;            }
  for(k1=1; k1<=m;k1++){            else if (j <= jmin){
    for(i1=1; i1<=ncodemax[k1];i1++){              jmin=j;
      jj1++;              ijmin=i;
      if (cptcovn > 0) {            }
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
        for (cpt=1; cpt<=cptcoveff;cpt++)            /*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]);*/
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            if(j<0){
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              nberr++;
      }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      /* Pij */              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      fprintf(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);                sum=sum+j;
      /* Quasi-incidences */          }
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>          jk= j/stepm;
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          jl= j -jk*stepm;
        /* Stable prevalence in each health state */          ju= j -(jk+1)*stepm;
        for(cpt=1; cpt<nlstate;cpt++){          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>            if(jl==0){
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              dh[mi][i]=jk;
        }              bh[mi][i]=0;
      for(cpt=1; cpt<=nlstate;cpt++) {            }else{ /* We want a negative bias in order to only have interpolation ie
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>                    * to avoid the price of an extra matrix product in likelihood */
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              dh[mi][i]=jk+1;
      }              bh[mi][i]=ju;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            }
 health expectancies in states (1) and (2): e%s%d.png<br>          }else{
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            if(jl <= -ju){
    } /* end i1 */              dh[mi][i]=jk;
  }/* End k1 */              bh[mi][i]=jl;       /* bias is positive if real duration
  fprintf(fichtm,"</ul>");                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
             }
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n            else{
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n              dh[mi][i]=jk+1;
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n              bh[mi][i]=ju;
  - 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            if(dh[mi][i]==0){
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n              dh[mi][i]=1; /* At least one step */
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n              bh[mi][i]=ju; /* At least one step */
  - 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);              /*  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);*/
             }
  if(popforecast==1) fprintf(fichtm,"\n          } /* end if mle */
  - 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      } /* end wave */
         <br>",fileres,fileres,fileres,fileres);    }
  else    jmean=sum/k;
    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);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");    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);
    }
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
  jj1=0;  {
  for(k1=1; k1<=m;k1++){    /* Uses cptcovn+2*cptcovprod as the number of covariates */
    for(i1=1; i1<=ncodemax[k1];i1++){    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
      jj1++;  
      if (cptcovn > 0) {    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    int modmaxcovj=0; /* Modality max of covariates j */
        for (cpt=1; cpt<=cptcoveff;cpt++)    cptcoveff=0; 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);   
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    for (k=0; k<maxncov; k++) Ndum[k]=0;
      }    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
      for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
 interval) in state (%d): v%s%d%d.png <br>      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                                   modality of this covariate Vj*/ 
      }        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
    } /* end i1 */                                        modality of the nth covariate of individual i. */
  }/* End k1 */        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
  fprintf(fichtm,"</ul>");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 fclose(fichtm);        if (ij > modmaxcovj) modmaxcovj=ij; 
 }        /* getting the maximum value of the modality of the covariate
            (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
 /******************* Gnuplot file **************/           female is 1, then modmaxcovj=1.*/
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      }
       /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
   int ng;        if( Ndum[i] != 0 )
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          ncodemax[j]++; 
     printf("Problem with file %s",optionfilegnuplot);        /* Number of modalities of the j th covariate. In fact
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);           ncodemax[j]=2 (dichotom. variables only) but it could be more for
   }           historical reasons */
       } /* Ndum[-1] number of undefined modalities */
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
 #endif      ij=1; 
 m=pow(2,cptcoveff);      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
          for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
  /* 1eme*/          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   for (cpt=1; cpt<= nlstate ; cpt ++) {            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
    for (k1=1; k1<= m ; k1 ++) {                                       k is a modality. If we have model=V1+V1*sex 
                                        then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
 #ifdef windows            ij++;
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          }
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);          if (ij > ncodemax[j]) break; 
 #endif        }  /* end of loop on */
 #ifdef unix      } /* end of loop on modality */ 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    
 #endif    for (k=0; k< maxncov; k++) Ndum[k]=0;
     
 for (i=1; i<= nlstate ; i ++) {    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
 }     Ndum[ij]++;
     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 ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");   ij=1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
 }     if((Ndum[i]!=0) && (i<=ncovcol)){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);       Tvaraff[ij]=i; /*For printing */
      for (i=1; i<= nlstate ; i ++) {       ij++;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");     }
   else fprintf(ficgp," \%%*lf (\%%*lf)");   }
 }     ij--;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));   cptcoveff=ij; /*Number of simple covariates*/
 #ifdef unix  }
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");  
 #endif  /*********** Health Expectancies ****************/
    }  
   }  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   /*2 eme*/  
   {
   for (k1=1; k1<= m ; k1 ++) {    /* Health expectancies, no variances */
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    int nhstepma, nstepma; /* Decreasing with age */
        double age, agelim, hf;
     for (i=1; i<= nlstate+1 ; i ++) {    double ***p3mat;
       k=2*i;    double eip;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    pstamp(ficreseij);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficreseij,"# Age");
 }      for(i=1; i<=nlstate;i++){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      for(j=1; j<=nlstate;j++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        fprintf(ficreseij," e%1d%1d ",i,j);
     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 ++) {      fprintf(ficreseij," e%1d. ",i);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
         else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficreseij,"\n");
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");    
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    if(estepm < stepm){
       for (j=1; j<= nlstate+1 ; j ++) {      printf ("Problem %d lower than %d\n",estepm, stepm);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    else  hstepm=estepm;   
 }      /* We compute the life expectancy from trapezoids spaced every estepm months
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");     * This is mainly to measure the difference between two models: for example
       else fprintf(ficgp,"\" t\"\" w l 0,");     * if stepm=24 months pijx are given only every 2 years and by summing them
     }     * we are calculating an estimate of the Life Expectancy assuming a linear 
   }     * progression in between and thus overestimating or underestimating according
       * to the curvature of the survival function. If, for the same date, we 
   /*3eme*/     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
   for (k1=1; k1<= m ; k1 ++) {     * hypothesis. A more precise result, taking into account a more precise
     for (cpt=1; cpt<= nlstate ; cpt ++) {     * curvature will be obtained if estepm is as small as stepm. */
       k=2+nlstate*(2*cpt-2);  
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);       nhstepm is the number of hstepm from age to agelim 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");       nstepm is the number of stepm from age to agelin. 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);       Look at hpijx to understand the reason of that which relies in memory size
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);       and note for a fixed period like estepm months */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
 */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for (i=1; i< nlstate ; i ++) {       results. So we changed our mind and took the option of the best precision.
         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);    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       }  
     }    agelim=AGESUP;
   }    /* If stepm=6 months */
        /* Computed by stepm unit matrices, product of hstepm matrices, stored
   /* CV preval stat */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     for (k1=1; k1<= m ; k1 ++) {      
     for (cpt=1; cpt<nlstate ; cpt ++) {  /* nhstepm age range expressed in number of stepm */
       k=3;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for (i=1; i< nlstate ; i ++)    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    for (age=bage; age<=fage; age ++){ 
            nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       l=3+(nlstate+ndeath)*cpt;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      /* if (stepm >= YEARM) hstepm=1;*/
       for (i=1; i< nlstate ; i ++) {      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);      /* If stepm=6 months */
       }      /* Computed by stepm unit matrices, product of hstepma matrices, stored
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);           in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     }      
   }        hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
        
   /* proba elementaires */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    for(i=1,jk=1; i <=nlstate; i++){      
     for(k=1; k <=(nlstate+ndeath); k++){      printf("%d|",(int)age);fflush(stdout);
       if (k != i) {      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(j=1; j <=ncovmodel; j++){      
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      /* Computing expectancies */
           jk++;      for(i=1; i<=nlstate;i++)
           fprintf(ficgp,"\n");        for(j=1; j<=nlstate;j++)
         }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     }            
    }            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
    for(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(ficreseij,"%3.0f",age );
        if (ng==2)      for(i=1; i<=nlstate;i++){
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");        eip=0;
        else        for(j=1; j<=nlstate;j++){
          fprintf(ficgp,"\nset title \"Probability\"\n");          eip +=eij[i][j][(int)age];
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
        i=1;        }
        for(k2=1; k2<=nlstate; k2++) {        fprintf(ficreseij,"%9.4f", eip );
          k3=i;      }
          for(k=1; k<=(nlstate+ndeath); k++) {      fprintf(ficreseij,"\n");
            if (k != k2){      
              if(ng==2)    }
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              else    printf("\n");
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    fprintf(ficlog,"\n");
              ij=1;    
              for(j=3; j <=ncovmodel; j++) {  }
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  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[] )
                  ij++;  
                }  {
                else    /* Covariances of health expectancies eij and of total life expectancies according
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);     to initial status i, ei. .
              }    */
              fprintf(ficgp,")/(1");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
                  int nhstepma, nstepma; /* Decreasing with age */
              for(k1=1; k1 <=nlstate; k1++){      double age, agelim, hf;
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    double ***p3matp, ***p3matm, ***varhe;
                ij=1;    double **dnewm,**doldm;
                for(j=3; j <=ncovmodel; j++){    double *xp, *xm;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double **gp, **gm;
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double ***gradg, ***trgradg;
                    ij++;    int theta;
                  }  
                  else    double eip, vip;
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
                }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
                fprintf(ficgp,")");    xp=vector(1,npar);
              }    xm=vector(1,npar);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    dnewm=matrix(1,nlstate*nlstate,1,npar);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
              i=i+ncovmodel;    
            }    pstamp(ficresstdeij);
          } /* end k */    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
        } /* end k2 */    fprintf(ficresstdeij,"# Age");
      } /* end jk */    for(i=1; i<=nlstate;i++){
    } /* end ng */      for(j=1; j<=nlstate;j++)
    fclose(ficgp);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
 }  /* end gnuplot */      fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
 /*************** Moving average **************/  
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   int i, cpt, cptcod;    fprintf(ficrescveij,"# Age");
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    for(i=1; i<=nlstate;i++)
       for (i=1; i<=nlstate;i++)      for(j=1; j<=nlstate;j++){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        cptj= (j-1)*nlstate+i;
           mobaverage[(int)agedeb][i][cptcod]=0.;        for(i2=1; i2<=nlstate;i2++)
              for(j2=1; j2<=nlstate;j2++){
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){            cptj2= (j2-1)*nlstate+i2;
       for (i=1; i<=nlstate;i++){            if(cptj2 <= cptj)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           for (cpt=0;cpt<=4;cpt++){          }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      }
           }    fprintf(ficrescveij,"\n");
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    
         }    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
     }    }
        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
      * if stepm=24 months pijx are given only every 2 years and by summing them
 /************** Forecasting ******************/     * we are calculating an estimate of the Life Expectancy assuming a linear 
 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){     * progression in between and thus overestimating or underestimating according
       * to the curvature of the survival function. If, for the same date, we 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   int *popage;     * to compare the new estimate of Life expectancy with the same linear 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;     * hypothesis. A more precise result, taking into account a more precise
   double *popeffectif,*popcount;     * curvature will be obtained if estepm is as small as stepm. */
   double ***p3mat;  
   char fileresf[FILENAMELENGTH];    /* 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. 
  agelim=AGESUP;       nhstepm is the number of hstepm from age to agelim 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);       and note for a fixed period like estepm months */
      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         survival function given by stepm (the optimization length). Unfortunately it
   strcpy(fileresf,"f");       means that if the survival funtion is printed only each two years of age and if
   strcat(fileresf,fileres);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   if((ficresf=fopen(fileresf,"w"))==NULL) {       results. So we changed our mind and took the option of the best precision.
     printf("Problem with forecast resultfile: %s\n", fileresf);    */
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);    /* If stepm=6 months */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   if (mobilav==1) {    /* if (stepm >= YEARM) hstepm=1;*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     movingaverage(agedeb, fage, ageminpar, mobaverage);    
   }    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   if (stepm<=12) stepsize=1;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   agelim=AGESUP;    gm=matrix(0,nhstepm,1,nlstate*nlstate);
    
   hstepm=1;    for (age=bage; age<=fage; age ++){ 
   hstepm=hstepm/stepm;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   yp1=modf(dateintmean,&yp);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   anprojmean=yp;      /* if (stepm >= YEARM) hstepm=1;*/
   yp2=modf((yp1*12),&yp);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   mprojmean=yp;  
   yp1=modf((yp2*30.5),&yp);      /* If stepm=6 months */
   jprojmean=yp;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   if(jprojmean==0) jprojmean=1;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   if(mprojmean==0) jprojmean=1;      
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
        /* Computing  Variances of health expectancies */
   for(cptcov=1;cptcov<=i2;cptcov++){      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){         decrease memory allocation */
       k=k+1;      for(theta=1; theta <=npar; theta++){
       fprintf(ficresf,"\n#******");        for(i=1; i<=npar; i++){ 
       for(j=1;j<=cptcoveff;j++) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       }        }
       fprintf(ficresf,"******\n");        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       fprintf(ficresf,"# StartingAge FinalAge");        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    
              for(j=1; j<= nlstate; j++){
                for(i=1; i<=nlstate; i++){
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {            for(h=0; h<=nhstepm-1; h++){
         fprintf(ficresf,"\n");              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        }
           nhstepm = nhstepm/hstepm;       
                  for(ij=1; ij<= nlstate*nlstate; ij++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(h=0; h<=nhstepm-1; h++){
           oldm=oldms;savm=savms;            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
              }/* End theta */
           for (h=0; h<=nhstepm; h++){      
             if (h==(int) (calagedate+YEARM*cpt)) {      
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      for(h=0; h<=nhstepm-1; h++)
             }        for(j=1; j<=nlstate*nlstate;j++)
             for(j=1; j<=nlstate+ndeath;j++) {          for(theta=1; theta <=npar; theta++)
               kk1=0.;kk2=0;            trgradg[h][j][theta]=gradg[h][theta][j];
               for(i=1; i<=nlstate;i++) {                    
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];       for(ij=1;ij<=nlstate*nlstate;ij++)
                 else {        for(ji=1;ji<=nlstate*nlstate;ji++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          varhe[ij][ji][(int)age] =0.;
                 }  
                       printf("%d|",(int)age);fflush(stdout);
               }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
               if (h==(int)(calagedate+12*cpt)){       for(h=0;h<=nhstepm-1;h++){
                 fprintf(ficresf," %.3f", kk1);        for(k=0;k<=nhstepm-1;k++){
                                  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]);
             }          for(ij=1;ij<=nlstate*nlstate;ij++)
           }            for(ji=1;ji<=nlstate*nlstate;ji++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }        }
       }      }
     }  
   }      /* Computing expectancies */
              hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   fclose(ficresf);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 }            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
 /************** Forecasting ******************/            
 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){            /* 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]);*/
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          }
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      fprintf(ficresstdeij,"%3.0f",age );
   double *popeffectif,*popcount;      for(i=1; i<=nlstate;i++){
   double ***p3mat,***tabpop,***tabpopprev;        eip=0.;
   char filerespop[FILENAMELENGTH];        vip=0.;
         for(j=1; j<=nlstate;j++){
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          eip += eij[i][j][(int)age];
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   agelim=AGESUP;            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
          }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
        }
        fprintf(ficresstdeij,"\n");
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);      fprintf(ficrescveij,"%3.0f",age );
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      for(i=1; i<=nlstate;i++)
     printf("Problem with forecast resultfile: %s\n", filerespop);        for(j=1; j<=nlstate;j++){
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);          cptj= (j-1)*nlstate+i;
   }          for(i2=1; i2<=nlstate;i2++)
   printf("Computing forecasting: result on file '%s' \n", filerespop);            for(j2=1; j2<=nlstate;j2++){
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);              cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
   if (mobilav==1) {        }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficrescveij,"\n");
     movingaverage(agedeb, fage, ageminpar, mobaverage);     
   }    }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   if (stepm<=12) stepsize=1;    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   agelim=AGESUP;    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   hstepm=1;    printf("\n");
   hstepm=hstepm/stepm;    fprintf(ficlog,"\n");
    
   if (popforecast==1) {    free_vector(xm,1,npar);
     if((ficpop=fopen(popfile,"r"))==NULL) {    free_vector(xp,1,npar);
       printf("Problem with population file : %s\n",popfile);exit(0);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     popage=ivector(0,AGESUP);  }
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);  /************ Variance ******************/
      void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
     i=1;    {
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    /* Variance of health expectancies */
        /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     imx=i;    /* double **newm;*/
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    double **dnewm,**doldm;
   }    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
   for(cptcov=1;cptcov<=i2;cptcov++){    int k, cptcode;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double *xp;
       k=k+1;    double **gp, **gm;  /* for var eij */
       fprintf(ficrespop,"\n#******");    double ***gradg, ***trgradg; /*for var eij */
       for(j=1;j<=cptcoveff;j++) {    double **gradgp, **trgradgp; /* for var p point j */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double *gpp, *gmp; /* for var p point j */
       }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       fprintf(ficrespop,"******\n");    double ***p3mat;
       fprintf(ficrespop,"# Age");    double age,agelim, hf;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    double ***mobaverage;
       if (popforecast==1)  fprintf(ficrespop," [Population]");    int theta;
          char digit[4];
       for (cpt=0; cpt<=0;cpt++) {    char digitp[25];
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
            char fileresprobmorprev[FILENAMELENGTH];
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    if(popbased==1){
           nhstepm = nhstepm/hstepm;      if(mobilav!=0)
                  strcpy(digitp,"-populbased-mobilav-");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      else strcpy(digitp,"-populbased-nomobil-");
           oldm=oldms;savm=savms;    }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      else 
              strcpy(digitp,"-stablbased-");
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    if (mobilav!=0) {
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
             for(j=1; j<=nlstate+ndeath;j++) {        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
               kk1=0.;kk2=0;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
               for(i=1; i<=nlstate;i++) {                    }
                 if (mobilav==1)    }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {    strcpy(fileresprobmorprev,"prmorprev"); 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    sprintf(digit,"%-d",ij);
                 }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
               }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
               if (h==(int)(calagedate+12*cpt)){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    strcat(fileresprobmorprev,fileres);
                   /*fprintf(ficrespop," %.3f", kk1);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      printf("Problem with resultfile: %s\n", fileresprobmorprev);
               }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
             }    }
             for(i=1; i<=nlstate;i++){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
               kk1=0.;   
                 for(j=1; j<=nlstate;j++){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    pstamp(ficresprobmorprev);
                 }    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);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
             }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      for(i=1; i<=nlstate;i++)
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           }    }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresprobmorprev,"\n");
         }    fprintf(ficgp,"\n# Routine varevsij");
       }    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   /******/    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      pstamp(ficresvij);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    if(popbased==1)
           nhstepm = nhstepm/hstepm;      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
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
           oldm=oldms;savm=savms;    fprintf(ficresvij,"# Age");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      for(i=1; i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){      for(j=1; j<=nlstate;j++)
             if (h==(int) (calagedate+YEARM*cpt)) {        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficresvij,"\n");
             }  
             for(j=1; j<=nlstate+ndeath;j++) {    xp=vector(1,npar);
               kk1=0.;kk2=0;    dnewm=matrix(1,nlstate,1,npar);
               for(i=1; i<=nlstate;i++) {                  doldm=matrix(1,nlstate,1,nlstate);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
               }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  
             }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           }    gpp=vector(nlstate+1,nlstate+ndeath);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    gmp=vector(nlstate+1,nlstate+ndeath);
         }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       }    
    }    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
   if (popforecast==1) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     free_ivector(popage,0,AGESUP);       nhstepm is the number of hstepm from age to agelim 
     free_vector(popeffectif,0,AGESUP);       nstepm is the number of stepm from age to agelin. 
     free_vector(popcount,0,AGESUP);       Look at function hpijx to understand why (it is linked to memory size questions) */
   }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       survival function given by stepm (the optimization length). Unfortunately it
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       means that if the survival funtion is printed every two years of age and if
   fclose(ficrespop);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 }       results. So we changed our mind and took the option of the best precision.
     */
 /***********************************************/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 /**************** Main Program *****************/    agelim = AGESUP;
 /***********************************************/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 int main(int argc, char *argv[])      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      gp=matrix(0,nhstepm,1,nlstate);
   double agedeb, agefin,hf;      gm=matrix(0,nhstepm,1,nlstate);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
   
   double fret;      for(theta=1; theta <=npar; theta++){
   double **xi,tmp,delta;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   double dum; /* Dummy variable */        }
   double ***p3mat;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   int *indx;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   char line[MAXLINE], linepar[MAXLINE];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];        if (popbased==1) {
   int firstobs=1, lastobs=10;          if(mobilav ==0){
   int sdeb, sfin; /* Status at beginning and end */            for(i=1; i<=nlstate;i++)
   int c,  h , cpt,l;              prlim[i][i]=probs[(int)age][i][ij];
   int ju,jl, mi;          }else{ /* mobilav */ 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            for(i=1; i<=nlstate;i++)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              prlim[i][i]=mobaverage[(int)age][i][ij];
   int mobilav=0,popforecast=0;          }
   int hstepm, nhstepm;        }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    
         for(j=1; j<= nlstate; j++){
   double bage, fage, age, agelim, agebase;          for(h=0; h<=nhstepm; h++){
   double ftolpl=FTOL;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   double **prlim;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   double *severity;          }
   double ***param; /* Matrix of parameters */        }
   double  *p;        /* This for computing probability of death (h=1 means
   double **matcov; /* Matrix of covariance */           computed over hstepm matrices product = hstepm*stepm months) 
   double ***delti3; /* Scale */           as a weighted average of prlim.
   double *delti; /* Scale */        */
   double ***eij, ***vareij;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   double **varpl; /* Variances of prevalence limits by age */          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   double *epj, vepp;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   double kk1, kk2;        }    
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        /* end probability of death */
    
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   char *alph[]={"a","a","b","c","d","e"}, str[4];          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   char z[1]="c", occ;   
 #include <sys/time.h>        if (popbased==1) {
 #include <time.h>          if(mobilav ==0){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
   /* long total_usecs;          }else{ /* mobilav */ 
   struct timeval start_time, end_time;            for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          }
   getcwd(pathcd, size);        }
   
   printf("\n%s",version);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   if(argc <=1){          for(h=0; h<=nhstepm; h++){
     printf("\nEnter the parameter file name: ");            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     scanf("%s",pathtot);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
   else{        }
     strcpy(pathtot,argv[1]);        /* This for computing probability of death (h=1 means
   }           computed over hstepm matrices product = hstepm*stepm months) 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/           as a weighted average of prlim.
   /*cygwin_split_path(pathtot,path,optionfile);        */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   /* cutv(path,optionfile,pathtot,'\\');*/          for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        }    
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        /* end probability of death */
   chdir(path);  
   replace(pathc,path);        for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
 /*-------- arguments in the command line --------*/            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   /* Log file */  
   strcat(filelog, optionfilefiname);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   strcat(filelog,".log");    /* */          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   if((ficlog=fopen(filelog,"w"))==NULL)    {        }
     printf("Problem with logfile %s\n",filelog);  
     goto end;      } /* End theta */
   }  
   fprintf(ficlog,"Log filename:%s\n",filelog);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   fprintf(ficlog,"\n%s",version);  
   fprintf(ficlog,"\nEnter the parameter file name: ");      for(h=0; h<=nhstepm; h++) /* veij */
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        for(j=1; j<=nlstate;j++)
   fflush(ficlog);          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   /* */  
   strcpy(fileres,"r");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   strcat(fileres, optionfilefiname);        for(theta=1; theta <=npar; theta++)
   strcat(fileres,".txt");    /* Other files have txt extension */          trgradgp[j][theta]=gradgp[theta][j];
     
   /*---------arguments file --------*/  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      for(i=1;i<=nlstate;i++)
     printf("Problem with optionfile %s\n",optionfile);        for(j=1;j<=nlstate;j++)
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);          vareij[i][j][(int)age] =0.;
     goto end;  
   }      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
   strcpy(filereso,"o");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   strcat(filereso,fileres);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   if((ficparo=fopen(filereso,"w"))==NULL) {          for(i=1;i<=nlstate;i++)
     printf("Problem with Output resultfile: %s\n", filereso);            for(j=1;j<=nlstate;j++)
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     goto end;        }
   }      }
     
   /* Reads comments: lines beginning with '#' */      /* pptj */
   while((c=getc(ficpar))=='#' && c!= EOF){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     ungetc(c,ficpar);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     fgets(line, MAXLINE, ficpar);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     puts(line);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     fputs(line,ficparo);          varppt[j][i]=doldmp[j][i];
   }      /* end ppptj */
   ungetc(c,ficpar);      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   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);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);   
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);      if (popbased==1) {
 while((c=getc(ficpar))=='#' && c!= EOF){        if(mobilav ==0){
     ungetc(c,ficpar);          for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);            prlim[i][i]=probs[(int)age][i][ij];
     puts(line);        }else{ /* mobilav */ 
     fputs(line,ficparo);          for(i=1; i<=nlstate;i++)
   }            prlim[i][i]=mobaverage[(int)age][i][ij];
   ungetc(c,ficpar);        }
        }
                   
   covar=matrix(0,NCOVMAX,1,n);      /* This for computing probability of death (h=1 means
   cptcovn=0;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;         as a weighted average of prlim.
       */
   ncovmodel=2+cptcovn;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   /* Read guess parameters */      }    
   /* Reads comments: lines beginning with '#' */      /* end probability of death */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     fgets(line, MAXLINE, ficpar);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     puts(line);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     fputs(line,ficparo);        for(i=1; i<=nlstate;i++){
   }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   ungetc(c,ficpar);        }
        } 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      fprintf(ficresprobmorprev,"\n");
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){      fprintf(ficresvij,"%.0f ",age );
       fscanf(ficpar,"%1d%1d",&i1,&j1);      for(i=1; i<=nlstate;i++)
       fprintf(ficparo,"%1d%1d",i1,j1);        for(j=1; j<=nlstate;j++){
       if(mle==1)          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         printf("%1d%1d",i,j);        }
       fprintf(ficlog,"%1d%1d",i,j);      fprintf(ficresvij,"\n");
       for(k=1; k<=ncovmodel;k++){      free_matrix(gp,0,nhstepm,1,nlstate);
         fscanf(ficpar," %lf",&param[i][j][k]);      free_matrix(gm,0,nhstepm,1,nlstate);
         if(mle==1){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
           printf(" %lf",param[i][j][k]);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           fprintf(ficlog," %lf",param[i][j][k]);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    } /* End age */
         else    free_vector(gpp,nlstate+1,nlstate+ndeath);
           fprintf(ficlog," %lf",param[i][j][k]);    free_vector(gmp,nlstate+1,nlstate+ndeath);
         fprintf(ficparo," %lf",param[i][j][k]);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       fscanf(ficpar,"\n");    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
       if(mle==1)    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
         printf("\n");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       fprintf(ficlog,"\n");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficparo,"\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    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));
   p=param[1][1];    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   /* Reads comments: lines beginning with '#' */    /*  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);
   while((c=getc(ficpar))=='#' && c!= EOF){  */
     ungetc(c,ficpar);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fgets(line, MAXLINE, ficpar);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     puts(line);  
     fputs(line,ficparo);    free_vector(xp,1,npar);
   }    free_matrix(doldm,1,nlstate,1,nlstate);
   ungetc(c,ficpar);    free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   for(i=1; i <=nlstate; i++){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for(j=1; j <=nlstate+ndeath-1; j++){    fclose(ficresprobmorprev);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fflush(ficgp);
       printf("%1d%1d",i,j);    fflush(fichtm); 
       fprintf(ficparo,"%1d%1d",i1,j1);  }  /* end varevsij */
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);  /************ Variance of prevlim ******************/
         printf(" %le",delti3[i][j][k]);  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[])
         fprintf(ficparo," %le",delti3[i][j][k]);  {
       }    /* Variance of prevalence limit */
       fscanf(ficpar,"\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       printf("\n");    double **newm;
       fprintf(ficparo,"\n");    double **dnewm,**doldm;
     }    int i, j, nhstepm, hstepm;
   }    int k, cptcode;
   delti=delti3[1][1];    double *xp;
      double *gp, *gm;
   /* Reads comments: lines beginning with '#' */    double **gradg, **trgradg;
   while((c=getc(ficpar))=='#' && c!= EOF){    double age,agelim;
     ungetc(c,ficpar);    int theta;
     fgets(line, MAXLINE, ficpar);    
     puts(line);    pstamp(ficresvpl);
     fputs(line,ficparo);    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   }    fprintf(ficresvpl,"# Age");
   ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %1d-%1d",i,i);
   matcov=matrix(1,npar,1,npar);    fprintf(ficresvpl,"\n");
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);    xp=vector(1,npar);
     if(mle==1)    dnewm=matrix(1,nlstate,1,npar);
       printf("%s",str);    doldm=matrix(1,nlstate,1,nlstate);
     fprintf(ficlog,"%s",str);    
     fprintf(ficparo,"%s",str);    hstepm=1*YEARM; /* Every year of age */
     for(j=1; j <=i; j++){    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       fscanf(ficpar," %le",&matcov[i][j]);    agelim = AGESUP;
       if(mle==1){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         printf(" %.5le",matcov[i][j]);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         fprintf(ficlog," %.5le",matcov[i][j]);      if (stepm >= YEARM) hstepm=1;
       }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       else      gradg=matrix(1,npar,1,nlstate);
         fprintf(ficlog," %.5le",matcov[i][j]);      gp=vector(1,nlstate);
       fprintf(ficparo," %.5le",matcov[i][j]);      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++)
   for(i=1; i <=npar; i++)          gp[i] = prlim[i][i];
     for(j=i+1;j<=npar;j++)      
       matcov[i][j]=matcov[j][i];        for(i=1; i<=npar; i++) /* Computes gradient */
              xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if(mle==1)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("\n");        for(i=1;i<=nlstate;i++)
   fprintf(ficlog,"\n");          gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
     /*-------- Rewriting paramater file ----------*/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
      strcpy(rfileres,"r");    /* "Rparameterfile */      } /* End theta */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
      strcat(rfileres,".");    /* */      trgradg =matrix(1,nlstate,1,npar);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  
     if((ficres =fopen(rfileres,"w"))==NULL) {      for(j=1; j<=nlstate;j++)
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        for(theta=1; theta <=npar; theta++)
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;          trgradg[j][theta]=gradg[theta][j];
     }  
     fprintf(ficres,"#%s\n",version);      for(i=1;i<=nlstate;i++)
            varpl[i][(int)age] =0.;
     /*-------- data file ----------*/      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     if((fic=fopen(datafile,"r"))==NULL)    {      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       printf("Problem with datafile: %s\n", datafile);goto end;      for(i=1;i<=nlstate;i++)
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     }  
       fprintf(ficresvpl,"%.0f ",age );
     n= lastobs;      for(i=1; i<=nlstate;i++)
     severity = vector(1,maxwav);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     outcome=imatrix(1,maxwav+1,1,n);      fprintf(ficresvpl,"\n");
     num=ivector(1,n);      free_vector(gp,1,nlstate);
     moisnais=vector(1,n);      free_vector(gm,1,nlstate);
     annais=vector(1,n);      free_matrix(gradg,1,npar,1,nlstate);
     moisdc=vector(1,n);      free_matrix(trgradg,1,nlstate,1,npar);
     andc=vector(1,n);    } /* End age */
     agedc=vector(1,n);  
     cod=ivector(1,n);    free_vector(xp,1,npar);
     weight=vector(1,n);    free_matrix(doldm,1,nlstate,1,npar);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    free_matrix(dnewm,1,nlstate,1,nlstate);
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);  }
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);      /************ Variance of one-step probabilities  ******************/
     tab=ivector(1,NCOVMAX);  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[])
     ncodemax=ivector(1,8);  {
     int i, j=0,  i1, k1, l1, t, tj;
     i=1;    int k2, l2, j1,  z1;
     while (fgets(line, MAXLINE, fic) != NULL)    {    int k=0,l, cptcode;
       if ((i >= firstobs) && (i <=lastobs)) {    int first=1, first1;
            double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         for (j=maxwav;j>=1;j--){    double **dnewm,**doldm;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    double *xp;
           strcpy(line,stra);    double *gp, *gm;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double **gradg, **trgradg;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double **mu;
         }    double age,agelim, cov[NCOVMAX];
            double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    int theta;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    char fileresprobcor[FILENAMELENGTH];
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
     double ***varpij;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncovcol;j>=1;j--){    strcpy(fileresprob,"prob"); 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    strcat(fileresprob,fileres);
         }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
         num[i]=atol(stra);      printf("Problem with resultfile: %s\n", fileresprob);
              fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    }
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
         i=i+1;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprobcov);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     /* printf("ii=%d", ij);    }
        scanf("%d",i);*/    strcpy(fileresprobcor,"probcor"); 
   imx=i-1; /* Number of individuals */    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   /* for (i=1; i<=imx; i++){      printf("Problem with resultfile: %s\n", fileresprobcor);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    }
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    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);
    /*  for (i=1; i<=imx; i++){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      if (s[4][i]==9)  s[4][i]=-1;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      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]));}*/    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      pstamp(ficresprob);
   /* Calculation of the number of parameter from char model*/    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */    fprintf(ficresprob,"# Age");
   Tprod=ivector(1,15);    pstamp(ficresprobcov);
   Tvaraff=ivector(1,15);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   Tvard=imatrix(1,15,1,2);    fprintf(ficresprobcov,"# Age");
   Tage=ivector(1,15);          pstamp(ficresprobcor);
        fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   if (strlen(model) >1){    fprintf(ficresprobcor,"# Age");
     j=0, j1=0, k1=1, k2=1;  
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');    for(i=1; i<=nlstate;i++)
     cptcovn=j+1;      for(j=1; j<=(nlstate+ndeath);j++){
     cptcovprod=j1;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
            fprintf(ficresprobcov," p%1d-%1d ",i,j);
     strcpy(modelsav,model);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      }  
       printf("Error. Non available option model=%s ",model);   /* fprintf(ficresprob,"\n");
       fprintf(ficlog,"Error. Non available option model=%s ",model);    fprintf(ficresprobcov,"\n");
       goto end;    fprintf(ficresprobcor,"\n");
     }   */
        xp=vector(1,npar);
     for(i=(j+1); i>=1;i--){    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       /*scanf("%d",i);*/    first=1;
       if (strchr(strb,'*')) {  /* Model includes a product */    fprintf(ficgp,"\n# Routine varprob");
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         if (strcmp(strc,"age")==0) { /* Vn*age */    fprintf(fichtm,"\n");
           cptcovprod--;  
           cutv(strb,stre,strd,'V');    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
           cptcovage++;    file %s<br>\n",optionfilehtmcov);
             Tage[cptcovage]=i;    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
             /*printf("stre=%s ", stre);*/  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");
         else if (strcmp(strd,"age")==0) { /* or age*Vn */    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. \
           cptcovprod--;  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
           cutv(strb,stre,strc,'V');  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
           Tvar[i]=atoi(stre);  standard deviations wide on each axis. <br>\
           cptcovage++;   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
           Tage[cptcovage]=i;   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
         }  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
         else {  /* Age is not in the model */  
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/    cov[1]=1;
           Tvar[i]=ncovcol+k1;    tj=cptcoveff;
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
           Tprod[k1]=i;    j1=0;
           Tvard[k1][1]=atoi(strc); /* m*/    for(t=1; t<=tj;t++){
           Tvard[k1][2]=atoi(stre); /* n */      for(i1=1; i1<=ncodemax[t];i1++){ 
           Tvar[cptcovn+k2]=Tvard[k1][1];        j1++;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        if  (cptcovn>0) {
           for (k=1; k<=lastobs;k++)          fprintf(ficresprob, "\n#********** Variable "); 
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           k1++;          fprintf(ficresprob, "**********\n#\n");
           k2=k2+2;          fprintf(ficresprobcov, "\n#********** Variable "); 
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresprobcov, "**********\n#\n");
       else { /* no more sum */          
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          fprintf(ficgp, "\n#********** Variable "); 
        /*  scanf("%d",i);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       cutv(strd,strc,strb,'V');          fprintf(ficgp, "**********\n#\n");
       Tvar[i]=atoi(strc);          
       }          
       strcpy(modelsav,stra);            fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         scanf("%d",i);*/          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     } /* end of loop + */          
   } /* end model */          fprintf(ficresprobcor, "\n#********** Variable ");    
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          fprintf(ficresprobcor, "**********\n#");    
   printf("cptcovprod=%d ", cptcovprod);        }
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);        
   scanf("%d ",i);*/        for (age=bage; age<=fage; age ++){ 
     fclose(fic);          cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
     /*  if(mle==1){*/            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     if (weightopt != 1) { /* Maximisation without weights*/          }
       for(i=1;i<=n;i++) weight[i]=1.0;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }          for (k=1; k<=cptcovprod;k++)
     /*-calculation of age at interview from date of interview and age at death -*/            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     agev=matrix(1,maxwav,1,imx);          
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     for (i=1; i<=imx; i++) {          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       for(m=2; (m<= maxwav); m++) {          gp=vector(1,(nlstate)*(nlstate+ndeath));
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          gm=vector(1,(nlstate)*(nlstate+ndeath));
          anint[m][i]=9999;      
          s[m][i]=-1;          for(theta=1; theta <=npar; theta++){
        }            for(i=1; i<=npar; i++)
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       }            
     }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
     for (i=1; i<=imx; i++)  {            k=0;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            for(i=1; i<= (nlstate); i++){
       for(m=1; (m<= maxwav); m++){              for(j=1; j<=(nlstate+ndeath);j++){
         if(s[m][i] >0){                k=k+1;
           if (s[m][i] >= nlstate+1) {                gp[k]=pmmij[i][j];
             if(agedc[i]>0)              }
               if(moisdc[i]!=99 && andc[i]!=9999)            }
                 agev[m][i]=agedc[i];            
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            for(i=1; i<=npar; i++)
            else {              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
               if (andc[i]!=9999){      
               printf("Warning negative age at death: %d line:%d\n",num[i],i);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);            k=0;
               agev[m][i]=-1;            for(i=1; i<=(nlstate); i++){
               }              for(j=1; j<=(nlstate+ndeath);j++){
             }                k=k+1;
           }                gm[k]=pmmij[i][j];
           else if(s[m][i] !=9){ /* Should no more exist */              }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            }
             if(mint[m][i]==99 || anint[m][i]==9999)       
               agev[m][i]=1;            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
             else if(agev[m][i] <agemin){              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
               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);*/  
             }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             else if(agev[m][i] >agemax){            for(theta=1; theta <=npar; theta++)
               agemax=agev[m][i];              trgradg[j][theta]=gradg[theta][j];
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          
             }          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
             /*agev[m][i]=anint[m][i]-annais[i];*/          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
             /*   agev[m][i] = age[i]+2*m;*/          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           }          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           else { /* =9 */          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
             agev[m][i]=1;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
             s[m][i]=-1;  
           }          pmij(pmmij,cov,ncovmodel,x,nlstate);
         }          
         else /*= 0 Unknown */          k=0;
           agev[m][i]=1;          for(i=1; i<=(nlstate); i++){
       }            for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
     }              mu[k][(int) age]=pmmij[i][j];
     for (i=1; i<=imx; i++)  {            }
       for(m=1; (m<= maxwav); m++){          }
         if (s[m][i] > (nlstate+ndeath)) {          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);              for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
           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);                varpij[i][j][(int)age] = doldm[i][j];
           goto end;  
         }          /*printf("\n%d ",(int)age);
       }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     }            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
 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);  
           fprintf(ficresprob,"\n%d ",(int)age);
     free_vector(severity,1,maxwav);          fprintf(ficresprobcov,"\n%d ",(int)age);
     free_imatrix(outcome,1,maxwav+1,1,n);          fprintf(ficresprobcor,"\n%d ",(int)age);
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     /* free_matrix(mint,1,maxwav,1,n);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
        free_matrix(anint,1,maxwav,1,n);*/          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     free_vector(moisdc,1,n);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     free_vector(andc,1,n);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
              i=0;
     wav=ivector(1,imx);          for (k=1; k<=(nlstate);k++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            for (l=1; l<=(nlstate+ndeath);l++){ 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              i=i++;
                  fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     /* Concatenates waves */              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       Tcode=ivector(1,100);              }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            }
       ncodemax[1]=1;          }/* end of loop for state */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        } /* end of loop for age */
        
    codtab=imatrix(1,100,1,10);        /* Confidence intervalle of pij  */
    h=0;        /*
    m=pow(2,cptcoveff);          fprintf(ficgp,"\nunset parametric;unset label");
            fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
    for(k=1;k<=cptcoveff; k++){          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
      for(i=1; i <=(m/pow(2,k));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);
        for(j=1; j <= ncodemax[k]; j++){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
            h++;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        */
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/  
          }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
        }        first1=1;
      }        for (k2=1; k2<=(nlstate);k2++){
    }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            if(l2==k2) continue;
       codtab[1][2]=1;codtab[2][2]=2; */            j=(k2-1)*(nlstate+ndeath)+l2;
    /* for(i=1; i <=m ;i++){            for (k1=1; k1<=(nlstate);k1++){
       for(k=1; k <=cptcovn; k++){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                if(l1==k1) continue;
       }                i=(k1-1)*(nlstate+ndeath)+l1;
       printf("\n");                if(i<=j) continue;
       }                for (age=bage; age<=fage; age ++){ 
       scanf("%d",i);*/                  if ((int)age %5==0){
                        v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
    /* Calculates basic frequencies. Computes observed prevalence at single age                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
        and prints on file fileres'p'. */                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                        mu2=mu[j][(int) age]/stepm*YEARM;
                        c12=cv12/sqrt(v1*v2);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    /* Computing eigen value of matrix of covariance */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    if ((lc2 <0) || (lc1 <0) ){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                      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);
     /* For Powell, parameters are in a vector p[] starting at p[1]                      lc1=fabs(lc1);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                      lc2=fabs(lc2);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */                    }
   
     if(mle==1){                    /* Eigen vectors */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     }                    /*v21=sqrt(1.-v11*v11); *//* error */
                        v21=(lc1-v1)/cv12*v11;
     /*--------- results files --------------*/                    v12=-v21;
     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);                    v22=v11;
                      tnalp=v21/v11;
                     if(first1==1){
    jk=1;                      first1=0;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\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);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                    }
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                    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);
    for(i=1,jk=1; i <=nlstate; i++){                    /*printf(fignu*/
      for(k=1; k <=(nlstate+ndeath); k++){                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
        if (k != i)                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
          {                    if(first==1){
            printf("%d%d ",i,k);                      first=0;
            fprintf(ficlog,"%d%d ",i,k);                      fprintf(ficgp,"\nset parametric;unset label");
            fprintf(ficres,"%1d%1d ",i,k);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
            for(j=1; j <=ncovmodel; j++){                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
              printf("%f ",p[jk]);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
              fprintf(ficlog,"%f ",p[jk]);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
              fprintf(ficres,"%f ",p[jk]);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
              jk++;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
            }                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
            printf("\n");                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
            fprintf(ficlog,"\n");                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
            fprintf(ficres,"\n");                      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);
      }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
    }                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
    if(mle==1){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
      /* Computing hessian and covariance matrix */                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
      ftolhess=ftol; /* Usually correct */                    }else{
      hesscov(matcov, p, npar, delti, ftolhess, func);                      first=0;
    }                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
    printf("# Scales (for hessian or gradient estimation)\n");                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
    for(i=1,jk=1; i <=nlstate; i++){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
      for(j=1; j <=nlstate+ndeath; j++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
        if (j!=i) {                    }/* if first */
          fprintf(ficres,"%1d%1d",i,j);                  } /* age mod 5 */
          printf("%1d%1d",i,j);                } /* end loop age */
          fprintf(ficlog,"%1d%1d",i,j);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
          for(k=1; k<=ncovmodel;k++){                first=1;
            printf(" %.5e",delti[jk]);              } /*l12 */
            fprintf(ficlog," %.5e",delti[jk]);            } /* k12 */
            fprintf(ficres," %.5e",delti[jk]);          } /*l1 */
            jk++;        }/* k1 */
          }      } /* loop covariates */
          printf("\n");    }
          fprintf(ficlog,"\n");    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
          fprintf(ficres,"\n");    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
        }    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      }    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
    }    free_vector(xp,1,npar);
        fclose(ficresprob);
    k=1;    fclose(ficresprobcov);
    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");    fclose(ficresprobcor);
    if(mle==1)    fflush(ficgp);
      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");    fflush(fichtmcov);
    fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");  }
    for(i=1;i<=npar;i++){  
      /*  if (k>nlstate) k=1;  
          i1=(i-1)/(ncovmodel*nlstate)+1;  /******************* Printing html file ***********/
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
          printf("%s%d%d",alph[k],i1,tab[i]);*/                    int lastpass, int stepm, int weightopt, char model[],\
      fprintf(ficres,"%3d",i);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
      if(mle==1)                    int popforecast, int estepm ,\
        printf("%3d",i);                    double jprev1, double mprev1,double anprev1, \
      fprintf(ficlog,"%3d",i);                    double jprev2, double mprev2,double anprev2){
      for(j=1; j<=i;j++){    int jj1, k1, i1, cpt;
        fprintf(ficres," %.5e",matcov[i][j]);  
        if(mle==1)     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
          printf(" %.5e",matcov[i][j]);     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
        fprintf(ficlog," %.5e",matcov[i][j]);  </ul>");
      }     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
      fprintf(ficres,"\n");   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
      if(mle==1)             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
        printf("\n");     fprintf(fichtm,"\
      fprintf(ficlog,"\n");   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
      k++;             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
    }     fprintf(fichtm,"\
       - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
    while((c=getc(ficpar))=='#' && c!= EOF){             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      ungetc(c,ficpar);     fprintf(fichtm,"\
      fgets(line, MAXLINE, ficpar);   - (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): \
      puts(line);     <a href=\"%s\">%s</a> <br>\n",
      fputs(line,ficparo);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
    }     fprintf(fichtm,"\
    ungetc(c,ficpar);   - Population projections by age and states: \
    estepm=0;     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
    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;  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    if (fage <= 2) {  
      bage = ageminpar;   m=cptcoveff;
      fage = agemaxpar;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    }  
       jj1=0;
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");   for(k1=1; k1<=m;k1++){
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);     for(i1=1; i1<=ncodemax[k1];i1++){
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);       jj1++;
           if (cptcovn > 0) {
    while((c=getc(ficpar))=='#' && c!= EOF){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
      ungetc(c,ficpar);         for (cpt=1; cpt<=cptcoveff;cpt++) 
      fgets(line, MAXLINE, ficpar);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
      puts(line);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      fputs(line,ficparo);       }
    }       /* Pij */
    ungetc(c,ficpar);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
    <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);       /* Quasi-incidences */
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   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); 
    while((c=getc(ficpar))=='#' && c!= EOF){         /* Period (stable) prevalence in each health state */
      ungetc(c,ficpar);         for(cpt=1; cpt<nlstate;cpt++){
      fgets(line, MAXLINE, ficpar);           fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
      puts(line);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
      fputs(line,ficparo);         }
    }       for(cpt=1; cpt<=nlstate;cpt++) {
    ungetc(c,ficpar);          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
    <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;     } /* end i1 */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;   }/* End k1 */
    fprintf(fichtm,"</ul>");
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
   fprintf(ficparo,"pop_based=%d\n",popbased);    
   fprintf(ficres,"pop_based=%d\n",popbased);     fprintf(fichtm,"\
    \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
   while((c=getc(ficpar))=='#' && c!= EOF){   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     puts(line);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
     fputs(line,ficparo);   fprintf(fichtm,"\
   }   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   ungetc(c,ficpar);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
   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);   fprintf(fichtm,"\
 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);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
 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);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
 while((c=getc(ficpar))=='#' && c!= EOF){     <a href=\"%s\">%s</a> <br>\n</li>",
     ungetc(c,ficpar);             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
     fgets(line, MAXLINE, ficpar);   fprintf(fichtm,"\
     puts(line);   - (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): \
     fputs(line,ficparo);     <a href=\"%s\">%s</a> <br>\n</li>",
   }             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
   ungetc(c,ficpar);   fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);   fprintf(fichtm,"\
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
 /*------------ gnuplot -------------*/           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".gp");  /*  if(popforecast==1) fprintf(fichtm,"\n */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
     printf("Problem with file %s",optionfilegnuplot);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   }  /*      <br>",fileres,fileres,fileres,fileres); */
   fclose(ficgp);  /*  else  */
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);  /*    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); */
 /*--------- index.htm --------*/   fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");   m=cptcoveff;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }   jj1=0;
    for(k1=1; k1<=m;k1++){
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n     for(i1=1; i1<=ncodemax[k1];i1++){
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n       jj1++;
 \n       if (cptcovn > 0) {
 Total number of observations=%d <br>\n         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n         for (cpt=1; cpt<=cptcoveff;cpt++) 
 <hr  size=\"2\" color=\"#EC5E5E\">           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
  <ul><li><h4>Parameter files</h4>\n         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
  - 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(cpt=1; cpt<=nlstate;cpt++) {
  - 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(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   fclose(fichtm);  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);  
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);       }
         fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 /*------------ free_vector  -------------*/  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
  chdir(path);  true period expectancies (those weighted with period prevalences are also\
     drawn in addition to the population based expectancies computed using\
  free_ivector(wav,1,imx);   observed and cahotic prevalences: %s%d.png<br>\
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);       } /* end i1 */
  free_ivector(num,1,n);   }/* End k1 */
  free_vector(agedc,1,n);   fprintf(fichtm,"</ul>");
  /*free_matrix(covar,1,NCOVMAX,1,n);*/   fflush(fichtm);
  fclose(ficparo);  }
  fclose(ficres);  
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   /*--------------- Prevalence limit --------------*/  
      char dirfileres[132],optfileres[132];
   strcpy(filerespl,"pl");    int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   strcat(filerespl,fileres);    int ng=0;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  /*     printf("Problem with file %s",optionfilegnuplot); */
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   }  /*   } */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);    /*#ifdef windows */
   fprintf(ficrespl,"#Prevalence limit\n");    fprintf(ficgp,"cd \"%s\" \n",pathc);
   fprintf(ficrespl,"#Age ");      /*#endif */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    m=pow(2,cptcoveff);
   fprintf(ficrespl,"\n");  
      strcpy(dirfileres,optionfilefiname);
   prlim=matrix(1,nlstate,1,nlstate);    strcpy(optfileres,"vpl");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   /* 1eme*/
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (cpt=1; cpt<= nlstate ; cpt ++) {
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     for (k1=1; k1<= m ; k1 ++) {
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   k=0;       fprintf(ficgp,"set xlabel \"Age\" \n\
   agebase=ageminpar;  set ylabel \"Probability\" \n\
   agelim=agemaxpar;  set ter png small\n\
   ftolpl=1.e-10;  set size 0.65,0.65\n\
   i1=cptcoveff;  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   if (cptcovn < 1){i1=1;}  
        for (i=1; i<= nlstate ; i ++) {
   for(cptcov=1;cptcov<=i1;cptcov++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         else        fprintf(ficgp," \%%*lf (\%%*lf)");
         k=k+1;       }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/       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);
         fprintf(ficrespl,"\n#******");       for (i=1; i<= nlstate ; i ++) {
         printf("\n#******");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficlog,"\n#******");         else fprintf(ficgp," \%%*lf (\%%*lf)");
         for(j=1;j<=cptcoveff;j++) {       } 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       for (i=1; i<= nlstate ; i ++) {
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         }         else fprintf(ficgp," \%%*lf (\%%*lf)");
         fprintf(ficrespl,"******\n");       }  
         printf("******\n");       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
         fprintf(ficlog,"******\n");     }
            }
         for (age=agebase; age<=agelim; age++){    /*2 eme*/
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    
           fprintf(ficrespl,"%.0f",age );    for (k1=1; k1<= m ; k1 ++) { 
           for(i=1; i<=nlstate;i++)      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
           fprintf(ficrespl," %.5f", prlim[i][i]);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
           fprintf(ficrespl,"\n");      
         }      for (i=1; i<= nlstate+1 ; i ++) {
       }        k=2*i;
     }        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   fclose(ficrespl);        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   /*------------- h Pij x at various ages ------------*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;        for (j=1; j<= nlstate+1 ; j ++) {
   }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   printf("Computing pij: result on file '%s' \n", filerespij);          else fprintf(ficgp," \%%*lf (\%%*lf)");
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);        }   
          fprintf(ficgp,"\" t\"\" w l 0,");
   stepsize=(int) (stepm+YEARM-1)/YEARM;        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   /*if (stepm<=24) stepsize=2;*/        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   agelim=AGESUP;          else fprintf(ficgp," \%%*lf (\%%*lf)");
   hstepm=stepsize*YEARM; /* Every year of age */        }   
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
   /* hstepm=1;   aff par mois*/      }
     }
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    /*3eme*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    for (k1=1; k1<= m ; k1 ++) { 
         fprintf(ficrespij,"\n#****** ");      for (cpt=1; cpt<= nlstate ; cpt ++) {
         for(j=1;j<=cptcoveff;j++)        /*       k=2+nlstate*(2*cpt-2); */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        k=2+(nlstate+1)*(cpt-1);
         fprintf(ficrespij,"******\n");        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
                fprintf(ficgp,"set ter png small\n\
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  set size 0.65,0.65\n\
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           /*      nhstepm=nhstepm*YEARM; aff par mois*/          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           oldm=oldms;savm=savms;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            
           fprintf(ficrespij,"# Age");        */
           for(i=1; i<=nlstate;i++)        for (i=1; i< nlstate ; i ++) {
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
               fprintf(ficrespij," %1d-%1d",i,j);          /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           fprintf(ficrespij,"\n");          
            for (h=0; h<=nhstepm; h++){        } 
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
             for(i=1; i<=nlstate;i++)      }
               for(j=1; j<=nlstate+ndeath;j++)    }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    
             fprintf(ficrespij,"\n");    /* CV preval stable (period) */
              }    for (k1=1; k1<= m ; k1 ++) { 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (cpt=1; cpt<=nlstate ; cpt ++) {
           fprintf(ficrespij,"\n");        k=3;
         }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
     }        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   }  set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
   fclose(ficrespij);        for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   /*---------- Forecasting ------------------*/        
   if((stepm == 1) && (strcmp(model,".")==0)){        l=3+(nlstate+ndeath)*cpt;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        for (i=1; i< nlstate ; i ++) {
   }          l=3+(nlstate+ndeath)*cpt;
   else{          fprintf(ficgp,"+$%d",l+i+1);
     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(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     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);      } 
   }    }  
      
     /* proba elementaires */
   /*---------- Health expectancies and variances ------------*/    for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
   strcpy(filerest,"t");        if (k != i) {
   strcat(filerest,fileres);          for(j=1; j <=ncovmodel; j++){
   if((ficrest=fopen(filerest,"w"))==NULL) {            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            jk++; 
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;            fprintf(ficgp,"\n");
   }          }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        }
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);      }
      }
   
   strcpy(filerese,"e");     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   strcat(filerese,fileres);       for(jk=1; jk <=m; jk++) {
   if((ficreseij=fopen(filerese,"w"))==NULL) {         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);         if (ng==2)
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   }         else
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);           fprintf(ficgp,"\nset title \"Probability\"\n");
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
   strcpy(fileresv,"v");         for(k2=1; k2<=nlstate; k2++) {
   strcat(fileresv,fileres);           k3=i;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {           for(k=1; k<=(nlstate+ndeath); k++) {
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);             if (k != k2){
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);               if(ng==2)
   }                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);               else
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   calagedate=-1;               ij=1;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);               for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   k=0;                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   for(cptcov=1;cptcov<=i1;cptcov++){                   ij++;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                 }
       k=k+1;                 else
       fprintf(ficrest,"\n#****** ");                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       for(j=1;j<=cptcoveff;j++)               }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);               fprintf(ficgp,")/(1");
       fprintf(ficrest,"******\n");               
                for(k1=1; k1 <=nlstate; k1++){   
       fprintf(ficreseij,"\n#****** ");                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       for(j=1;j<=cptcoveff;j++)                 ij=1;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                 for(j=3; j <=ncovmodel; j++){
       fprintf(ficreseij,"******\n");                   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]]]);
       fprintf(ficresvij,"\n#****** ");                     ij++;
       for(j=1;j<=cptcoveff;j++)                   }
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                   else
       fprintf(ficresvij,"******\n");                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                 fprintf(ficgp,")");
       oldm=oldms;savm=savms;               }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);                 fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                 if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);               i=i+ncovmodel;
       oldm=oldms;savm=savms;             }
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);           } /* end k */
       if(popbased==1){         } /* end k2 */
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);       } /* end jk */
        }     } /* end ng */
      fflush(ficgp); 
    }  /* end gnuplot */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");  /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){    int i, cpt, cptcod;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    int modcovmax =1;
         if (popbased==1) {    int mobilavrange, mob;
           for(i=1; i<=nlstate;i++)    double age;
             prlim[i][i]=probs[(int)age][i][k];  
         }    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                                     a covariate has 2 modalities */
         fprintf(ficrest," %4.0f",age);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      if(mobilav==1) mobilavrange=5; /* default */
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      else mobilavrange=mobilav;
           }      for (age=bage; age<=fage; age++)
           epj[nlstate+1] +=epj[j];        for (i=1; i<=nlstate;i++)
         }          for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
         for(i=1, vepp=0.;i <=nlstate;i++)      /* We keep the original values on the extreme ages bage, fage and for 
           for(j=1;j <=nlstate;j++)         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
             vepp += vareij[i][j][(int)age];         we use a 5 terms etc. until the borders are no more concerned. 
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));      */ 
         for(j=1;j <=nlstate;j++){      for (mob=3;mob <=mobilavrange;mob=mob+2){
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
         }          for (i=1; i<=nlstate;i++){
         fprintf(ficrest,"\n");            for (cptcod=1;cptcod<=modcovmax;cptcod++){
       }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
     }                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
 free_matrix(mint,1,maxwav,1,n);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                }
     free_vector(weight,1,n);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   fclose(ficreseij);            }
   fclose(ficresvij);          }
   fclose(ficrest);        }/* end age */
   fclose(ficpar);      }/* end mob */
   free_vector(epj,1,nlstate+1);    }else return -1;
      return 0;
   /*------- Variance limit prevalence------*/    }/* End movingaverage */
   
   strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);  /************** Forecasting ******************/
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  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){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    /* proj1, year, month, day of starting projection 
     exit(0);       agemin, agemax range of age
   }       dateprev1 dateprev2 range of dates during which prevalence is computed
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);       anproj2 year of en of projection (same day and month as proj1).
     */
   k=0;    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   for(cptcov=1;cptcov<=i1;cptcov++){    int *popage;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double agec; /* generic age */
       k=k+1;    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
       fprintf(ficresvpl,"\n#****** ");    double *popeffectif,*popcount;
       for(j=1;j<=cptcoveff;j++)    double ***p3mat;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ***mobaverage;
       fprintf(ficresvpl,"******\n");    char fileresf[FILENAMELENGTH];
        
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    agelim=AGESUP;
       oldm=oldms;savm=savms;    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);   
     }    strcpy(fileresf,"f"); 
  }    strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
   fclose(ficresvpl);      printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   /*---------- End : free ----------------*/    }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    printf("Computing forecasting: result on file '%s' \n", fileresf);
      fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
    
      if (mobilav!=0) {
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        }
   free_matrix(matcov,1,npar,1,npar);    }
   free_vector(delti,1,npar);  
   free_matrix(agev,1,maxwav,1,imx);    stepsize=(int) (stepm+YEARM-1)/YEARM;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    if (stepm<=12) stepsize=1;
     if(estepm < stepm){
   fprintf(fichtm,"\n</body>");      printf ("Problem %d lower than %d\n",estepm, stepm);
   fclose(fichtm);    }
   fclose(ficgp);    else  hstepm=estepm;   
    
     hstepm=hstepm/stepm; 
   if(erreur >0){    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
     printf("End of Imach with error or warning %d\n",erreur);                                 fractional in yp1 */
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);    anprojmean=yp;
   }else{    yp2=modf((yp1*12),&yp);
    printf("End of Imach\n");    mprojmean=yp;
    fprintf(ficlog,"End of Imach\n");    yp1=modf((yp2*30.5),&yp);
   }    jprojmean=yp;
   printf("See log file on %s\n",filelog);    if(jprojmean==0) jprojmean=1;
   fclose(ficlog);    if(mprojmean==0) jprojmean=1;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
      i1=cptcoveff;
   /* 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);*/    if (cptcovn < 1){i1=1;}
   /*printf("Total time was %d uSec.\n", total_usecs);*/    
   /*------ End -----------*/    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
  end:  
 #ifdef windows  /*            if (h==(int)(YEARM*yearp)){ */
   /* chdir(pathcd);*/    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
 #endif      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
  /*system("wgnuplot graph.plt");*/        k=k+1;
  /*system("../gp37mgw/wgnuplot graph.plt");*/        fprintf(ficresf,"\n#******");
  /*system("cd ../gp37mgw");*/        for(j=1;j<=cptcoveff;j++) {
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          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]]);
  strcpy(plotcmd,GNUPLOTPROGRAM);        }
  strcat(plotcmd," ");        fprintf(ficresf,"******\n");
  strcat(plotcmd,optionfilegnuplot);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
  system(plotcmd);        for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
 #ifdef windows            fprintf(ficresf," p%d%d",i,j);
   while (z[0] != 'q') {          fprintf(ficresf," p.%d",j);
     /* chdir(path); */        }
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     scanf("%s",z);          fprintf(ficresf,"\n");
     if (z[0] == 'c') system("./imach");          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
     else if (z[0] == 'e') system(optionfilehtm);  
     else if (z[0] == 'g') system(plotcmd);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
     else if (z[0] == 'q') exit(0);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
   }            nhstepm = nhstepm/hstepm; 
 #endif            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 }            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\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 (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for(k=cptcovn; k>=1;k--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 
                                       */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
           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);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
             Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
             Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
             k1++;
             k2=k2+2;
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutv(strd,strc,strb,'V');
           Tvar[k]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     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); /* hard coded ? */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,15); 
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2); /* For V3*V2 Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     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.1.52  
changed lines
  Added in v.1.139


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