Diff for /imach/src/imach.c between versions 1.52 and 1.143

version 1.52, 2002/07/19 18:49:30 version 1.143, 2014/01/26 09:45:38
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.143  2014/01/26 09:45:38  brouard
      Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   first survey ("cross") where individuals from different ages are    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.142  2014/01/26 03:57:36  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.141  2014/01/26 02:42:01  brouard
   simplest model is the multinomial logistic model where pij is the    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.140  2011/09/02 10:37:54  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: times.h is ok with mingw32 now.
   '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 1.139  2010/06/14 07:50:17  brouard
   where the markup *Covariates have to be included here again* invites    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   you to do it.  More covariates you add, slower the    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   convergence.  
     Revision 1.138  2010/04/30 18:19:40  brouard
   The advantage of this computer programme, compared to a simple    *** empty log message ***
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.137  2010/04/29 18:11:38  brouard
   intermediate interview, the information is lost, but taken into    (Module): Checking covariates for more complex models
   account using an interpolation or extrapolation.      than V1+V2. A lot of change to be done. Unstable.
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.136  2010/04/26 20:30:53  brouard
   conditional to the observed state i at age x. The delay 'h' can be    (Module): merging some libgsl code. Fixing computation
   split into an exact number (nh*stepm) of unobserved intermediate    of likelione (using inter/intrapolation if mle = 0) in order to
   states. This elementary transition (by month or quarter trimester,    get same likelihood as if mle=1.
   semester or year) is model as a multinomial logistic.  The hPx    Some cleaning of code and comments added.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.135  2009/10/29 15:33:14  brouard
   hPijx.    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.134  2009/10/29 13:18:53  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.133  2009/07/06 10:21:25  brouard
            Institut national d'études démographiques, Paris.    just nforces
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.132  2009/07/06 08:22:05  brouard
   It is copyrighted identically to a GNU software product, ie programme and    Many tings
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.131  2009/06/20 16:22:47  brouard
   **********************************************************************/    Some dimensions resccaled
    
 #include <math.h>    Revision 1.130  2009/05/26 06:44:34  brouard
 #include <stdio.h>    (Module): Max Covariate is now set to 20 instead of 8. A
 #include <stdlib.h>    lot of cleaning with variables initialized to 0. Trying to make
 #include <unistd.h>    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
 #define MAXLINE 256    Revision 1.129  2007/08/31 13:49:27  lievre
 #define GNUPLOTPROGRAM "gnuplot"    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.128  2006/06/30 13:02:05  brouard
 /*#define DEBUG*/    (Module): Clarifications on computing e.j
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.127  2006/04/28 18:11:50  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    loop. Now we define nhstepma in the age loop.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
 #define NINTERVMAX 8    and then all the health expectancies with variances or standard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    deviation (needs data from the Hessian matrices) which slows the
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    computation.
 #define NCOVMAX 8 /* Maximum number of covariates */    In the future we should be able to stop the program is only health
 #define MAXN 20000    expectancies and graph are needed without standard deviations.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.126  2006/04/28 17:23:28  brouard
 #define AGEBASE 40    (Module): Yes the sum of survivors was wrong since
 #ifdef windows    imach-114 because nhstepm was no more computed in the age
 #define DIRSEPARATOR '\\'    loop. Now we define nhstepma in the age loop.
 #define ODIRSEPARATOR '/'    Version 0.98h
 #else  
 #define DIRSEPARATOR '/'    Revision 1.125  2006/04/04 15:20:31  lievre
 #define ODIRSEPARATOR '\\'    Errors in calculation of health expectancies. Age was not initialized.
 #endif    Forecasting file added.
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Revision 1.124  2006/03/22 17:13:53  lievre
 int erreur; /* Error number */    Parameters are printed with %lf instead of %f (more numbers after the comma).
 int nvar;    The log-likelihood is printed in the log file
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.123  2006/03/20 10:52:43  brouard
 int nlstate=2; /* Number of live states */    * imach.c (Module): <title> changed, corresponds to .htm file
 int ndeath=1; /* Number of dead states */    name. <head> headers where missing.
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 int *wav; /* Number of waves for this individuual 0 is possible */    otherwise the weight is truncated).
 int maxwav; /* Maxim number of waves */    Modification of warning when the covariates values are not 0 or
 int jmin, jmax; /* min, max spacing between 2 waves */    1.
 int mle, weightopt;    Version 0.98g
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.122  2006/03/20 09:45:41  brouard
 double jmean; /* Mean space between 2 waves */    (Module): Weights can have a decimal point as for
 double **oldm, **newm, **savm; /* Working pointers to matrices */    English (a comma might work with a correct LC_NUMERIC environment,
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    otherwise the weight is truncated).
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Modification of warning when the covariates values are not 0 or
 FILE *ficlog;    1.
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    Version 0.98g
 FILE *ficresprobmorprev;  
 FILE *fichtm; /* Html File */    Revision 1.121  2006/03/16 17:45:01  lievre
 FILE *ficreseij;    * imach.c (Module): Comments concerning covariates added
 char filerese[FILENAMELENGTH];  
 FILE  *ficresvij;    * imach.c (Module): refinements in the computation of lli if
 char fileresv[FILENAMELENGTH];    status=-2 in order to have more reliable computation if stepm is
 FILE  *ficresvpl;    not 1 month. Version 0.98f
 char fileresvpl[FILENAMELENGTH];  
 char title[MAXLINE];    Revision 1.120  2006/03/16 15:10:38  lievre
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    (Module): refinements in the computation of lli if
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
 char filelog[FILENAMELENGTH]; /* Log file */    Revision 1.119  2006/03/15 17:42:26  brouard
 char filerest[FILENAMELENGTH];    (Module): Bug if status = -2, the loglikelihood was
 char fileregp[FILENAMELENGTH];    computed as likelihood omitting the logarithm. Version O.98e
 char popfile[FILENAMELENGTH];  
     Revision 1.118  2006/03/14 18:20:07  brouard
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 #define NR_END 1    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define FREE_ARG char*    (Module): Function pstamp added
 #define FTOL 1.0e-10    (Module): Version 0.98d
   
 #define NRANSI    Revision 1.117  2006/03/14 17:16:22  brouard
 #define ITMAX 200    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 #define TOL 2.0e-4    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 #define CGOLD 0.3819660    (Module): Version 0.98d
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.116  2006/03/06 10:29:27  brouard
     (Module): Variance-covariance wrong links and
 #define GOLD 1.618034    varian-covariance of ej. is needed (Saito).
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.114  2006/02/26 12:57:58  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Some improvements in processing parameter
      filename with strsep.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 static double sqrarg;    datafile was not closed, some imatrix were not freed and on matrix
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    allocation too.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.112  2006/01/30 09:55:26  brouard
 int imx;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 int estepm;    (Module): Comments can be added in data file. Missing date values
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    can be a simple dot '.'.
   
 int m,nb;    Revision 1.110  2006/01/25 00:51:50  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): Lots of cleaning and bugs added (Gompertz)
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.109  2006/01/24 19:37:15  brouard
 double dateintmean=0;    (Module): Comments (lines starting with a #) are allowed in data.
   
 double *weight;    Revision 1.108  2006/01/19 18:05:42  lievre
 int **s; /* Status */    Gnuplot problem appeared...
 double *agedc, **covar, idx;    To be fixed
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.107  2006/01/19 16:20:37  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Test existence of gnuplot in imach path
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.106  2006/01/19 13:24:36  brouard
 /**************** split *************************/    Some cleaning and links added in html output
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.105  2006/01/05 20:23:19  lievre
    char *s;                             /* pointer */    *** empty log message ***
    int  l1, l2;                         /* length counters */  
     Revision 1.104  2005/09/30 16:11:43  lievre
    l1 = strlen( path );                 /* length of path */    (Module): sump fixed, loop imx fixed, and simplifications.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): If the status is missing at the last wave but we know
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    that the person is alive, then we can code his/her status as -2
    if ( s == NULL ) {                   /* no directory, so use current */    (instead of missing=-1 in earlier versions) and his/her
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    contributions to the likelihood is 1 - Prob of dying from last
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #if     defined(__bsd__)                /* get current working directory */    the healthy state at last known wave). Version is 0.98
       extern char       *getwd( );  
     Revision 1.103  2005/09/30 15:54:49  lievre
       if ( getwd( dirc ) == NULL ) {    (Module): sump fixed, loop imx fixed, and simplifications.
 #else  
       extern char       *getcwd( );    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.101  2004/09/15 10:38:38  brouard
          return( GLOCK_ERROR_GETCWD );    Fix on curr_time
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.100  2004/07/12 18:29:06  brouard
    } else {                             /* strip direcotry from path */    Add version for Mac OS X. Just define UNIX in Makefile
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.99  2004/06/05 08:57:40  brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    *** empty log message ***
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.98  2004/05/16 15:05:56  brouard
       dirc[l1-l2] = 0;                  /* add zero */    New version 0.97 . First attempt to estimate force of mortality
    }    directly from the data i.e. without the need of knowing the health
    l1 = strlen( dirc );                 /* length of directory */    state at each age, but using a Gompertz model: log u =a + b*age .
 #ifdef windows    This is the basic analysis of mortality and should be done before any
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    other analysis, in order to test if the mortality estimated from the
 #else    cross-longitudinal survey is different from the mortality estimated
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    from other sources like vital statistic data.
 #endif  
    s = strrchr( name, '.' );            /* find last / */    The same imach parameter file can be used but the option for mle should be -3.
    s++;  
    strcpy(ext,s);                       /* save extension */    Agnès, who wrote this part of the code, tried to keep most of the
    l1= strlen( name);    former routines in order to include the new code within the former code.
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    The output is very simple: only an estimate of the intercept and of
    finame[l1-l2]= 0;    the slope with 95% confident intervals.
    return( 0 );                         /* we're done */  
 }    Current limitations:
     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.
 /******************************************/    B) There is no computation of Life Expectancy nor Life Table.
   
 void replace(char *s, char*t)    Revision 1.97  2004/02/20 13:25:42  lievre
 {    Version 0.96d. Population forecasting command line is (temporarily)
   int i;    suppressed.
   int lg=20;  
   i=0;    Revision 1.96  2003/07/15 15:38:55  brouard
   lg=strlen(t);    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   for(i=0; i<= lg; i++) {    rewritten within the same printf. Workaround: many printfs.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.95  2003/07/08 07:54:34  brouard
   }    * imach.c (Repository):
 }    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
 int nbocc(char *s, char occ)  
 {    Revision 1.94  2003/06/27 13:00:02  brouard
   int i,j=0;    Just cleaning
   int lg=20;  
   i=0;    Revision 1.93  2003/06/25 16:33:55  brouard
   lg=strlen(s);    (Module): On windows (cygwin) function asctime_r doesn't
   for(i=0; i<= lg; i++) {    exist so I changed back to asctime which exists.
   if  (s[i] == occ ) j++;    (Module): Version 0.96b
   }  
   return j;    Revision 1.92  2003/06/25 16:30:45  brouard
 }    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.91  2003/06/25 15:30:29  brouard
   /* cuts string t into u and v where u is ended by char occ excluding it    * imach.c (Repository): Duplicated warning errors corrected.
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    (Repository): Elapsed time after each iteration is now output. It
      gives u="abcedf" and v="ghi2j" */    helps to forecast when convergence will be reached. Elapsed time
   int i,lg,j,p=0;    is stamped in powell.  We created a new html file for the graphs
   i=0;    concerning matrix of covariance. It has extension -cov.htm.
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.90  2003/06/24 12:34:15  brouard
   }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
   lg=strlen(t);    of the covariance matrix to be input.
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Revision 1.89  2003/06/24 12:30:52  brouard
   }    (Module): Some bugs corrected for windows. Also, when
      u[p]='\0';    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.88  2003/06/23 17:54:56  brouard
   }    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 }  
     Revision 1.87  2003/06/18 12:26:01  brouard
 /********************** nrerror ********************/    Version 0.96
   
 void nrerror(char error_text[])    Revision 1.86  2003/06/17 20:04:08  brouard
 {    (Module): Change position of html and gnuplot routines and added
   fprintf(stderr,"ERREUR ...\n");    routine fileappend.
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Revision 1.85  2003/06/17 13:12:43  brouard
 }    * imach.c (Repository): Check when date of death was earlier that
 /*********************** vector *******************/    current date of interview. It may happen when the death was just
 double *vector(int nl, int nh)    prior to the death. In this case, dh was negative and likelihood
 {    was wrong (infinity). We still send an "Error" but patch by
   double *v;    assuming that the date of death was just one stepm after the
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    interview.
   if (!v) nrerror("allocation failure in vector");    (Repository): Because some people have very long ID (first column)
   return v-nl+NR_END;    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)
 /************************ free vector ******************/    (Repository): No more line truncation errors.
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.84  2003/06/13 21:44:43  brouard
   free((FREE_ARG)(v+nl-NR_END));    * imach.c (Repository): Replace "freqsummary" at a correct
 }    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 /************************ivector *******************************/    parcimony.
 int *ivector(long nl,long nh)    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 {  
   int *v;    Revision 1.83  2003/06/10 13:39:11  lievre
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    *** empty log message ***
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    Revision 1.82  2003/06/05 15:57:20  brouard
 }    Add log in  imach.c and  fullversion number is now printed.
   
 /******************free ivector **************************/  */
 void free_ivector(int *v, long nl, long nh)  /*
 {     Interpolated Markov Chain
   free((FREE_ARG)(v+nl-NR_END));  
 }    Short summary of the programme:
     
 /******************* imatrix *******************************/    This program computes Healthy Life Expectancies from
 int **imatrix(long nrl, long nrh, long ncl, long nch)    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    first survey ("cross") where individuals from different ages are
 {    interviewed on their health status or degree of disability (in the
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    case of a health survey which is our main interest) -2- at least a
   int **m;    second wave of interviews ("longitudinal") which measure each change
      (if any) in individual health status.  Health expectancies are
   /* allocate pointers to rows */    computed from the time spent in each health state according to a
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    model. More health states you consider, more time is necessary to reach the
   if (!m) nrerror("allocation failure 1 in matrix()");    Maximum Likelihood of the parameters involved in the model.  The
   m += NR_END;    simplest model is the multinomial logistic model where pij is the
   m -= nrl;    probability to be observed in state j at the second wave
      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
   /* allocate rows and set pointers to them */    'age' is age and 'sex' is a covariate. If you want to have a more
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    complex model than "constant and age", you should modify the program
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    where the markup *Covariates have to be included here again* invites
   m[nrl] += NR_END;    you to do it.  More covariates you add, slower the
   m[nrl] -= ncl;    convergence.
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    The advantage of this computer programme, compared to a simple
      multinomial logistic model, is clear when the delay between waves is not
   /* return pointer to array of pointers to rows */    identical for each individual. Also, if a individual missed an
   return m;    intermediate interview, the information is lost, but taken into
 }    account using an interpolation or extrapolation.  
   
 /****************** free_imatrix *************************/    hPijx is the probability to be observed in state i at age x+h
 void free_imatrix(m,nrl,nrh,ncl,nch)    conditional to the observed state i at age x. The delay 'h' can be
       int **m;    split into an exact number (nh*stepm) of unobserved intermediate
       long nch,ncl,nrh,nrl;    states. This elementary transition (by month, quarter,
      /* free an int matrix allocated by imatrix() */    semester or year) is modelled as a multinomial logistic.  The hPx
 {    matrix is simply the matrix product of nh*stepm elementary matrices
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    and the contribution of each individual to the likelihood is simply
   free((FREE_ARG) (m+nrl-NR_END));    hPijx.
 }  
     Also this programme outputs the covariance matrix of the parameters but also
 /******************* matrix *******************************/    of the life expectancies. It also computes the period (stable) prevalence. 
 double **matrix(long nrl, long nrh, long ncl, long nch)    
 {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;             Institut national d'études démographiques, Paris.
   double **m;    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    It is copyrighted identically to a GNU software product, ie programme and
   if (!m) nrerror("allocation failure 1 in matrix()");    software can be distributed freely for non commercial use. Latest version
   m += NR_END;    can be accessed at http://euroreves.ined.fr/imach .
   m -= nrl;  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    **********************************************************************/
   m[nrl] -= ncl;  /*
     main
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    read parameterfile
   return m;    read datafile
 }    concatwav
     freqsummary
 /*************************free matrix ************************/    if (mle >= 1)
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)      mlikeli
 {    print results files
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if mle==1 
   free((FREE_ARG)(m+nrl-NR_END));       computes hessian
 }    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 /******************* ma3x *******************************/    open gnuplot file
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    open html file
 {    period (stable) prevalence
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;     for age prevalim()
   double ***m;    h Pij x
     variance of p varprob
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    forecasting if prevfcast==1 prevforecast call prevalence()
   if (!m) nrerror("allocation failure 1 in matrix()");    health expectancies
   m += NR_END;    Variance-covariance of DFLE
   m -= nrl;    prevalence()
      movingaverage()
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    varevsij() 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if popbased==1 varevsij(,popbased)
   m[nrl] += NR_END;    total life expectancies
   m[nrl] -= ncl;    Variance of period (stable) prevalence
    end
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  */
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;   
   m[nrl][ncl] -= nll;  #include <math.h>
   for (j=ncl+1; j<=nch; j++)  #include <stdio.h>
     m[nrl][j]=m[nrl][j-1]+nlay;  #include <stdlib.h>
    #include <string.h>
   for (i=nrl+1; i<=nrh; i++) {  #include <unistd.h>
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  #include <limits.h>
       m[i][j]=m[i][j-1]+nlay;  #include <sys/types.h>
   }  #include <sys/stat.h>
   return m;  #include <errno.h>
 }  extern int errno;
   
 /*************************free ma3x ************************/  #ifdef LINUX
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #include <time.h>
 {  #include "timeval.h"
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #else
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #include <sys/time.h>
   free((FREE_ARG)(m+nrl-NR_END));  #endif
 }  
   #ifdef GSL
 /***************** f1dim *************************/  #include <gsl/gsl_errno.h>
 extern int ncom;  #include <gsl/gsl_multimin.h>
 extern double *pcom,*xicom;  #endif
 extern double (*nrfunc)(double []);  
    /* #include <libintl.h> */
 double f1dim(double x)  /* #define _(String) gettext (String) */
 {  
   int j;  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   double f;  
   double *xt;  #define GNUPLOTPROGRAM "gnuplot"
    /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   xt=vector(1,ncom);  #define FILENAMELENGTH 132
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   free_vector(xt,1,ncom);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   return f;  
 }  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   int iter;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   double a,b,d,etemp;  #define NCOVMAX 20 /* Maximum number of covariates */
   double fu,fv,fw,fx;  #define MAXN 20000
   double ftemp;  #define YEARM 12. /* Number of months per year */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define AGESUP 130
   double e=0.0;  #define AGEBASE 40
    #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   a=(ax < cx ? ax : cx);  #ifdef UNIX
   b=(ax > cx ? ax : cx);  #define DIRSEPARATOR '/'
   x=w=v=bx;  #define CHARSEPARATOR "/"
   fw=fv=fx=(*f)(x);  #define ODIRSEPARATOR '\\'
   for (iter=1;iter<=ITMAX;iter++) {  #else
     xm=0.5*(a+b);  #define DIRSEPARATOR '\\'
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #define CHARSEPARATOR "\\"
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #define ODIRSEPARATOR '/'
     printf(".");fflush(stdout);  #endif
     fprintf(ficlog,".");fflush(ficlog);  
 #ifdef DEBUG  /* $Id$ */
     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);  /* $State$ */
     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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 #endif  char fullversion[]="$Revision$ $Date$"; 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  char strstart[80];
       *xmin=x;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       return fx;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     }  int nvar=0, nforce=0; /* Number of variables, number of forces */
     ftemp=fu;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
     if (fabs(e) > tol1) {  int npar=NPARMAX;
       r=(x-w)*(fx-fv);  int nlstate=2; /* Number of live states */
       q=(x-v)*(fx-fw);  int ndeath=1; /* Number of dead states */
       p=(x-v)*q-(x-w)*r;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       q=2.0*(q-r);  int popbased=0;
       if (q > 0.0) p = -p;  
       q=fabs(q);  int *wav; /* Number of waves for this individuual 0 is possible */
       etemp=e;  int maxwav=0; /* Maxim number of waves */
       e=d;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       else {                     to the likelihood and the sum of weights (done by funcone)*/
         d=p/q;  int mle=1, weightopt=0;
         u=x+d;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
         if (u-a < tol2 || b-u < tol2)  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
           d=SIGN(tol1,xm-x);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     } else {  double jmean=1; /* Mean space between 2 waves */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  double **oldm, **newm, **savm; /* Working pointers to matrices */
     }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /*FILE *fic ; */ /* Used in readdata only */
     fu=(*f)(u);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     if (fu <= fx) {  FILE *ficlog, *ficrespow;
       if (u >= x) a=x; else b=x;  int globpr=0; /* Global variable for printing or not */
       SHFT(v,w,x,u)  double fretone; /* Only one call to likelihood */
         SHFT(fv,fw,fx,fu)  long ipmx=0; /* Number of contributions */
         } else {  double sw; /* Sum of weights */
           if (u < x) a=u; else b=u;  char filerespow[FILENAMELENGTH];
           if (fu <= fw || w == x) {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
             v=w;  FILE *ficresilk;
             w=u;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
             fv=fw;  FILE *ficresprobmorprev;
             fw=fu;  FILE *fichtm, *fichtmcov; /* Html File */
           } else if (fu <= fv || v == x || v == w) {  FILE *ficreseij;
             v=u;  char filerese[FILENAMELENGTH];
             fv=fu;  FILE *ficresstdeij;
           }  char fileresstde[FILENAMELENGTH];
         }  FILE *ficrescveij;
   }  char filerescve[FILENAMELENGTH];
   nrerror("Too many iterations in brent");  FILE  *ficresvij;
   *xmin=x;  char fileresv[FILENAMELENGTH];
   return fx;  FILE  *ficresvpl;
 }  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 /****************** mnbrak ***********************/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
             double (*func)(double))  char command[FILENAMELENGTH];
 {  int  outcmd=0;
   double ulim,u,r,q, dum;  
   double fu;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    
   *fa=(*func)(*ax);  char filelog[FILENAMELENGTH]; /* Log file */
   *fb=(*func)(*bx);  char filerest[FILENAMELENGTH];
   if (*fb > *fa) {  char fileregp[FILENAMELENGTH];
     SHFT(dum,*ax,*bx,dum)  char popfile[FILENAMELENGTH];
       SHFT(dum,*fb,*fa,dum)  
       }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   while (*fb > *fc) {  struct timezone tzp;
     r=(*bx-*ax)*(*fb-*fc);  extern int gettimeofday();
     q=(*bx-*cx)*(*fb-*fa);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  long time_value;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  extern long time();
     ulim=(*bx)+GLIMIT*(*cx-*bx);  char strcurr[80], strfor[80];
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  char *endptr;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  long lval;
       fu=(*func)(u);  double dval;
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define NR_END 1
           SHFT(*fb,*fc,fu,(*func)(u))  #define FREE_ARG char*
           }  #define FTOL 1.0e-10
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  #define NRANSI 
       fu=(*func)(u);  #define ITMAX 200 
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);  #define TOL 2.0e-4 
       fu=(*func)(u);  
     }  #define CGOLD 0.3819660 
     SHFT(*ax,*bx,*cx,u)  #define ZEPS 1.0e-10 
       SHFT(*fa,*fb,*fc,fu)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       }  
 }  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 /*************** linmin ************************/  #define TINY 1.0e-20 
   
 int ncom;  static double maxarg1,maxarg2;
 double *pcom,*xicom;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 double (*nrfunc)(double []);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 {  #define rint(a) floor(a+0.5)
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  static double sqrarg;
   double f1dim(double x);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
               double *fc, double (*func)(double));  int agegomp= AGEGOMP;
   int j;  
   double xx,xmin,bx,ax;  int imx; 
   double fx,fb,fa;  int stepm=1;
    /* Stepm, step in month: minimum step interpolation*/
   ncom=n;  
   pcom=vector(1,n);  int estepm;
   xicom=vector(1,n);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   nrfunc=func;  
   for (j=1;j<=n;j++) {  int m,nb;
     pcom[j]=p[j];  long *num;
     xicom[j]=xi[j];  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   ax=0.0;  double **pmmij, ***probs;
   xx=1.0;  double *ageexmed,*agecens;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  double dateintmean=0;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  double *weight;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  int **s; /* Status */
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double *agedc;
 #endif  double  **covar; /**< covar[i,j], value of jth covariate for individual i,
   for (j=1;j<=n;j++) {                    * covar=matrix(0,NCOVMAX,1,n); 
     xi[j] *= xmin;                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
     p[j] += xi[j];  double  idx; 
   }  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   free_vector(xicom,1,n);  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   free_vector(pcom,1,n);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 }  double *lsurv, *lpop, *tpop;
   
 /*************** powell ************************/  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  double ftolhess; /**< Tolerance for computing hessian */
             double (*func)(double []))  
 {  /**************** split *************************/
   void linmin(double p[], double xi[], int n, double *fret,  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
               double (*func)(double []));  {
   int i,ibig,j;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double del,t,*pt,*ptt,*xit;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double fp,fptt;    */ 
   double *xits;    char  *ss;                            /* pointer */
   pt=vector(1,n);    int   l1, l2;                         /* length counters */
   ptt=vector(1,n);  
   xit=vector(1,n);    l1 = strlen(path );                   /* length of path */
   xits=vector(1,n);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   *fret=(*func)(p);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   for (j=1;j<=n;j++) pt[j]=p[j];    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   for (*iter=1;;++(*iter)) {      strcpy( name, path );               /* we got the fullname name because no directory */
     fp=(*fret);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     ibig=0;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     del=0.0;      /* get current working directory */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      /*    extern  char* getcwd ( char *buf , int len);*/
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     for (i=1;i<=n;i++)        return( GLOCK_ERROR_GETCWD );
       printf(" %d %.12f",i, p[i]);      }
     fprintf(ficlog," %d %.12f",i, p[i]);      /* got dirc from getcwd*/
     printf("\n");      printf(" DIRC = %s \n",dirc);
     fprintf(ficlog,"\n");    } else {                              /* strip direcotry from path */
     for (i=1;i<=n;i++) {      ss++;                               /* after this, the filename */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      l2 = strlen( ss );                  /* length of filename */
       fptt=(*fret);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 #ifdef DEBUG      strcpy( name, ss );         /* save file name */
       printf("fret=%lf \n",*fret);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       fprintf(ficlog,"fret=%lf \n",*fret);      dirc[l1-l2] = 0;                    /* add zero */
 #endif      printf(" DIRC2 = %s \n",dirc);
       printf("%d",i);fflush(stdout);    }
       fprintf(ficlog,"%d",i);fflush(ficlog);    /* We add a separator at the end of dirc if not exists */
       linmin(p,xit,n,fret,func);    l1 = strlen( dirc );                  /* length of directory */
       if (fabs(fptt-(*fret)) > del) {    if( dirc[l1-1] != DIRSEPARATOR ){
         del=fabs(fptt-(*fret));      dirc[l1] =  DIRSEPARATOR;
         ibig=i;      dirc[l1+1] = 0; 
       }      printf(" DIRC3 = %s \n",dirc);
 #ifdef DEBUG    }
       printf("%d %.12e",i,(*fret));    ss = strrchr( name, '.' );            /* find last / */
       fprintf(ficlog,"%d %.12e",i,(*fret));    if (ss >0){
       for (j=1;j<=n;j++) {      ss++;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      strcpy(ext,ss);                     /* save extension */
         printf(" x(%d)=%.12e",j,xit[j]);      l1= strlen( name);
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);      l2= strlen(ss)+1;
       }      strncpy( finame, name, l1-l2);
       for(j=1;j<=n;j++) {      finame[l1-l2]= 0;
         printf(" p=%.12e",p[j]);    }
         fprintf(ficlog," p=%.12e",p[j]);  
       }    return( 0 );                          /* we're done */
       printf("\n");  }
       fprintf(ficlog,"\n");  
 #endif  
     }  /******************************************/
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  void replace_back_to_slash(char *s, char*t)
       int k[2],l;  {
       k[0]=1;    int i;
       k[1]=-1;    int lg=0;
       printf("Max: %.12e",(*func)(p));    i=0;
       fprintf(ficlog,"Max: %.12e",(*func)(p));    lg=strlen(t);
       for (j=1;j<=n;j++) {    for(i=0; i<= lg; i++) {
         printf(" %.12e",p[j]);      (s[i] = t[i]);
         fprintf(ficlog," %.12e",p[j]);      if (t[i]== '\\') s[i]='/';
       }    }
       printf("\n");  }
       fprintf(ficlog,"\n");  
       for(l=0;l<=1;l++) {  char *trimbb(char *out, char *in)
         for (j=1;j<=n;j++) {  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    char *s;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    s=out;
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    while (*in != '\0'){
         }      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        in++;
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      }
       }      *out++ = *in++;
 #endif    }
     *out='\0';
     return s;
       free_vector(xit,1,n);  }
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  char *cutv(char *blocc, char *alocc, char *in, char occ)
       free_vector(pt,1,n);  {
       return;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     }       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       gives blocc="abcdef2ghi" and alocc="j".
     for (j=1;j<=n;j++) {       If occ is not found blocc is null and alocc is equal to in. Returns alocc
       ptt[j]=2.0*p[j]-pt[j];    */
       xit[j]=p[j]-pt[j];    char *s, *t;
       pt[j]=p[j];    t=in;s=in;
     }    while (*in != '\0'){
     fptt=(*func)(ptt);      while( *in == occ){
     if (fptt < fp) {        *blocc++ = *in++;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        s=in;
       if (t < 0.0) {      }
         linmin(p,xit,n,fret,func);      *blocc++ = *in++;
         for (j=1;j<=n;j++) {    }
           xi[j][ibig]=xi[j][n];    if (s == t) /* occ not found */
           xi[j][n]=xit[j];      *(blocc-(in-s))='\0';
         }    else
 #ifdef DEBUG      *(blocc-(in-s)-1)='\0';
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    in=s;
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    while ( *in != '\0'){
         for(j=1;j<=n;j++){      *alocc++ = *in++;
           printf(" %.12e",xit[j]);    }
           fprintf(ficlog," %.12e",xit[j]);  
         }    *alocc='\0';
         printf("\n");    return s;
         fprintf(ficlog,"\n");  }
 #endif  
       }  int nbocc(char *s, char occ)
     }  {
   }    int i,j=0;
 }    int lg=20;
     i=0;
 /**** Prevalence limit ****************/    lg=strlen(s);
     for(i=0; i<= lg; i++) {
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    if  (s[i] == occ ) j++;
 {    }
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    return j;
      matrix by transitions matrix until convergence is reached */  }
   
   int i, ii,j,k;  /* void cutv(char *u,char *v, char*t, char occ) */
   double min, max, maxmin, maxmax,sumnew=0.;  /* { */
   double **matprod2();  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   double **out, cov[NCOVMAX], **pmij();  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   double **newm;  /*      gives u="abcdef2ghi" and v="j" *\/ */
   double agefin, delaymax=50 ; /* Max number of years to converge */  /*   int i,lg,j,p=0; */
   /*   i=0; */
   for (ii=1;ii<=nlstate+ndeath;ii++)  /*   lg=strlen(t); */
     for (j=1;j<=nlstate+ndeath;j++){  /*   for(j=0; j<=lg-1; j++) { */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
     }  /*   } */
   
    cov[1]=1.;  /*   for(j=0; j<p; j++) { */
    /*     (u[j] = t[j]); */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*   } */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  /*      u[p]='\0'; */
     newm=savm;  
     /* Covariates have to be included here again */  /*    for(j=0; j<= lg; j++) { */
      cov[2]=agefin;  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
    /*   } */
       for (k=1; k<=cptcovn;k++) {  /* } */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  /********************** nrerror ********************/
       }  
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  void nrerror(char error_text[])
       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]]];    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    exit(EXIT_FAILURE);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  }
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  /*********************** vector *******************/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  double *vector(int nl, int nh)
   {
     savm=oldm;    double *v;
     oldm=newm;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     maxmax=0.;    if (!v) nrerror("allocation failure in vector");
     for(j=1;j<=nlstate;j++){    return v-nl+NR_END;
       min=1.;  }
       max=0.;  
       for(i=1; i<=nlstate; i++) {  /************************ free vector ******************/
         sumnew=0;  void free_vector(double*v, int nl, int nh)
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  {
         prlim[i][j]= newm[i][j]/(1-sumnew);    free((FREE_ARG)(v+nl-NR_END));
         max=FMAX(max,prlim[i][j]);  }
         min=FMIN(min,prlim[i][j]);  
       }  /************************ivector *******************************/
       maxmin=max-min;  int *ivector(long nl,long nh)
       maxmax=FMAX(maxmax,maxmin);  {
     }    int *v;
     if(maxmax < ftolpl){    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       return prlim;    if (!v) nrerror("allocation failure in ivector");
     }    return v-nl+NR_END;
   }  }
 }  
   /******************free ivector **************************/
 /*************** transition probabilities ***************/  void free_ivector(int *v, long nl, long nh)
   {
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    free((FREE_ARG)(v+nl-NR_END));
 {  }
   double s1, s2;  
   /*double t34;*/  /************************lvector *******************************/
   int i,j,j1, nc, ii, jj;  long *lvector(long nl,long nh)
   {
     for(i=1; i<= nlstate; i++){    long *v;
     for(j=1; j<i;j++){    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if (!v) nrerror("allocation failure in ivector");
         /*s2 += param[i][j][nc]*cov[nc];*/    return v-nl+NR_END;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  }
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  /******************free lvector **************************/
       ps[i][j]=s2;  void free_lvector(long *v, long nl, long nh)
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  {
     }    free((FREE_ARG)(v+nl-NR_END));
     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];  /******************* imatrix *******************************/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       ps[i][j]=s2;  { 
     }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   }    int **m; 
     /*ps[3][2]=1;*/    
     /* allocate pointers to rows */ 
   for(i=1; i<= nlstate; i++){    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
      s1=0;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     for(j=1; j<i; j++)    m += NR_END; 
       s1+=exp(ps[i][j]);    m -= nrl; 
     for(j=i+1; j<=nlstate+ndeath; j++)    
       s1+=exp(ps[i][j]);    
     ps[i][i]=1./(s1+1.);    /* 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))); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     for(j=i+1; j<=nlstate+ndeath; j++)    m[nrl] += NR_END; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    m[nrl] -= ncl; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    
   } /* end i */    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    /* return pointer to array of pointers to rows */ 
     for(jj=1; jj<= nlstate+ndeath; jj++){    return m; 
       ps[ii][jj]=0;  } 
       ps[ii][ii]=1;  
     }  /****************** free_imatrix *************************/
   }  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
         long nch,ncl,nrh,nrl; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){       /* free an int matrix allocated by imatrix() */ 
     for(jj=1; jj<= nlstate+ndeath; jj++){  { 
      printf("%lf ",ps[ii][jj]);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
    }    free((FREE_ARG) (m+nrl-NR_END)); 
     printf("\n ");  } 
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  /******************* matrix *******************************/
 /*  double **matrix(long nrl, long nrh, long ncl, long nch)
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  {
   goto end;*/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     return ps;    double **m;
 }  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 /**************** Product of 2 matrices ******************/    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    m -= nrl;
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   /* in, b, out are matrice of pointers which should have been initialized    m[nrl] += NR_END;
      before: only the contents of out is modified. The function returns    m[nrl] -= ncl;
      a pointer to pointers identical to out */  
   long i, j, k;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for(i=nrl; i<= nrh; i++)    return m;
     for(k=ncolol; k<=ncoloh; k++)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)     */
         out[i][k] +=in[i][j]*b[j][k];  }
   
   return out;  /*************************free matrix ************************/
 }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 /************* Higher Matrix Product ***************/    free((FREE_ARG)(m+nrl-NR_END));
   }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  /******************* ma3x *******************************/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
      duration (i.e. until  {
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    double ***m;
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      included manually here.    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
      */    m -= nrl;
   
   int i, j, d, h, k;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double **out, cov[NCOVMAX];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double **newm;    m[nrl] += NR_END;
     m[nrl] -= ncl;
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       po[i][j][0]=(i==j ? 1.0 : 0.0);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     }    m[nrl][ncl] += NR_END;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m[nrl][ncl] -= nll;
   for(h=1; h <=nhstepm; h++){    for (j=ncl+1; j<=nch; j++) 
     for(d=1; d <=hstepm; d++){      m[nrl][j]=m[nrl][j-1]+nlay;
       newm=savm;    
       /* Covariates have to be included here again */    for (i=nrl+1; i<=nrh; i++) {
       cov[1]=1.;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      for (j=ncl+1; j<=nch; j++) 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        m[i][j]=m[i][j-1]+nlay;
       for (k=1; k<=cptcovage;k++)    }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    return m; 
       for (k=1; k<=cptcovprod;k++)    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
   }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /*************************free ma3x ************************/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  {
       savm=oldm;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       oldm=newm;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     }    free((FREE_ARG)(m+nrl-NR_END));
     for(i=1; i<=nlstate+ndeath; i++)  }
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  /*************** function subdirf ***********/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  char *subdirf(char fileres[])
          */  {
       }    /* Caution optionfilefiname is hidden */
   } /* end h */    strcpy(tmpout,optionfilefiname);
   return po;    strcat(tmpout,"/"); /* Add to the right */
 }    strcat(tmpout,fileres);
     return tmpout;
   }
 /*************** log-likelihood *************/  
 double func( double *x)  /*************** function subdirf2 ***********/
 {  char *subdirf2(char fileres[], char *preop)
   int i, ii, j, k, mi, d, kk;  {
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    
   double **out;    /* Caution optionfilefiname is hidden */
   double sw; /* Sum of weights */    strcpy(tmpout,optionfilefiname);
   double lli; /* Individual log likelihood */    strcat(tmpout,"/");
   long ipmx;    strcat(tmpout,preop);
   /*extern weight */    strcat(tmpout,fileres);
   /* We are differentiating ll according to initial status */    return tmpout;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  }
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);  /*************** function subdirf3 ***********/
   */  char *subdirf3(char fileres[], char *preop, char *preop2)
   cov[1]=1.;  {
     
   for(k=1; k<=nlstate; k++) ll[k]=0.;    /* Caution optionfilefiname is hidden */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    strcpy(tmpout,optionfilefiname);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    strcat(tmpout,"/");
     for(mi=1; mi<= wav[i]-1; mi++){    strcat(tmpout,preop);
       for (ii=1;ii<=nlstate+ndeath;ii++)    strcat(tmpout,preop2);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    strcat(tmpout,fileres);
       for(d=0; d<dh[mi][i]; d++){    return tmpout;
         newm=savm;  }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  /***************** f1dim *************************/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  extern int ncom; 
         }  extern double *pcom,*xicom;
          extern double (*nrfunc)(double []); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,   
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  double f1dim(double x) 
         savm=oldm;  { 
         oldm=newm;    int j; 
            double f;
            double *xt; 
       } /* end mult */   
          xt=vector(1,ncom); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    f=(*nrfunc)(xt); 
       ipmx +=1;    free_vector(xt,1,ncom); 
       sw += weight[i];    return f; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  } 
     } /* end of wave */  
   } /* end of individual */  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  { 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    int iter; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    double a,b,d,etemp;
   return -l;    double fu,fv,fw,fx;
 }    double ftemp;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
 /*********** Maximum Likelihood Estimation ***************/   
     a=(ax < cx ? ax : cx); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    b=(ax > cx ? ax : cx); 
 {    x=w=v=bx; 
   int i,j, iter;    fw=fv=fx=(*f)(x); 
   double **xi,*delti;    for (iter=1;iter<=ITMAX;iter++) { 
   double fret;      xm=0.5*(a+b); 
   xi=matrix(1,npar,1,npar);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for (i=1;i<=npar;i++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for (j=1;j<=npar;j++)      printf(".");fflush(stdout);
       xi[i][j]=(i==j ? 1.0 : 0.0);      fprintf(ficlog,".");fflush(ficlog);
   printf("Powell\n");  fprintf(ficlog,"Powell\n");  #ifdef DEBUG
   powell(p,xi,npar,ftol,&iter,&fret,func);      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);
       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);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  #endif
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
 }        return fx; 
       } 
 /**** Computes Hessian and covariance matrix ***/      ftemp=fu;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      if (fabs(e) > tol1) { 
 {        r=(x-w)*(fx-fv); 
   double  **a,**y,*x,pd;        q=(x-v)*(fx-fw); 
   double **hess;        p=(x-v)*q-(x-w)*r; 
   int i, j,jk;        q=2.0*(q-r); 
   int *indx;        if (q > 0.0) p = -p; 
         q=fabs(q); 
   double hessii(double p[], double delta, int theta, double delti[]);        etemp=e; 
   double hessij(double p[], double delti[], int i, int j);        e=d; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   void ludcmp(double **a, int npar, int *indx, double *d) ;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
   hess=matrix(1,npar,1,npar);          d=p/q; 
           u=x+d; 
   printf("\nCalculation of the hessian matrix. Wait...\n");          if (u-a < tol2 || b-u < tol2) 
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");            d=SIGN(tol1,xm-x); 
   for (i=1;i<=npar;i++){        } 
     printf("%d",i);fflush(stdout);      } else { 
     fprintf(ficlog,"%d",i);fflush(ficlog);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     hess[i][i]=hessii(p,ftolhess,i,delti);      } 
     /*printf(" %f ",p[i]);*/      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     /*printf(" %lf ",hess[i][i]);*/      fu=(*f)(u); 
   }      if (fu <= fx) { 
          if (u >= x) a=x; else b=x; 
   for (i=1;i<=npar;i++) {        SHFT(v,w,x,u) 
     for (j=1;j<=npar;j++)  {          SHFT(fv,fw,fx,fu) 
       if (j>i) {          } else { 
         printf(".%d%d",i,j);fflush(stdout);            if (u < x) a=u; else b=u; 
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);            if (fu <= fw || w == x) { 
         hess[i][j]=hessij(p,delti,i,j);              v=w; 
         hess[j][i]=hess[i][j];                  w=u; 
         /*printf(" %lf ",hess[i][j]);*/              fv=fw; 
       }              fw=fu; 
     }            } else if (fu <= fv || v == x || v == w) { 
   }              v=u; 
   printf("\n");              fv=fu; 
   fprintf(ficlog,"\n");            } 
           } 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    } 
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    nrerror("Too many iterations in brent"); 
      *xmin=x; 
   a=matrix(1,npar,1,npar);    return fx; 
   y=matrix(1,npar,1,npar);  } 
   x=vector(1,npar);  
   indx=ivector(1,npar);  /****************** mnbrak ***********************/
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   ludcmp(a,npar,indx,&pd);              double (*func)(double)) 
   { 
   for (j=1;j<=npar;j++) {    double ulim,u,r,q, dum;
     for (i=1;i<=npar;i++) x[i]=0;    double fu; 
     x[j]=1;   
     lubksb(a,npar,indx,x);    *fa=(*func)(*ax); 
     for (i=1;i<=npar;i++){    *fb=(*func)(*bx); 
       matcov[i][j]=x[i];    if (*fb > *fa) { 
     }      SHFT(dum,*ax,*bx,dum) 
   }        SHFT(dum,*fb,*fa,dum) 
         } 
   printf("\n#Hessian matrix#\n");    *cx=(*bx)+GOLD*(*bx-*ax); 
   fprintf(ficlog,"\n#Hessian matrix#\n");    *fc=(*func)(*cx); 
   for (i=1;i<=npar;i++) {    while (*fb > *fc) { 
     for (j=1;j<=npar;j++) {      r=(*bx-*ax)*(*fb-*fc); 
       printf("%.3e ",hess[i][j]);      q=(*bx-*cx)*(*fb-*fa); 
       fprintf(ficlog,"%.3e ",hess[i][j]);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     printf("\n");      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     fprintf(ficlog,"\n");      if ((*bx-u)*(u-*cx) > 0.0) { 
   }        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
   /* Recompute Inverse */        fu=(*func)(u); 
   for (i=1;i<=npar;i++)        if (fu < *fc) { 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   ludcmp(a,npar,indx,&pd);            SHFT(*fb,*fc,fu,(*func)(u)) 
             } 
   /*  printf("\n#Hessian matrix recomputed#\n");      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
   for (j=1;j<=npar;j++) {        fu=(*func)(u); 
     for (i=1;i<=npar;i++) x[i]=0;      } else { 
     x[j]=1;        u=(*cx)+GOLD*(*cx-*bx); 
     lubksb(a,npar,indx,x);        fu=(*func)(u); 
     for (i=1;i<=npar;i++){      } 
       y[i][j]=x[i];      SHFT(*ax,*bx,*cx,u) 
       printf("%.3e ",y[i][j]);        SHFT(*fa,*fb,*fc,fu) 
       fprintf(ficlog,"%.3e ",y[i][j]);        } 
     }  } 
     printf("\n");  
     fprintf(ficlog,"\n");  /*************** linmin ************************/
   }  
   */  int ncom; 
   double *pcom,*xicom;
   free_matrix(a,1,npar,1,npar);  double (*nrfunc)(double []); 
   free_matrix(y,1,npar,1,npar);   
   free_vector(x,1,npar);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   free_ivector(indx,1,npar);  { 
   free_matrix(hess,1,npar,1,npar);    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
 }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
 /*************** hessian matrix ****************/    int j; 
 double hessii( double x[], double delta, int theta, double delti[])    double xx,xmin,bx,ax; 
 {    double fx,fb,fa;
   int i;   
   int l=1, lmax=20;    ncom=n; 
   double k1,k2;    pcom=vector(1,n); 
   double p2[NPARMAX+1];    xicom=vector(1,n); 
   double res;    nrfunc=func; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    for (j=1;j<=n;j++) { 
   double fx;      pcom[j]=p[j]; 
   int k=0,kmax=10;      xicom[j]=xi[j]; 
   double l1;    } 
     ax=0.0; 
   fx=func(x);    xx=1.0; 
   for (i=1;i<=npar;i++) p2[i]=x[i];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   for(l=0 ; l <=lmax; l++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     l1=pow(10,l);  #ifdef DEBUG
     delts=delt;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for(k=1 ; k <kmax; k=k+1){    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       delt = delta*(l1*k);  #endif
       p2[theta]=x[theta] +delt;    for (j=1;j<=n;j++) { 
       k1=func(p2)-fx;      xi[j] *= xmin; 
       p2[theta]=x[theta]-delt;      p[j] += xi[j]; 
       k2=func(p2)-fx;    } 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    free_vector(xicom,1,n); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    free_vector(pcom,1,n); 
        } 
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  char *asc_diff_time(long time_sec, char ascdiff[])
       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    long sec_left, days, hours, minutes;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    days = (time_sec) / (60*60*24);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    sec_left = (time_sec) % (60*60*24);
         k=kmax;    hours = (sec_left) / (60*60) ;
       }    sec_left = (sec_left) %(60*60);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    minutes = (sec_left) /60;
         k=kmax; l=lmax*10.;    sec_left = (sec_left) % (60);
       }    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    return ascdiff;
         delts=delt;  }
       }  
     }  /*************** powell ************************/
   }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   delti[theta]=delts;              double (*func)(double [])) 
   return res;  { 
      void linmin(double p[], double xi[], int n, double *fret, 
 }                double (*func)(double [])); 
     int i,ibig,j; 
 double hessij( double x[], double delti[], int thetai,int thetaj)    double del,t,*pt,*ptt,*xit;
 {    double fp,fptt;
   int i;    double *xits;
   int l=1, l1, lmax=20;    int niterf, itmp;
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];    pt=vector(1,n); 
   int k;    ptt=vector(1,n); 
     xit=vector(1,n); 
   fx=func(x);    xits=vector(1,n); 
   for (k=1; k<=2; k++) {    *fret=(*func)(p); 
     for (i=1;i<=npar;i++) p2[i]=x[i];    for (j=1;j<=n;j++) pt[j]=p[j]; 
     p2[thetai]=x[thetai]+delti[thetai]/k;    for (*iter=1;;++(*iter)) { 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      fp=(*fret); 
     k1=func(p2)-fx;      ibig=0; 
        del=0.0; 
     p2[thetai]=x[thetai]+delti[thetai]/k;      last_time=curr_time;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      (void) gettimeofday(&curr_time,&tzp);
     k2=func(p2)-fx;      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);
     p2[thetai]=x[thetai]-delti[thetai]/k;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;     for (i=1;i<=n;i++) {
     k3=func(p2)-fx;        printf(" %d %.12f",i, p[i]);
          fprintf(ficlog," %d %.12lf",i, p[i]);
     p2[thetai]=x[thetai]-delti[thetai]/k;        fprintf(ficrespow," %.12lf", p[i]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      }
     k4=func(p2)-fx;      printf("\n");
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      fprintf(ficlog,"\n");
 #ifdef DEBUG      fprintf(ficrespow,"\n");fflush(ficrespow);
     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);      if(*iter <=3){
     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);        tm = *localtime(&curr_time.tv_sec);
 #endif        strcpy(strcurr,asctime(&tm));
   }  /*       asctime_r(&tm,strcurr); */
   return res;        forecast_time=curr_time; 
 }        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 /************** Inverse of matrix **************/          strcurr[itmp-1]='\0';
 void ludcmp(double **a, int n, int *indx, double *d)        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 {        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   int i,imax,j,k;        for(niterf=10;niterf<=30;niterf+=10){
   double big,dum,sum,temp;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   double *vv;          tmf = *localtime(&forecast_time.tv_sec);
    /*      asctime_r(&tmf,strfor); */
   vv=vector(1,n);          strcpy(strfor,asctime(&tmf));
   *d=1.0;          itmp = strlen(strfor);
   for (i=1;i<=n;i++) {          if(strfor[itmp-1]=='\n')
     big=0.0;          strfor[itmp-1]='\0';
     for (j=1;j<=n;j++)          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       if ((temp=fabs(a[i][j])) > big) big=temp;          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);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        }
     vv[i]=1.0/big;      }
   }      for (i=1;i<=n;i++) { 
   for (j=1;j<=n;j++) {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     for (i=1;i<j;i++) {        fptt=(*fret); 
       sum=a[i][j];  #ifdef DEBUG
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        printf("fret=%lf \n",*fret);
       a[i][j]=sum;        fprintf(ficlog,"fret=%lf \n",*fret);
     }  #endif
     big=0.0;        printf("%d",i);fflush(stdout);
     for (i=j;i<=n;i++) {        fprintf(ficlog,"%d",i);fflush(ficlog);
       sum=a[i][j];        linmin(p,xit,n,fret,func); 
       for (k=1;k<j;k++)        if (fabs(fptt-(*fret)) > del) { 
         sum -= a[i][k]*a[k][j];          del=fabs(fptt-(*fret)); 
       a[i][j]=sum;          ibig=i; 
       if ( (dum=vv[i]*fabs(sum)) >= big) {        } 
         big=dum;  #ifdef DEBUG
         imax=i;        printf("%d %.12e",i,(*fret));
       }        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     if (j != imax) {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       for (k=1;k<=n;k++) {          printf(" x(%d)=%.12e",j,xit[j]);
         dum=a[imax][k];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         a[imax][k]=a[j][k];        }
         a[j][k]=dum;        for(j=1;j<=n;j++) {
       }          printf(" p=%.12e",p[j]);
       *d = -(*d);          fprintf(ficlog," p=%.12e",p[j]);
       vv[imax]=vv[j];        }
     }        printf("\n");
     indx[j]=imax;        fprintf(ficlog,"\n");
     if (a[j][j] == 0.0) a[j][j]=TINY;  #endif
     if (j != n) {      } 
       dum=1.0/(a[j][j]);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  #ifdef DEBUG
     }        int k[2],l;
   }        k[0]=1;
   free_vector(vv,1,n);  /* Doesn't work */        k[1]=-1;
 ;        printf("Max: %.12e",(*func)(p));
 }        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
 void lubksb(double **a, int n, int *indx, double b[])          printf(" %.12e",p[j]);
 {          fprintf(ficlog," %.12e",p[j]);
   int i,ii=0,ip,j;        }
   double sum;        printf("\n");
          fprintf(ficlog,"\n");
   for (i=1;i<=n;i++) {        for(l=0;l<=1;l++) {
     ip=indx[i];          for (j=1;j<=n;j++) {
     sum=b[ip];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     b[ip]=b[i];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     if (ii)            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          }
     else if (sum) ii=i;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     b[i]=sum;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   }        }
   for (i=n;i>=1;i--) {  #endif
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];        free_vector(xit,1,n); 
   }        free_vector(xits,1,n); 
 }        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
 /************ Frequencies ********************/        return; 
 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 */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
        for (j=1;j<=n;j++) { 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        ptt[j]=2.0*p[j]-pt[j]; 
   int first;        xit[j]=p[j]-pt[j]; 
   double ***freq; /* Frequencies */        pt[j]=p[j]; 
   double *pp;      } 
   double pos, k2, dateintsum=0,k2cpt=0;      fptt=(*func)(ptt); 
   FILE *ficresp;      if (fptt < fp) { 
   char fileresp[FILENAMELENGTH];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
          if (t < 0.0) { 
   pp=vector(1,nlstate);          linmin(p,xit,n,fret,func); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (j=1;j<=n;j++) { 
   strcpy(fileresp,"p");            xi[j][ibig]=xi[j][n]; 
   strcat(fileresp,fileres);            xi[j][n]=xit[j]; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {          }
     printf("Problem with prevalence resultfile: %s\n", fileresp);  #ifdef DEBUG
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     exit(0);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   }          for(j=1;j<=n;j++){
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            printf(" %.12e",xit[j]);
   j1=0;            fprintf(ficlog," %.12e",xit[j]);
            }
   j=cptcoveff;          printf("\n");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          fprintf(ficlog,"\n");
   #endif
   first=1;        }
       } 
   for(k1=1; k1<=j;k1++){    } 
     for(i1=1; i1<=ncodemax[k1];i1++){  } 
       j1++;  
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  /**** Prevalence limit (stable or period prevalence)  ****************/
         scanf("%d", i);*/  
       for (i=-1; i<=nlstate+ndeath; i++)    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         for (jk=-1; jk<=nlstate+ndeath; jk++)    {
           for(m=agemin; m <= agemax+3; m++)    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
             freq[i][jk][m]=0;       matrix by transitions matrix until convergence is reached */
        
       dateintsum=0;    int i, ii,j,k;
       k2cpt=0;    double min, max, maxmin, maxmax,sumnew=0.;
       for (i=1; i<=imx; i++) {    double **matprod2();
         bool=1;    double **out, cov[NCOVMAX+1], **pmij();
         if  (cptcovn>0) {    double **newm;
           for (z1=1; z1<=cptcoveff; z1++)    double agefin, delaymax=50 ; /* Max number of years to converge */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;    for (ii=1;ii<=nlstate+ndeath;ii++)
         }      for (j=1;j<=nlstate+ndeath;j++){
         if (bool==1) {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=firstpass; m<=lastpass; m++){      }
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {     cov[1]=1.;
               if(agev[m][i]==0) agev[m][i]=agemax+1;   
               if(agev[m][i]==1) agev[m][i]=agemax+2;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
               if (m<lastpass) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      newm=savm;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      /* Covariates have to be included here again */
               }      cov[2]=agefin;
                    
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      for (k=1; k<=cptcovn;k++) {
                 dateintsum=dateintsum+k2;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                 k2cpt++;        /*        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 (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           }      for (k=1; k<=cptcovprod;k++)
         }        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       }      
              /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       if  (cptcovn>0) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
         fprintf(ficresp, "\n#********** Variable ");      
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      savm=oldm;
         fprintf(ficresp, "**********\n#");      oldm=newm;
       }      maxmax=0.;
       for(i=1; i<=nlstate;i++)      for(j=1;j<=nlstate;j++){
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        min=1.;
       fprintf(ficresp, "\n");        max=0.;
              for(i=1; i<=nlstate; i++) {
       for(i=(int)agemin; i <= (int)agemax+3; i++){          sumnew=0;
         if(i==(int)agemax+3){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           fprintf(ficlog,"Total");          prlim[i][j]= newm[i][j]/(1-sumnew);
         }else{          max=FMAX(max,prlim[i][j]);
           if(first==1){          min=FMIN(min,prlim[i][j]);
             first=0;        }
             printf("See log file for details...\n");        maxmin=max-min;
           }        maxmax=FMAX(maxmax,maxmin);
           fprintf(ficlog,"Age %d", i);      }
         }      if(maxmax < ftolpl){
         for(jk=1; jk <=nlstate ; jk++){        return prlim;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      }
             pp[jk] += freq[jk][m][i];    }
         }  }
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)  /*************** transition probabilities ***************/ 
             pos += freq[jk][m][i];  
           if(pp[jk]>=1.e-10){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
             if(first==1){  {
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    /* According to parameters values stored in x and the covariate's values stored in cov,
             }       computes the probability to be observed in state j being in state i by appying the
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);       model to the ncovmodel covariates (including constant and age).
           }else{       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
             if(first==1)       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       ncth covariate in the global vector x is given by the formula:
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           }       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
         }       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
         for(jk=1; jk <=nlstate ; jk++){       Outputs ps[i][j] the probability to be observed in j being in j according to
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
             pp[jk] += freq[jk][m][i];    */
         }    double s1, lnpijopii;
     /*double t34;*/
         for(jk=1,pos=0; jk <=nlstate ; jk++)    int i,j,j1, nc, ii, jj;
           pos += pp[jk];  
         for(jk=1; jk <=nlstate ; jk++){      for(i=1; i<= nlstate; i++){
           if(pos>=1.e-5){        for(j=1; j<i;j++){
             if(first==1)          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            /*lnpijopii += param[i][j][nc]*cov[nc];*/
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           }else{  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
             if(first==1)          }
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           }        }
           if( i <= (int) agemax){        for(j=i+1; j<=nlstate+ndeath;j++){
             if(pos>=1.e-5){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
               probs[i][jk][j1]= pp[jk]/pos;            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
             }          }
             else          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        }
           }      }
         }      
              for(i=1; i<= nlstate; i++){
         for(jk=-1; jk <=nlstate+ndeath; jk++)        s1=0;
           for(m=-1; m <=nlstate+ndeath; m++)        for(j=1; j<i; j++){
             if(freq[jk][m][i] !=0 ) {          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
             if(first==1)          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        }
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);        for(j=i+1; j<=nlstate+ndeath; j++){
             }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         if(i <= (int) agemax)          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           fprintf(ficresp,"\n");        }
         if(first==1)        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
           printf("Others in log...\n");        ps[i][i]=1./(s1+1.);
         fprintf(ficlog,"\n");        /* Computing other pijs */
       }        for(j=1; j<i; j++)
     }          ps[i][j]= exp(ps[i][j])*ps[i][i];
   }        for(j=i+1; j<=nlstate+ndeath; j++)
   dateintmean=dateintsum/k2cpt;          ps[i][j]= exp(ps[i][j])*ps[i][i];
          /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   fclose(ficresp);      } /* end i */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      
   free_vector(pp,1,nlstate);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
          for(jj=1; jj<= nlstate+ndeath; jj++){
   /* End of Freq */          ps[ii][jj]=0;
 }          ps[ii][ii]=1;
         }
 /************ Prevalence ********************/      }
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      
 {  /* Some frequencies */  
    /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   double ***freq; /* Frequencies */  /*         printf("ddd %lf ",ps[ii][jj]); */
   double *pp;  /*       } */
   double pos, k2;  /*       printf("\n "); */
   /*        } */
   pp=vector(1,nlstate);  /*        printf("\n ");printf("%lf ",cov[2]); */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);         /*
          for(i=1; i<= npar; i++) printf("%f ",x[i]);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        goto end;*/
   j1=0;      return ps;
    }
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /**************** Product of 2 matrices ******************/
    
   for(k1=1; k1<=j;k1++){  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     for(i1=1; i1<=ncodemax[k1];i1++){  {
       j1++;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
             b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for (i=-1; i<=nlstate+ndeath; i++)      /* in, b, out are matrice of pointers which should have been initialized 
         for (jk=-1; jk<=nlstate+ndeath; jk++)         before: only the contents of out is modified. The function returns
           for(m=agemin; m <= agemax+3; m++)       a pointer to pointers identical to out */
             freq[i][jk][m]=0;    long i, j, k;
          for(i=nrl; i<= nrh; i++)
       for (i=1; i<=imx; i++) {      for(k=ncolol; k<=ncoloh; k++)
         bool=1;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         if  (cptcovn>0) {          out[i][k] +=in[i][j]*b[j][k];
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    return out;
               bool=0;  }
         }  
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){  /************* Higher Matrix Product ***************/
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
               if(agev[m][i]==0) agev[m][i]=agemax+1;  {
               if(agev[m][i]==1) agev[m][i]=agemax+2;    /* Computes the transition matrix starting at age 'age' over 
               if (m<lastpass) {       'nhstepm*hstepm*stepm' months (i.e. until
                 if (calagedate>0)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];       nhstepm*hstepm matrices. 
                 else       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];       (typically every 2 years instead of every month which is too big 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];       for the memory).
               }       Model is determined by parameters x and covariates have to be 
             }       included manually here. 
           }  
         }       */
       }  
       for(i=(int)agemin; i <= (int)agemax+3; i++){    int i, j, d, h, k;
         for(jk=1; jk <=nlstate ; jk++){    double **out, cov[NCOVMAX+1];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double **newm;
             pp[jk] += freq[jk][m][i];  
         }    /* Hstepm could be zero and should return the unit matrix */
         for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=nlstate+ndeath;i++)
           for(m=-1, pos=0; m <=0 ; m++)      for (j=1;j<=nlstate+ndeath;j++){
             pos += freq[jk][m][i];        oldm[i][j]=(i==j ? 1.0 : 0.0);
         }        po[i][j][0]=(i==j ? 1.0 : 0.0);
              }
         for(jk=1; jk <=nlstate ; jk++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    for(h=1; h <=nhstepm; h++){
             pp[jk] += freq[jk][m][i];      for(d=1; d <=hstepm; d++){
         }        newm=savm;
                /* Covariates have to be included here again */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        cov[1]=1.;
                cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for(jk=1; jk <=nlstate ; jk++){            for (k=1; k<=cptcovn;k++) 
           if( i <= (int) agemax){          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
             if(pos>=1.e-5){        for (k=1; k<=cptcovage;k++)
               probs[i][jk][j1]= pp[jk]/pos;          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]]];
         }/* end jk */  
       }/* end i */  
     } /* end i1 */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   } /* end k1 */        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                       pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        savm=oldm;
   free_vector(pp,1,nlstate);        oldm=newm;
        }
 }  /* End of Freq */      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
 /************* Waves Concatenation ***************/          po[i][j][h]=newm[i][j];
           /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        }
 {      /*printf("h=%d ",h);*/
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    } /* end h */
      Death is a valid wave (if date is known).  /*     printf("\n H=%d \n",h); */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    return po;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  }
      and mw[mi+1][i]. dh depends on stepm.  
      */  
   /*************** log-likelihood *************/
   int i, mi, m;  double func( double *x)
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  {
      double sum=0., jmean=0.;*/    int i, ii, j, k, mi, d, kk;
   int first;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   int j, k=0,jk, ju, jl;    double **out;
   double sum=0.;    double sw; /* Sum of weights */
   first=0;    double lli; /* Individual log likelihood */
   jmin=1e+5;    int s1, s2;
   jmax=-1;    double bbh, survp;
   jmean=0.;    long ipmx;
   for(i=1; i<=imx; i++){    /*extern weight */
     mi=0;    /* We are differentiating ll according to initial status */
     m=firstpass;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     while(s[m][i] <= nlstate){    /*for(i=1;i<imx;i++) 
       if(s[m][i]>=1)      printf(" %d\n",s[4][i]);
         mw[++mi][i]=m;    */
       if(m >=lastpass)    cov[1]=1.;
         break;  
       else    for(k=1; k<=nlstate; k++) ll[k]=0.;
         m++;  
     }/* end while */    if(mle==1){
     if (s[m][i] > nlstate){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       mi++;     /* Death is another wave */        /* Computes the values of the ncovmodel covariates of the model
       /* if(mi==0)  never been interviewed correctly before death */           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
          /* Only death is a correct wave */           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
       mw[mi][i]=m;           to be observed in j being in i according to the model.
     }         */
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     wav[i]=mi;        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     if(mi==0){           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       if(first==0){           has been calculated etc */
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);        for(mi=1; mi<= wav[i]-1; mi++){
         first=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
       if(first==1){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
     } /* end mi==0 */          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(i=1; i<=imx; i++){            for (kk=1; kk<=cptcovage;kk++) {
     for(mi=1; mi<wav[i];mi++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
       if (stepm <=0)            }
         dh[mi][i]=1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else{                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (s[mw[mi+1][i]][i] > nlstate) {            savm=oldm;
           if (agedc[i] < 2*AGESUP) {            oldm=newm;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          } /* end mult */
           if(j==0) j=1;  /* Survives at least one month after exam */        
           k=k+1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           if (j >= jmax) jmax=j;          /* But now since version 0.9 we anticipate for bias at large stepm.
           if (j <= jmin) jmin=j;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           sum=sum+j;           * (in months) between two waves is not a multiple of stepm, we rounded to 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */           * the nearest (and in case of equal distance, to the lowest) interval but now
           }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         else{           * probability in order to take into account the bias as a fraction of the way
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           k=k+1;           * -stepm/2 to stepm/2 .
           if (j >= jmax) jmax=j;           * For stepm=1 the results are the same as for previous versions of Imach.
           else if (j <= jmin)jmin=j;           * For stepm > 1 the results are less biased than in previous versions. 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */           */
           sum=sum+j;          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
         jk= j/stepm;          bbh=(double)bh[mi][i]/(double)stepm; 
         jl= j -jk*stepm;          /* bias bh is positive if real duration
         ju= j -(jk+1)*stepm;           * is higher than the multiple of stepm and negative otherwise.
         if(jl <= -ju)           */
           dh[mi][i]=jk;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         else          if( s2 > nlstate){ 
           dh[mi][i]=jk+1;            /* i.e. if s2 is a death state and if the date of death is known 
         if(dh[mi][i]==0)               then the contribution to the likelihood is the probability to 
           dh[mi][i]=1; /* At least one step */               die between last step unit time and current  step unit time, 
       }               which is also equal to probability to die before dh 
     }               minus probability to die before dh-stepm . 
   }               In version up to 0.92 likelihood was computed
   jmean=sum/k;          as if date of death was unknown. Death was treated as any other
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          health state: the date of the interview describes the actual state
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          and not the date of a change in health state. The former idea was
  }          to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
 /*********** Tricode ****************************/          introduced the exact date of death then we should have modified
 void tricode(int *Tvar, int **nbcode, int imx)          the contribution of an exact death to the likelihood. This new
 {          contribution is smaller and very dependent of the step unit
   int Ndum[20],ij=1, k, j, i;          stepm. It is no more the probability to die between last interview
   int cptcode=0;          and month of death but the probability to survive from last
   cptcoveff=0;          interview up to one month before death multiplied by the
            probability to die within a month. Thanks to Chris
   for (k=0; k<19; k++) Ndum[k]=0;          Jackson for correcting this bug.  Former versions increased
   for (k=1; k<=7; k++) ncodemax[k]=0;          mortality artificially. The bad side is that we add another loop
           which slows down the processing. The difference can be up to 10%
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          lower mortality.
     for (i=1; i<=imx; i++) {            */
       ij=(int)(covar[Tvar[j]][i]);            lli=log(out[s1][s2] - savm[s1][s2]);
       Ndum[ij]++;  
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;          } else if  (s2==-2) {
     }            for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for (i=0; i<=cptcode; i++) {            /*survp += out[s1][j]; */
       if(Ndum[i]!=0) ncodemax[j]++;            lli= log(survp);
     }          }
     ij=1;          
           else if  (s2==-4) { 
             for (j=3,survp=0. ; j<=nlstate; j++)  
     for (i=1; i<=ncodemax[j]; i++) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for (k=0; k<=19; k++) {            lli= log(survp); 
         if (Ndum[k] != 0) {          } 
           nbcode[Tvar[j]][ij]=k;  
                    else if  (s2==-5) { 
           ij++;            for (j=1,survp=0. ; j<=2; j++)  
         }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         if (ij > ncodemax[j]) break;            lli= log(survp); 
       }            } 
     }          
   }            else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
  for (k=0; k<19; k++) Ndum[k]=0;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
  for (i=1; i<=ncovmodel-2; i++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
    ij=Tvar[i];          /*if(lli ==000.0)*/
    Ndum[ij]++;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
  }          ipmx +=1;
           sw += weight[i];
  ij=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  for (i=1; i<=10; i++) {        } /* end of wave */
    if((Ndum[i]!=0) && (i<=ncovcol)){      } /* end of individual */
      Tvaraff[ij]=i;    }  else if(mle==2){
      ij++;      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 (ii=1;ii<=nlstate+ndeath;ii++)
  cptcoveff=ij-1;            for (j=1;j<=nlstate+ndeath;j++){
 }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /*********** Health Expectancies ****************/            }
           for(d=0; d<=dh[mi][i]; d++){
 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 )            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
   /* Health expectancies */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;            }
   double age, agelim, hf;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***p3mat,***varhe;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double **dnewm,**doldm;            savm=oldm;
   double *xp;            oldm=newm;
   double **gp, **gm;          } /* end mult */
   double ***gradg, ***trgradg;        
   int theta;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          bbh=(double)bh[mi][i]/(double)stepm; 
   xp=vector(1,npar);          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 */
   dnewm=matrix(1,nlstate*2,1,npar);          ipmx +=1;
   doldm=matrix(1,nlstate*2,1,nlstate*2);          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficreseij,"# Health expectancies\n");        } /* end of wave */
   fprintf(ficreseij,"# Age");      } /* end of individual */
   for(i=1; i<=nlstate;i++)    }  else if(mle==3){  /* exponential inter-extrapolation */
     for(j=1; j<=nlstate;j++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficreseij,"\n");        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   if(estepm < stepm){            for (j=1;j<=nlstate+ndeath;j++){
     printf ("Problem %d lower than %d\n",estepm, stepm);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   else  hstepm=estepm;              }
   /* We compute the life expectancy from trapezoids spaced every estepm months          for(d=0; d<dh[mi][i]; d++){
    * This is mainly to measure the difference between two models: for example            newm=savm;
    * if stepm=24 months pijx are given only every 2 years and by summing them            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
    * we are calculating an estimate of the Life Expectancy assuming a linear            for (kk=1; kk<=cptcovage;kk++) {
    * progression inbetween and thus overestimating or underestimating according              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
    * to the curvature of the survival function. If, for the same date, we            }
    * estimate the model with stepm=1 month, we can keep estepm to 24 months            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
    * to compare the new estimate of Life expectancy with the same linear                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
    * hypothesis. A more precise result, taking into account a more precise            savm=oldm;
    * curvature will be obtained if estepm is as small as stepm. */            oldm=newm;
           } /* end mult */
   /* 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.          s1=s[mw[mi][i]][i];
      nhstepm is the number of hstepm from age to agelim          s2=s[mw[mi+1][i]][i];
      nstepm is the number of stepm from age to agelin.          bbh=(double)bh[mi][i]/(double)stepm; 
      Look at hpijx to understand the reason of that which relies in memory size          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 */
      and note for a fixed period like estepm months */          ipmx +=1;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          sw += weight[i];
      survival function given by stepm (the optimization length). Unfortunately it          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      means that if the survival funtion is printed only each two years of age and if        } /* end of wave */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      } /* end of individual */
      results. So we changed our mind and took the option of the best precision.    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   agelim=AGESUP;          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            for (j=1;j<=nlstate+ndeath;j++){
     /* nhstepm age range expressed in number of stepm */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            }
     /* if (stepm >= YEARM) hstepm=1;*/          for(d=0; d<dh[mi][i]; d++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            newm=savm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);            for (kk=1; kk<=cptcovage;kk++) {
     gp=matrix(0,nhstepm,1,nlstate*2);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     gm=matrix(0,nhstepm,1,nlstate*2);            }
           
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              savm=oldm;
              oldm=newm;
           } /* end mult */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        
           s1=s[mw[mi][i]][i];
     /* Computing Variances of health expectancies */          s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
      for(theta=1; theta <=npar; theta++){            lli=log(out[s1][s2] - savm[s1][s2]);
       for(i=1; i<=npar; i++){          }else{
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }          }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ipmx +=1;
            sw += weight[i];
       cptj=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1; j<= nlstate; j++){  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         for(i=1; i<=nlstate; i++){        } /* end of wave */
           cptj=cptj+1;      } /* end of individual */
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      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 (ii=1;ii<=nlstate+ndeath;ii++)
                  for (j=1;j<=nlstate+ndeath;j++){
                    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(d=0; d<dh[mi][i]; d++){
                  newm=savm;
       cptj=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(j=1; j<= nlstate; j++){            for (kk=1; kk<=cptcovage;kk++) {
         for(i=1;i<=nlstate;i++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           cptj=cptj+1;            }
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
       }            oldm=newm;
       for(j=1; j<= nlstate*2; j++)          } /* end mult */
         for(h=0; h<=nhstepm-1; h++){        
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
      }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
              ipmx +=1;
 /* End theta */          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      trgradg =ma3x(0,nhstepm,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]);*/
         } /* end of wave */
      for(h=0; h<=nhstepm-1; h++)      } /* end of individual */
       for(j=1; j<=nlstate*2;j++)    } /* End of if */
         for(theta=1; theta <=npar; theta++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           trgradg[h][j][theta]=gradg[h][theta][j];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
      for(i=1;i<=nlstate*2;i++)  }
       for(j=1;j<=nlstate*2;j++)  
         varhe[i][j][(int)age] =0.;  /*************** log-likelihood *************/
   double funcone( double *x)
      printf("%d|",(int)age);fflush(stdout);  {
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    /* Same as likeli but slower because of a lot of printf and if */
      for(h=0;h<=nhstepm-1;h++){    int i, ii, j, k, mi, d, kk;
       for(k=0;k<=nhstepm-1;k++){    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    double **out;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    double lli; /* Individual log likelihood */
         for(i=1;i<=nlstate*2;i++)    double llt;
           for(j=1;j<=nlstate*2;j++)    int s1, s2;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    double bbh, survp;
       }    /*extern weight */
     }    /* We are differentiating ll according to initial status */
     /* Computing expectancies */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(i=1; i<=nlstate;i++)    /*for(i=1;i<imx;i++) 
       for(j=1; j<=nlstate;j++)      printf(" %d\n",s[4][i]);
         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;    cov[1]=1.;
            
 /* 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(k=1; k<=nlstate; k++) ll[k]=0.;
   
         }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficreseij,"%3.0f",age );      for(mi=1; mi<= wav[i]-1; mi++){
     cptj=0;        for (ii=1;ii<=nlstate+ndeath;ii++)
     for(i=1; i<=nlstate;i++)          for (j=1;j<=nlstate+ndeath;j++){
       for(j=1; j<=nlstate;j++){            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         cptj++;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          }
       }        for(d=0; d<dh[mi][i]; d++){
     fprintf(ficreseij,"\n");          newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_matrix(gm,0,nhstepm,1,nlstate*2);          for (kk=1; kk<=cptcovage;kk++) {
     free_matrix(gp,0,nhstepm,1,nlstate*2);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          }
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }          savm=oldm;
   printf("\n");          oldm=newm;
   fprintf(ficlog,"\n");        } /* end mult */
         
   free_vector(xp,1,npar);        s1=s[mw[mi][i]][i];
   free_matrix(dnewm,1,nlstate*2,1,npar);        s2=s[mw[mi+1][i]][i];
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        bbh=(double)bh[mi][i]/(double)stepm; 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        /* bias is positive if real duration
 }         * is higher than the multiple of stepm and negative otherwise.
          */
 /************ Variance ******************/        if( s2 > nlstate && (mle <5) ){  /* Jackson */
 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)          lli=log(out[s1][s2] - savm[s1][s2]);
 {        } else if  (s2==-2) {
   /* Variance of health expectancies */          for (j=1,survp=0. ; j<=nlstate; j++) 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /* double **newm;*/          lli= log(survp);
   double **dnewm,**doldm;        }else if (mle==1){
   double **dnewmp,**doldmp;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   int i, j, nhstepm, hstepm, h, nstepm ;        } else if(mle==2){
   int k, cptcode;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   double *xp;        } else if(mle==3){  /* exponential inter-extrapolation */
   double **gp, **gm;  /* for var eij */          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 */
   double ***gradg, ***trgradg; /*for var eij */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double **gradgp, **trgradgp; /* for var p point j */          lli=log(out[s1][s2]); /* Original formula */
   double *gpp, *gmp; /* for var p point j */        } else{  /* mle=0 back to 1 */
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double ***p3mat;          /*lli=log(out[s1][s2]); */ /* Original formula */
   double age,agelim, hf;        } /* End of if */
   int theta;        ipmx +=1;
   char digit[4];        sw += weight[i];
   char digitp[16];        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]); */
   char fileresprobmorprev[FILENAMELENGTH];        if(globpr){
           fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   if(popbased==1)   %11.6f %11.6f %11.6f ", \
     strcpy(digitp,"-populbased-");                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   else                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     strcpy(digitp,"-stablbased-");          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
   strcpy(fileresprobmorprev,"prmorprev");            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   sprintf(digit,"%-d",ij);          }
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/          fprintf(ficresilk," %10.6f\n", -llt);
   strcat(fileresprobmorprev,digit); /* Tvar to be done */        }
   strcat(fileresprobmorprev,digitp); /* Popbased or not */      } /* end of wave */
   strcat(fileresprobmorprev,fileres);    } /* end of individual */
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     printf("Problem with resultfile: %s\n", fileresprobmorprev);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   }    if(globpr==0){ /* First time we count the contributions and weights */
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      gipmx=ipmx;
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      gsw=sw;
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");    }
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    return -l;
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){  }
     fprintf(ficresprobmorprev," p.%-d SE",j);  
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);  /*************** function likelione ***********/
   }    void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   fprintf(ficresprobmorprev,"\n");  {
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    /* This routine should help understanding what is done with 
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);       the selection of individuals/waves and
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);       to check the exact contribution to the likelihood.
     exit(0);       Plotting could be done.
   }     */
   else{    int k;
     fprintf(ficgp,"\n# Routine varevsij");  
   }    if(*globpri !=0){ /* Just counts and sums, no printings */
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {      strcpy(fileresilk,"ilk"); 
     printf("Problem with html file: %s\n", optionfilehtm);      strcat(fileresilk,fileres);
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     exit(0);        printf("Problem with resultfile: %s\n", fileresilk);
   }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   else{      }
     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");      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 ");
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
   fprintf(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");        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   fprintf(ficresvij,"# Age");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   for(i=1; i<=nlstate;i++)    }
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    *fretone=(*funcone)(p);
   fprintf(ficresvij,"\n");    if(*globpri !=0){
       fclose(ficresilk);
   xp=vector(1,npar);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   dnewm=matrix(1,nlstate,1,npar);      fflush(fichtm); 
   doldm=matrix(1,nlstate,1,nlstate);    } 
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);    return;
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  }
   
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);  
   gpp=vector(nlstate+1,nlstate+ndeath);  /*********** Maximum Likelihood Estimation ***************/
   gmp=vector(nlstate+1,nlstate+ndeath);  
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    {
   if(estepm < stepm){    int i,j, iter;
     printf ("Problem %d lower than %d\n",estepm, stepm);    double **xi;
   }    double fret;
   else  hstepm=estepm;      double fretone; /* Only one call to likelihood */
   /* For example we decided to compute the life expectancy with the smallest unit */    /*  char filerespow[FILENAMELENGTH];*/
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    xi=matrix(1,npar,1,npar);
      nhstepm is the number of hstepm from age to agelim    for (i=1;i<=npar;i++)
      nstepm is the number of stepm from age to agelin.      for (j=1;j<=npar;j++)
      Look at hpijx to understand the reason of that which relies in memory size        xi[i][j]=(i==j ? 1.0 : 0.0);
      and note for a fixed period like k years */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    strcpy(filerespow,"pow"); 
      survival function given by stepm (the optimization length). Unfortunately it    strcat(filerespow,fileres);
      means that if the survival funtion is printed only each two years of age and if    if((ficrespow=fopen(filerespow,"w"))==NULL) {
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      printf("Problem with resultfile: %s\n", filerespow);
      results. So we changed our mind and took the option of the best precision.      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   agelim = AGESUP;    for (i=1;i<=nlstate;i++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for(j=1;j<=nlstate+ndeath;j++)
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    fprintf(ficrespow,"\n");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    powell(p,xi,npar,ftol,&iter,&fret,func);
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);    free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     for(theta=1; theta <=npar; theta++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for(i=1; i<=npar; i++){ /* Computes gradient */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         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);  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       if (popbased==1) {  {
         for(i=1; i<=nlstate;i++)    double  **a,**y,*x,pd;
           prlim[i][i]=probs[(int)age][i][ij];    double **hess;
       }    int i, j,jk;
      int *indx;
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    void lubksb(double **a, int npar, int *indx, double b[]) ;
         }    void ludcmp(double **a, int npar, int *indx, double *d) ;
       }    double gompertz(double p[]);
       /* This for computing forces of mortality (h=1)as a weighted average */    hess=matrix(1,npar,1,npar);
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){  
         for(i=1; i<= nlstate; i++)    printf("\nCalculation of the hessian matrix. Wait...\n");
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       }        for (i=1;i<=npar;i++){
       /* end force of mortality */      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
       for(i=1; i<=npar; i++) /* Computes gradient */     
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      /*  printf(" %f ",p[i]);
            printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       if (popbased==1) {    }
         for(i=1; i<=nlstate;i++)    
           prlim[i][i]=probs[(int)age][i][ij];    for (i=1;i<=npar;i++) {
       }      for (j=1;j<=npar;j++)  {
         if (j>i) { 
       for(j=1; j<= nlstate; j++){          printf(".%d%d",i,j);fflush(stdout);
         for(h=0; h<=nhstepm; h++){          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          hess[i][j]=hessij(p,delti,i,j,func,npar);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          
         }          hess[j][i]=hess[i][j];    
       }          /*printf(" %lf ",hess[i][j]);*/
       /* This for computing force of mortality (h=1)as a weighted average */        }
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){      }
         for(i=1; i<= nlstate; i++)    }
           gmp[j] += prlim[i][i]*p3mat[i][j][1];    printf("\n");
       }        fprintf(ficlog,"\n");
       /* end force of mortality */  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(j=1; j<= nlstate; j++) /* vareij */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         for(h=0; h<=nhstepm; h++){    
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    a=matrix(1,npar,1,npar);
         }    y=matrix(1,npar,1,npar);
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */    x=vector(1,npar);
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];    indx=ivector(1,npar);
       }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     } /* End theta */    ludcmp(a,npar,indx,&pd);
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
     for(h=0; h<=nhstepm; h++) /* veij */      x[j]=1;
       for(j=1; j<=nlstate;j++)      lubksb(a,npar,indx,x);
         for(theta=1; theta <=npar; theta++)      for (i=1;i<=npar;i++){ 
           trgradg[h][j][theta]=gradg[h][theta][j];        matcov[i][j]=x[i];
       }
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */    }
       for(theta=1; theta <=npar; theta++)  
         trgradgp[j][theta]=gradgp[theta][j];    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    for (i=1;i<=npar;i++) { 
     for(i=1;i<=nlstate;i++)      for (j=1;j<=npar;j++) { 
       for(j=1;j<=nlstate;j++)        printf("%.3e ",hess[i][j]);
         vareij[i][j][(int)age] =0.;        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
     for(h=0;h<=nhstepm;h++){      printf("\n");
       for(k=0;k<=nhstepm;k++){      fprintf(ficlog,"\n");
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)    /* Recompute Inverse */
           for(j=1;j<=nlstate;j++)    for (i=1;i<=npar;i++)
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       }    ludcmp(a,npar,indx,&pd);
     }  
     /*  printf("\n#Hessian matrix recomputed#\n");
     /* pptj */  
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);    for (j=1;j<=npar;j++) {
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);      for (i=1;i<=npar;i++) x[i]=0;
     for(j=nlstate+1;j<=nlstate+ndeath;j++)      x[j]=1;
       for(i=nlstate+1;i<=nlstate+ndeath;i++)      lubksb(a,npar,indx,x);
         varppt[j][i]=doldmp[j][i];      for (i=1;i<=npar;i++){ 
     /* end ppptj */        y[i][j]=x[i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);          printf("%.3e ",y[i][j]);
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);        fprintf(ficlog,"%.3e ",y[i][j]);
        }
     if (popbased==1) {      printf("\n");
       for(i=1; i<=nlstate;i++)      fprintf(ficlog,"\n");
         prlim[i][i]=probs[(int)age][i][ij];    }
     }    */
      
     /* This for computing force of mortality (h=1)as a weighted average */    free_matrix(a,1,npar,1,npar);
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    free_matrix(y,1,npar,1,npar);
       for(i=1; i<= nlstate; i++)    free_vector(x,1,npar);
         gmp[j] += prlim[i][i]*p3mat[i][j][1];    free_ivector(indx,1,npar);
     }        free_matrix(hess,1,npar,1,npar);
     /* end force of mortality */  
   
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);  }
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));  /*************** hessian matrix ****************/
       for(i=1; i<=nlstate;i++){  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);  {
       }    int i;
     }    int l=1, lmax=20;
     fprintf(ficresprobmorprev,"\n");    double k1,k2;
     double p2[MAXPARM+1]; /* identical to x */
     fprintf(ficresvij,"%.0f ",age );    double res;
     for(i=1; i<=nlstate;i++)    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       for(j=1; j<=nlstate;j++){    double fx;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    int k=0,kmax=10;
       }    double l1;
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);    fx=func(x);
     free_matrix(gm,0,nhstepm,1,nlstate);    for (i=1;i<=npar;i++) p2[i]=x[i];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    for(l=0 ; l <=lmax; l++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      l1=pow(10,l);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      delts=delt;
   } /* End age */      for(k=1 ; k <kmax; k=k+1){
   free_vector(gpp,nlstate+1,nlstate+ndeath);        delt = delta*(l1*k);
   free_vector(gmp,nlstate+1,nlstate+ndeath);        p2[theta]=x[theta] +delt;
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);        k1=func(p2)-fx;
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        p2[theta]=x[theta]-delt;
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");        k2=func(p2)-fx;
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */        /*res= (k1-2.0*fx+k2)/delt/delt; */
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);        
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);  #ifdef DEBUGHESS
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);  #endif
   /*  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);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);          k=kmax;
         }
   free_vector(xp,1,npar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   free_matrix(doldm,1,nlstate,1,nlstate);          k=kmax; l=lmax*10.;
   free_matrix(dnewm,1,nlstate,1,npar);        }
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);          delts=delt;
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        }
   fclose(ficresprobmorprev);      }
   fclose(ficgp);    }
   fclose(fichtm);    delti[theta]=delts;
     return res; 
 }    
   }
 /************ Variance of prevlim ******************/  
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {  {
   /* Variance of prevalence limit */    int i;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    int l=1, l1, lmax=20;
   double **newm;    double k1,k2,k3,k4,res,fx;
   double **dnewm,**doldm;    double p2[MAXPARM+1];
   int i, j, nhstepm, hstepm;    int k;
   int k, cptcode;  
   double *xp;    fx=func(x);
   double *gp, *gm;    for (k=1; k<=2; k++) {
   double **gradg, **trgradg;      for (i=1;i<=npar;i++) p2[i]=x[i];
   double age,agelim;      p2[thetai]=x[thetai]+delti[thetai]/k;
   int theta;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          k1=func(p2)-fx;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    
   fprintf(ficresvpl,"# Age");      p2[thetai]=x[thetai]+delti[thetai]/k;
   for(i=1; i<=nlstate;i++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       fprintf(ficresvpl," %1d-%1d",i,i);      k2=func(p2)-fx;
   fprintf(ficresvpl,"\n");    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   xp=vector(1,npar);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   dnewm=matrix(1,nlstate,1,npar);      k3=func(p2)-fx;
   doldm=matrix(1,nlstate,1,nlstate);    
        p2[thetai]=x[thetai]-delti[thetai]/k;
   hstepm=1*YEARM; /* Every year of age */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      k4=func(p2)-fx;
   agelim = AGESUP;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  #ifdef DEBUG
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      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);
     if (stepm >= YEARM) hstepm=1;      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);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  #endif
     gradg=matrix(1,npar,1,nlstate);    }
     gp=vector(1,nlstate);    return res;
     gm=vector(1,nlstate);  }
   
     for(theta=1; theta <=npar; theta++){  /************** Inverse of matrix **************/
       for(i=1; i<=npar; i++){ /* Computes gradient */  void ludcmp(double **a, int n, int *indx, double *d) 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  { 
       }    int i,imax,j,k; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double big,dum,sum,temp; 
       for(i=1;i<=nlstate;i++)    double *vv; 
         gp[i] = prlim[i][i];   
        vv=vector(1,n); 
       for(i=1; i<=npar; i++) /* Computes gradient */    *d=1.0; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    for (i=1;i<=n;i++) { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      big=0.0; 
       for(i=1;i<=nlstate;i++)      for (j=1;j<=n;j++) 
         gm[i] = prlim[i][i];        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       for(i=1;i<=nlstate;i++)      vv[i]=1.0/big; 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    } 
     } /* End theta */    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
     trgradg =matrix(1,nlstate,1,npar);        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     for(j=1; j<=nlstate;j++)        a[i][j]=sum; 
       for(theta=1; theta <=npar; theta++)      } 
         trgradg[j][theta]=gradg[theta][j];      big=0.0; 
       for (i=j;i<=n;i++) { 
     for(i=1;i<=nlstate;i++)        sum=a[i][j]; 
       varpl[i][(int)age] =0.;        for (k=1;k<j;k++) 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          sum -= a[i][k]*a[k][j]; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        a[i][j]=sum; 
     for(i=1;i<=nlstate;i++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          big=dum; 
           imax=i; 
     fprintf(ficresvpl,"%.0f ",age );        } 
     for(i=1; i<=nlstate;i++)      } 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      if (j != imax) { 
     fprintf(ficresvpl,"\n");        for (k=1;k<=n;k++) { 
     free_vector(gp,1,nlstate);          dum=a[imax][k]; 
     free_vector(gm,1,nlstate);          a[imax][k]=a[j][k]; 
     free_matrix(gradg,1,npar,1,nlstate);          a[j][k]=dum; 
     free_matrix(trgradg,1,nlstate,1,npar);        } 
   } /* End age */        *d = -(*d); 
         vv[imax]=vv[j]; 
   free_vector(xp,1,npar);      } 
   free_matrix(doldm,1,nlstate,1,npar);      indx[j]=imax; 
   free_matrix(dnewm,1,nlstate,1,nlstate);      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
 }        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 /************ 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)    } 
 {    free_vector(vv,1,n);  /* Doesn't work */
   int i, j=0,  i1, k1, l1, t, tj;  ;
   int k2, l2, j1,  z1;  } 
   int k=0,l, cptcode;  
   int first=1, first1;  void lubksb(double **a, int n, int *indx, double b[]) 
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;  { 
   double **dnewm,**doldm;    int i,ii=0,ip,j; 
   double *xp;    double sum; 
   double *gp, *gm;   
   double **gradg, **trgradg;    for (i=1;i<=n;i++) { 
   double **mu;      ip=indx[i]; 
   double age,agelim, cov[NCOVMAX];      sum=b[ip]; 
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */      b[ip]=b[i]; 
   int theta;      if (ii) 
   char fileresprob[FILENAMELENGTH];        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   char fileresprobcov[FILENAMELENGTH];      else if (sum) ii=i; 
   char fileresprobcor[FILENAMELENGTH];      b[i]=sum; 
     } 
   double ***varpij;    for (i=n;i>=1;i--) { 
       sum=b[i]; 
   strcpy(fileresprob,"prob");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   strcat(fileresprob,fileres);      b[i]=sum/a[i][i]; 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    } 
     printf("Problem with resultfile: %s\n", fileresprob);  } 
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);  
   }  void pstamp(FILE *fichier)
   strcpy(fileresprobcov,"probcov");  {
   strcat(fileresprobcov,fileres);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {  }
     printf("Problem with resultfile: %s\n", fileresprobcov);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);  /************ Frequencies ********************/
   }  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   strcpy(fileresprobcor,"probcor");  {  /* Some frequencies */
   strcat(fileresprobcor,fileres);    
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    int i, m, jk, k1,i1, j1, bool, z1,j;
     printf("Problem with resultfile: %s\n", fileresprobcor);    int first;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);    double ***freq; /* Frequencies */
   }    double *pp, **prop;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    char fileresp[FILENAMELENGTH];
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    pp=vector(1,nlstate);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    strcpy(fileresp,"p");
      strcat(fileresp,fileres);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    if((ficresp=fopen(fileresp,"w"))==NULL) {
   fprintf(ficresprob,"# Age");      printf("Problem with prevalence resultfile: %s\n", fileresp);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   fprintf(ficresprobcov,"# Age");      exit(0);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    }
   fprintf(ficresprobcov,"# Age");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
     
   for(i=1; i<=nlstate;i++)    j=cptcoveff;
     for(j=1; j<=(nlstate+ndeath);j++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    first=1;
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  
     }      for(k1=1; k1<=j;k1++){   /* Loop on covariates */
   fprintf(ficresprob,"\n");      for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
   fprintf(ficresprobcov,"\n");        j1++;
   fprintf(ficresprobcor,"\n");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   xp=vector(1,npar);          scanf("%d", i);*/
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);        for (i=-5; i<=nlstate+ndeath; i++)  
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);            for(m=iagemin; m <= iagemax+3; m++)
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);              freq[i][jk][m]=0;
   first=1;        
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        for (i=1; i<=nlstate; i++)  
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          for(m=iagemin; m <= iagemax+3; m++)
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);            prop[i][m]=0;
     exit(0);        
   }        dateintsum=0;
   else{        k2cpt=0;
     fprintf(ficgp,"\n# Routine varprob");        for (i=1; i<=imx; i++) {
   }          bool=1;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {          if  (cptcovn>0) {
     printf("Problem with html file: %s\n", optionfilehtm);            for (z1=1; z1<=cptcoveff; z1++) 
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     exit(0);                bool=0;
   }          }
   else{          if (bool==1){
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");            for(m=firstpass; m<=lastpass; m++){
     fprintf(fichtm,"\n");              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 if (m<lastpass) {
   }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                  }
   cov[1]=1;                
   tj=cptcoveff;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}                  dateintsum=dateintsum+k2;
   j1=0;                  k2cpt++;
   for(t=1; t<=tj;t++){                }
     for(i1=1; i1<=ncodemax[t];i1++){                /*}*/
       j1++;            }
                }
       if  (cptcovn>0) {        }
         fprintf(ficresprob, "\n#********** Variable ");         
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         fprintf(ficresprob, "**********\n#");        pstamp(ficresp);
         fprintf(ficresprobcov, "\n#********** Variable ");        if  (cptcovn>0) {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          fprintf(ficresp, "\n#********** Variable "); 
         fprintf(ficresprobcov, "**********\n#");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(ficresp, "**********\n#");
         fprintf(ficgp, "\n#********** Variable ");          fprintf(ficlog, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficgp, "**********\n#");          fprintf(ficlog, "**********\n#");
                }
                for(i=1; i<=nlstate;i++) 
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        fprintf(ficresp, "\n");
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");        
                for(i=iagemin; i <= iagemax+3; i++){
         fprintf(ficresprobcor, "\n#********** Variable ");              if(i==iagemax+3){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            fprintf(ficlog,"Total");
         fprintf(ficgp, "**********\n#");              }else{
       }            if(first==1){
                    first=0;
       for (age=bage; age<=fage; age ++){              printf("See log file for details...\n");
         cov[2]=age;            }
         for (k=1; k<=cptcovn;k++) {            fprintf(ficlog,"Age %d", i);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          }
         }          for(jk=1; jk <=nlstate ; jk++){
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         for (k=1; k<=cptcovprod;k++)              pp[jk] += freq[jk][m][i]; 
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          }
                  for(jk=1; jk <=nlstate ; jk++){
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));            for(m=-1, pos=0; m <=0 ; m++)
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);              pos += freq[jk][m][i];
         gp=vector(1,(nlstate)*(nlstate+ndeath));            if(pp[jk]>=1.e-10){
         gm=vector(1,(nlstate)*(nlstate+ndeath));              if(first==1){
                    printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for(theta=1; theta <=npar; theta++){              }
           for(i=1; i<=npar; i++)              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);            }else{
                        if(first==1)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                        fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           k=0;            }
           for(i=1; i<= (nlstate); i++){          }
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;          for(jk=1; jk <=nlstate ; jk++){
               gp[k]=pmmij[i][j];            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
             }              pp[jk] += freq[jk][m][i];
           }          }       
                    for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
           for(i=1; i<=npar; i++)            pos += pp[jk];
             xp[i] = x[i] - (i==theta ?delti[theta]:0);            posprop += prop[jk][i];
              }
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          for(jk=1; jk <=nlstate ; jk++){
           k=0;            if(pos>=1.e-5){
           for(i=1; i<=(nlstate); i++){              if(first==1)
             for(j=1; j<=(nlstate+ndeath);j++){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               k=k+1;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               gm[k]=pmmij[i][j];            }else{
             }              if(first==1)
           }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                    fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)            }
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              if( i <= iagemax){
         }              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)                /*probs[i][jk][j1]= pp[jk]/pos;*/
           for(theta=1; theta <=npar; theta++)                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
             trgradg[j][theta]=gradg[theta][j];              }
                      else
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);            }
                  }
         pmij(pmmij,cov,ncovmodel,x,nlstate);          
                  for(jk=-1; jk <=nlstate+ndeath; jk++)
         k=0;            for(m=-1; m <=nlstate+ndeath; m++)
         for(i=1; i<=(nlstate); i++){              if(freq[jk][m][i] !=0 ) {
           for(j=1; j<=(nlstate+ndeath);j++){              if(first==1)
             k=k+1;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
             mu[k][(int) age]=pmmij[i][j];                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           }              }
         }          if(i <= iagemax)
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)            fprintf(ficresp,"\n");
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)          if(first==1)
             varpij[i][j][(int)age] = doldm[i][j];            printf("Others in log...\n");
           fprintf(ficlog,"\n");
         /*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]));    dateintmean=dateintsum/k2cpt; 
      }*/   
     fclose(ficresp);
         fprintf(ficresprob,"\n%d ",(int)age);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         fprintf(ficresprobcov,"\n%d ",(int)age);    free_vector(pp,1,nlstate);
         fprintf(ficresprobcor,"\n%d ",(int)age);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)  }
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));  
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  /************ Prevalence ********************/
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);  {  
         }    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         i=0;       in each health status at the date of interview (if between dateprev1 and dateprev2).
         for (k=1; k<=(nlstate);k++){       We still use firstpass and lastpass as another selection.
           for (l=1; l<=(nlstate+ndeath);l++){    */
             i=i++;   
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    int i, m, jk, k1, i1, j1, bool, z1,j;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    double ***freq; /* Frequencies */
             for (j=1; j<=i;j++){    double *pp, **prop;
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    double pos,posprop; 
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));    double  y2; /* in fractional years */
             }    int iagemin, iagemax;
           }  
         }/* end of loop for state */    iagemin= (int) agemin;
       } /* end of loop for age */    iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
       /* Confidence intervalle of pij  */    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       /*    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       fprintf(ficgp,"\nset noparametric;unset label");    j1=0;
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");    
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    j=cptcoveff;
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);    
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);    for(k1=1; k1<=j;k1++){
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);      for(i1=1; i1<=ncodemax[k1];i1++){
       */        j1++;
         
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/        for (i=1; i<=nlstate; i++)  
       first1=1;          for(m=iagemin; m <= iagemax+3; m++)
       for (k2=1; k2<=(nlstate);k2++){            prop[i][m]=0.0;
         for (l2=1; l2<=(nlstate+ndeath);l2++){       
           if(l2==k2) continue;        for (i=1; i<=imx; i++) { /* Each individual */
           j=(k2-1)*(nlstate+ndeath)+l2;          bool=1;
           for (k1=1; k1<=(nlstate);k1++){          if  (cptcovn>0) {
             for (l1=1; l1<=(nlstate+ndeath);l1++){            for (z1=1; z1<=cptcoveff; z1++) 
               if(l1==k1) continue;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
               i=(k1-1)*(nlstate+ndeath)+l1;                bool=0;
               if(i<=j) continue;          } 
               for (age=bage; age<=fage; age ++){          if (bool==1) { 
                 if ((int)age %5==0){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   mu1=mu[i][(int) age]/stepm*YEARM ;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                   mu2=mu[j][(int) age]/stepm*YEARM;                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); 
                   c12=cv12/sqrt(v1*v2);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /* Computing eigen value of matrix of covariance */                  /*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]]);*/
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                  prop[s[m][i]][iagemax+3] += weight[i]; 
                   /* Eigen vectors */                } 
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));              }
                   /*v21=sqrt(1.-v11*v11); *//* error */            } /* end selection of waves */
                   v21=(lc1-v1)/cv12*v11;          }
                   v12=-v21;        }
                   v22=v11;        for(i=iagemin; i <= iagemax+3; i++){  
                   tnalp=v21/v11;          
                   if(first1==1){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                     first1=0;            posprop += prop[jk][i]; 
                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);          } 
                   }  
                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);          for(jk=1; jk <=nlstate ; jk++){     
                   /*printf(fignu*/            if( i <=  iagemax){ 
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */              if(posprop>=1.e-5){ 
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */                probs[i][jk][j1]= prop[jk][i]/posprop;
                   if(first==1){              } else
                     first=0;                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
                     fprintf(ficgp,"\nset parametric;unset label");            } 
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);          }/* end jk */ 
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        }/* end i */ 
                     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);      } /* end i1 */
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);    } /* end k1 */
                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);    
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);    /*free_vector(pp,1,nlstate);*/
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\  }  /* End of prevalence */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\  
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));  /************* Waves Concatenation ***************/
                   }else{  
                     first=0;  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)
                     fprintf(fichtm," %d (%.3f),",(int) age, c12);  {
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);       Death is a valid wave (if date is known).
                     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",\       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));       and mw[mi+1][i]. dh depends on stepm.
                   }/* if first */       */
                 } /* age mod 5 */  
               } /* end loop age */    int i, mi, m;
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
               first=1;       double sum=0., jmean=0.;*/
             } /*l12 */    int first;
           } /* k12 */    int j, k=0,jk, ju, jl;
         } /*l1 */    double sum=0.;
       }/* k1 */    first=0;
     } /* loop covariates */    jmin=1e+5;
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    jmax=-1;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    jmean=0.;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    for(i=1; i<=imx; i++){
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);      mi=0;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      m=firstpass;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      while(s[m][i] <= nlstate){
   }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   free_vector(xp,1,npar);          mw[++mi][i]=m;
   fclose(ficresprob);        if(m >=lastpass)
   fclose(ficresprobcov);          break;
   fclose(ficresprobcor);        else
   fclose(ficgp);          m++;
   fclose(fichtm);      }/* end while */
 }      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
 /******************* Printing html file ***********/           /* Only death is a correct wave */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \        mw[mi][i]=m;
                   int lastpass, int stepm, int weightopt, char model[],\      }
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\  
                   int popforecast, int estepm ,\      wav[i]=mi;
                   double jprev1, double mprev1,double anprev1, \      if(mi==0){
                   double jprev2, double mprev2,double anprev2){        nbwarn++;
   int jj1, k1, i1, cpt;        if(first==0){
   /*char optionfilehtm[FILENAMELENGTH];*/          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {          first=1;
     printf("Problem with %s \n",optionfilehtm), exit(0);        }
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);        if(first==1){
   }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n      } /* end mi==0 */
  - 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    } /* End individuals */
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n  
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    for(i=1; i<=imx; i++){
  - Life expectancies by age and initial health status (estepm=%2d months):      for(mi=1; mi<wav[i];mi++){
    <a href=\"e%s\">e%s</a> <br>\n</li>", \        if (stepm <=0)
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);          dh[mi][i]=1;
         else{
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
  m=cptcoveff;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
  jj1=0;                nberr++;
  for(k1=1; k1<=m;k1++){                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]);
    for(i1=1; i1<=ncodemax[k1];i1++){                j=1; /* Temporary Dangerous patch */
      jj1++;                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);
      if (cptcovn > 0) {                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
        for (cpt=1; cpt<=cptcoveff;cpt++)              }
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);              k=k+1;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              if (j >= jmax){
      }                jmax=j;
      /* Pij */                ijmax=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);                  if (j <= jmin){
      /* Quasi-incidences */                jmin=j;
      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>                ijmin=i;
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              }
        /* Stable prevalence in each health state */              sum=sum+j;
        for(cpt=1; cpt<nlstate;cpt++){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            }
        }          }
      for(cpt=1; cpt<=nlstate;cpt++) {          else{
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  /*        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<br>- Total life expectancy by age and            k=k+1;
 health expectancies in states (1) and (2): e%s%d.png<br>            if (j >= jmax) {
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              jmax=j;
    } /* end i1 */              ijmax=i;
  }/* End k1 */            }
  fprintf(fichtm,"</ul>");            else if (j <= jmin){
               jmin=j;
               ijmin=i;
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n            }
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n            /*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]);*/
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n            if(j<0){
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n              nberr++;
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n              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]);
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n              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]);
  - 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);            }
             sum=sum+j;
  if(popforecast==1) fprintf(fichtm,"\n          }
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n          jk= j/stepm;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          jl= j -jk*stepm;
         <br>",fileres,fileres,fileres,fileres);          ju= j -(jk+1)*stepm;
  else          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
    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);            if(jl==0){
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");              dh[mi][i]=jk;
               bh[mi][i]=0;
  m=cptcoveff;            }else{ /* We want a negative bias in order to only have interpolation ie
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                    * to avoid the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
  jj1=0;              bh[mi][i]=ju;
  for(k1=1; k1<=m;k1++){            }
    for(i1=1; i1<=ncodemax[k1];i1++){          }else{
      jj1++;            if(jl <= -ju){
      if (cptcovn > 0) {              dh[mi][i]=jk;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");              bh[mi][i]=jl;       /* bias is positive if real duration
        for (cpt=1; cpt<=cptcoveff;cpt++)                                   * is higher than the multiple of stepm and negative otherwise.
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);                                   */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            }
      }            else{
      for(cpt=1; cpt<=nlstate;cpt++) {              dh[mi][i]=jk+1;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              bh[mi][i]=ju;
 interval) in state (%d): v%s%d%d.png <br>            }
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              if(dh[mi][i]==0){
      }              dh[mi][i]=1; /* At least one step */
    } /* end i1 */              bh[mi][i]=ju; /* At least one step */
  }/* End k1 */              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
  fprintf(fichtm,"</ul>");            }
 fclose(fichtm);          } /* end if mle */
 }        }
       } /* end wave */
 /******************* Gnuplot file **************/    }
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    jmean=sum/k;
     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);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   int ng;   }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);  /*********** Tricode ****************************/
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);  void tricode(int *Tvar, int **nbcode, int imx)
   }  {
     /* Uses cptcovn+2*cptcovprod as the number of covariates */
 #ifdef windows    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
     fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
 m=pow(2,cptcoveff);    int modmaxcovj=0; /* Modality max of covariates j */
      cptcoveff=0; 
  /* 1eme*/   
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for (k=0; k<maxncov; k++) Ndum[k]=0;
    for (k1=1; k1<= m ; k1 ++) {    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   
 #ifdef windows    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
      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);                                 modality of this covariate Vj*/ 
 #endif        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
 #ifdef unix                                        modality of the nth covariate of individual i. */
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 #endif        if (ij > modmaxcovj) modmaxcovj=ij; 
         /* getting the maximum value of the modality of the covariate
 for (i=1; i<= nlstate ; i ++) {           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           female is 1, then modmaxcovj=1.*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }
 }      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     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=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
     for (i=1; i<= nlstate ; i ++) {        if( Ndum[i] != 0 )
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          ncodemax[j]++; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        /* Number of modalities of the j th covariate. In fact
 }           ncodemax[j]=2 (dichotom. variables only) but it could be more for
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);           historical reasons */
      for (i=1; i<= nlstate ; i ++) {      } /* Ndum[-1] number of undefined modalities */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
 }        ij=1; 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
 #ifdef unix        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
 #endif            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
    }                                       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; */
   /*2 eme*/            ij++;
           }
   for (k1=1; k1<= m ; k1 ++) {          if (ij > ncodemax[j]) break; 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);        }  /* end of loop on */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      } /* end of loop on modality */ 
        } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     for (i=1; i<= nlstate+1 ; i ++) {    
       k=2*i;    for (k=0; k< maxncov; k++) Ndum[k]=0;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    
       for (j=1; j<= nlstate+1 ; j ++) {    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
   if (j==i) 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]++;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");   }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);   ij=1;
       for (j=1; j<= nlstate+1 ; j ++) {   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");     if((Ndum[i]!=0) && (i<=ncovcol)){
         else fprintf(ficgp," \%%*lf (\%%*lf)");       Tvaraff[ij]=i; /*For printing */
 }         ij++;
       fprintf(ficgp,"\" t\"\" w l 0,");     }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);   }
       for (j=1; j<= nlstate+1 ; j ++) {   ij--;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");   cptcoveff=ij; /*Number of simple covariates*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  /*********** Health Expectancies ****************/
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   }  
    {
   /*3eme*/    /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   for (k1=1; k1<= m ; k1 ++) {    int nhstepma, nstepma; /* Decreasing with age */
     for (cpt=1; cpt<= nlstate ; cpt ++) {    double age, agelim, hf;
       k=2+nlstate*(2*cpt-2);    double ***p3mat;
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    double eip;
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    pstamp(ficreseij);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    fprintf(ficreseij,"# Age");
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    for(i=1; i<=nlstate;i++){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      for(j=1; j<=nlstate;j++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        fprintf(ficreseij," e%1d%1d ",i,j);
       }
 */      fprintf(ficreseij," e%1d. ",i);
       for (i=1; i< nlstate ; i ++) {    }
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);    fprintf(ficreseij,"\n");
   
       }    
     }    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   /* CV preval stat */    else  hstepm=estepm;   
     for (k1=1; k1<= m ; k1 ++) {    /* We compute the life expectancy from trapezoids spaced every estepm months
     for (cpt=1; cpt<nlstate ; cpt ++) {     * This is mainly to measure the difference between two models: for example
       k=3;     * if stepm=24 months pijx are given only every 2 years and by summing them
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
       for (i=1; i< nlstate ; i ++)     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         fprintf(ficgp,"+$%d",k+i+1);     * to compare the new estimate of Life expectancy with the same linear 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);     * hypothesis. A more precise result, taking into account a more precise
           * curvature will be obtained if estepm is as small as stepm. */
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    /* For example we decided to compute the life expectancy with the smallest unit */
       for (i=1; i< nlstate ; i ++) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         l=3+(nlstate+ndeath)*cpt;       nhstepm is the number of hstepm from age to agelim 
         fprintf(ficgp,"+$%d",l+i+1);       nstepm is the number of stepm from age to agelin. 
       }       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);         and note for a fixed period like estepm months */
     }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   }         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
   /* proba elementaires */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
    for(i=1,jk=1; i <=nlstate; i++){       results. So we changed our mind and took the option of the best precision.
     for(k=1; k <=(nlstate+ndeath); k++){    */
       if (k != i) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         for(j=1; j <=ncovmodel; j++){  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    agelim=AGESUP;
           jk++;    /* If stepm=6 months */
           fprintf(ficgp,"\n");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       }      
     }  /* nhstepm age range expressed in number of stepm */
    }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    /* if (stepm >= YEARM) hstepm=1;*/
      for(jk=1; jk <=m; jk++) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        if (ng==2)  
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    for (age=bage; age<=fage; age ++){ 
        else      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
          fprintf(ficgp,"\nset title \"Probability\"\n");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);      /* if (stepm >= YEARM) hstepm=1;*/
        i=1;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
        for(k2=1; k2<=nlstate; k2++) {  
          k3=i;      /* If stepm=6 months */
          for(k=1; k<=(nlstate+ndeath); k++) {      /* Computed by stepm unit matrices, product of hstepma matrices, stored
            if (k != k2){         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
              if(ng==2)      
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
              else      
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
              ij=1;      
              for(j=3; j <=ncovmodel; j++) {      printf("%d|",(int)age);fflush(stdout);
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      
                  ij++;      /* Computing expectancies */
                }      for(i=1; i<=nlstate;i++)
                else        for(j=1; j<=nlstate;j++)
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          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;
              fprintf(ficgp,")/(1");            
                          /* 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(k1=1; k1 <=nlstate; k1++){    
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          }
                ij=1;  
                for(j=3; j <=ncovmodel; j++){      fprintf(ficreseij,"%3.0f",age );
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for(i=1; i<=nlstate;i++){
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        eip=0;
                    ij++;        for(j=1; j<=nlstate;j++){
                  }          eip +=eij[i][j][(int)age];
                  else          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        }
                }        fprintf(ficreseij,"%9.4f", eip );
                fprintf(ficgp,")");      }
              }      fprintf(ficreseij,"\n");
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    }
              i=i+ncovmodel;    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            }    printf("\n");
          } /* end k */    fprintf(ficlog,"\n");
        } /* end k2 */    
      } /* end jk */  }
    } /* end ng */  
    fclose(ficgp);  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[] )
 }  /* end gnuplot */  
   {
     /* Covariances of health expectancies eij and of total life expectancies according
 /*************** Moving average **************/     to initial status i, ei. .
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   int i, cpt, cptcod;    int nhstepma, nstepma; /* Decreasing with age */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    double age, agelim, hf;
       for (i=1; i<=nlstate;i++)    double ***p3matp, ***p3matm, ***varhe;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    double **dnewm,**doldm;
           mobaverage[(int)agedeb][i][cptcod]=0.;    double *xp, *xm;
        double **gp, **gm;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    double ***gradg, ***trgradg;
       for (i=1; i<=nlstate;i++){    int theta;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){    double eip, vip;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    xp=vector(1,npar);
         }    xm=vector(1,npar);
       }    dnewm=matrix(1,nlstate*nlstate,1,npar);
     }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
        
 }    pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
 /************** Forecasting ******************/    for(i=1; i<=nlstate;i++){
 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){      for(j=1; j<=nlstate;j++)
          fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      fprintf(ficresstdeij," e%1d. ",i);
   int *popage;    }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    fprintf(ficresstdeij,"\n");
   double *popeffectif,*popcount;  
   double ***p3mat;    pstamp(ficrescveij);
   char fileresf[FILENAMELENGTH];    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
  agelim=AGESUP;    for(i=1; i<=nlstate;i++)
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(i2=1; i2<=nlstate;i2++)
            for(j2=1; j2<=nlstate;j2++){
              cptj2= (j2-1)*nlstate+i2;
   strcpy(fileresf,"f");            if(cptj2 <= cptj)
   strcat(fileresf,fileres);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   if((ficresf=fopen(fileresf,"w"))==NULL) {          }
     printf("Problem with forecast resultfile: %s\n", fileresf);      }
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    fprintf(ficrescveij,"\n");
   }    
   printf("Computing forecasting: result on file '%s' \n", fileresf);    if(estepm < stepm){
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   if (mobilav==1) {     * This is mainly to measure the difference between two models: for example
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * if stepm=24 months pijx are given only every 2 years and by summing them
     movingaverage(agedeb, fage, ageminpar, mobaverage);     * 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 
   stepsize=(int) (stepm+YEARM-1)/YEARM;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   if (stepm<=12) stepsize=1;     * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
   agelim=AGESUP;     * curvature will be obtained if estepm is as small as stepm. */
    
   hstepm=1;    /* For example we decided to compute the life expectancy with the smallest unit */
   hstepm=hstepm/stepm;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   yp1=modf(dateintmean,&yp);       nhstepm is the number of hstepm from age to agelim 
   anprojmean=yp;       nstepm is the number of stepm from age to agelin. 
   yp2=modf((yp1*12),&yp);       Look at hpijx to understand the reason of that which relies in memory size
   mprojmean=yp;       and note for a fixed period like estepm months */
   yp1=modf((yp2*30.5),&yp);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   jprojmean=yp;       survival function given by stepm (the optimization length). Unfortunately it
   if(jprojmean==0) jprojmean=1;       means that if the survival funtion is printed only each two years of age and if
   if(mprojmean==0) jprojmean=1;       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.
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   for(cptcov=1;cptcov<=i2;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /* If stepm=6 months */
       k=k+1;    /* nhstepm age range expressed in number of stepm */
       fprintf(ficresf,"\n#******");    agelim=AGESUP;
       for(j=1;j<=cptcoveff;j++) {    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       }    /* if (stepm >= YEARM) hstepm=1;*/
       fprintf(ficresf,"******\n");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fprintf(ficresf,"# StartingAge FinalAge");    
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         fprintf(ficresf,"\n");    gp=matrix(0,nhstepm,1,nlstate*nlstate);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    for (age=bage; age<=fage; age ++){ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           nhstepm = nhstepm/hstepm;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                /* if (stepm >= YEARM) hstepm=1;*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        /* If stepm=6 months */
              /* Computed by stepm unit matrices, product of hstepma matrices, stored
           for (h=0; h<=nhstepm; h++){         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
             if (h==(int) (calagedate+YEARM*cpt)) {      
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             }  
             for(j=1; j<=nlstate+ndeath;j++) {      /* Computing  Variances of health expectancies */
               kk1=0.;kk2=0;      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
               for(i=1; i<=nlstate;i++) {                       decrease memory allocation */
                 if (mobilav==1)      for(theta=1; theta <=npar; theta++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        for(i=1; i<=npar; i++){ 
                 else {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          xm[i] = x[i] - (i==theta ?delti[theta]:0);
                 }        }
                        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
               }        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
               if (h==(int)(calagedate+12*cpt)){    
                 fprintf(ficresf," %.3f", kk1);        for(j=1; j<= nlstate; j++){
                                  for(i=1; i<=nlstate; i++){
               }            for(h=0; h<=nhstepm-1; h++){
             }              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
           }              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
         }          }
       }        }
     }       
   }        for(ij=1; ij<= nlstate*nlstate; ij++)
                  for(h=0; h<=nhstepm-1; h++){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
   fclose(ficresf);      }/* End theta */
 }      
 /************** 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){      for(h=0; h<=nhstepm-1; h++)
          for(j=1; j<=nlstate*nlstate;j++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          for(theta=1; theta <=npar; theta++)
   int *popage;            trgradg[h][j][theta]=gradg[h][theta][j];
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;       for(ij=1;ij<=nlstate*nlstate;ij++)
   char filerespop[FILENAMELENGTH];        for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       printf("%d|",(int)age);fflush(stdout);
   agelim=AGESUP;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;       for(h=0;h<=nhstepm-1;h++){
          for(k=0;k<=nhstepm-1;k++){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          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++)
   strcpy(filerespop,"pop");            for(ji=1;ji<=nlstate*nlstate;ji++)
   strcat(filerespop,fileres);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        }
     printf("Problem with forecast resultfile: %s\n", filerespop);      }
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);  
   }      /* Computing expectancies */
   printf("Computing forecasting: result on file '%s' \n", filerespop);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          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;
   if (mobilav==1) {            
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            /* 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]);*/
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }          }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;      fprintf(ficresstdeij,"%3.0f",age );
   if (stepm<=12) stepsize=1;      for(i=1; i<=nlstate;i++){
          eip=0.;
   agelim=AGESUP;        vip=0.;
          for(j=1; j<=nlstate;j++){
   hstepm=1;          eip += eij[i][j][(int)age];
   hstepm=hstepm/stepm;          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
              vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   if (popforecast==1) {          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
     if((ficpop=fopen(popfile,"r"))==NULL) {        }
       printf("Problem with population file : %s\n",popfile);exit(0);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);      }
     }      fprintf(ficresstdeij,"\n");
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);      fprintf(ficrescveij,"%3.0f",age );
     popcount=vector(0,AGESUP);      for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++){
     i=1;            cptj= (j-1)*nlstate+i;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          for(i2=1; i2<=nlstate;i2++)
                for(j2=1; j2<=nlstate;j2++){
     imx=i;              cptj2= (j2-1)*nlstate+i2;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];              if(cptj2 <= cptj)
   }                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
   for(cptcov=1;cptcov<=i2;cptcov++){        }
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fprintf(ficrescveij,"\n");
       k=k+1;     
       fprintf(ficrespop,"\n#******");    }
       for(j=1;j<=cptcoveff;j++) {    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       fprintf(ficrespop,"******\n");    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       fprintf(ficrespop,"# Age");    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if (popforecast==1)  fprintf(ficrespop," [Population]");    printf("\n");
          fprintf(ficlog,"\n");
       for (cpt=0; cpt<=0;cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      free_vector(xm,1,npar);
            free_vector(xp,1,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           nhstepm = nhstepm/hstepm;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
            }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;  /************ Variance ******************/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    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[])
          {
           for (h=0; h<=nhstepm; h++){    /* Variance of health expectancies */
             if (h==(int) (calagedate+YEARM*cpt)) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    /* double **newm;*/
             }    double **dnewm,**doldm;
             for(j=1; j<=nlstate+ndeath;j++) {    double **dnewmp,**doldmp;
               kk1=0.;kk2=0;    int i, j, nhstepm, hstepm, h, nstepm ;
               for(i=1; i<=nlstate;i++) {                  int k, cptcode;
                 if (mobilav==1)    double *xp;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    double **gp, **gm;  /* for var eij */
                 else {    double ***gradg, ***trgradg; /*for var eij */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double **gradgp, **trgradgp; /* for var p point j */
                 }    double *gpp, *gmp; /* for var p point j */
               }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
               if (h==(int)(calagedate+12*cpt)){    double ***p3mat;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    double age,agelim, hf;
                   /*fprintf(ficrespop," %.3f", kk1);    double ***mobaverage;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    int theta;
               }    char digit[4];
             }    char digitp[25];
             for(i=1; i<=nlstate;i++){  
               kk1=0.;    char fileresprobmorprev[FILENAMELENGTH];
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    if(popbased==1){
                 }      if(mobilav!=0)
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        strcpy(digitp,"-populbased-mobilav-");
             }      else strcpy(digitp,"-populbased-nomobil-");
     }
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    else 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      strcpy(digitp,"-stablbased-");
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if (mobilav!=0) {
         }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   /******/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    strcpy(fileresprobmorprev,"prmorprev"); 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    sprintf(digit,"%-d",ij);
           nhstepm = nhstepm/hstepm;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
              strcat(fileresprobmorprev,digit); /* Tvar to be done */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           oldm=oldms;savm=savms;    strcat(fileresprobmorprev,fileres);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           for (h=0; h<=nhstepm; h++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
             if (h==(int) (calagedate+YEARM*cpt)) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    }
             }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             for(j=1; j<=nlstate+ndeath;j++) {   
               kk1=0.;kk2=0;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
               for(i=1; i<=nlstate;i++) {                  pstamp(ficresprobmorprev);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
               }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
             }      fprintf(ficresprobmorprev," p.%-d SE",j);
           }      for(i=1; i<=nlstate;i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         }    }  
       }    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");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
   if (popforecast==1) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_ivector(popage,0,AGESUP);    pstamp(ficresvij);
     free_vector(popeffectif,0,AGESUP);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     free_vector(popcount,0,AGESUP);    if(popbased==1)
   }      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    else
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   fclose(ficrespop);    fprintf(ficresvij,"# Age");
 }    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
 /***********************************************/        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
 /**************** Main Program *****************/    fprintf(ficresvij,"\n");
 /***********************************************/  
     xp=vector(1,npar);
 int main(int argc, char *argv[])    dnewm=matrix(1,nlstate,1,npar);
 {    doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double agedeb, agefin,hf;  
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
   double fret;    gmp=vector(nlstate+1,nlstate+ndeath);
   double **xi,tmp,delta;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
   double dum; /* Dummy variable */    if(estepm < stepm){
   double ***p3mat;      printf ("Problem %d lower than %d\n",estepm, stepm);
   int *indx;    }
   char line[MAXLINE], linepar[MAXLINE];    else  hstepm=estepm;   
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];    /* For example we decided to compute the life expectancy with the smallest unit */
   int firstobs=1, lastobs=10;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   int sdeb, sfin; /* Status at beginning and end */       nhstepm is the number of hstepm from age to agelim 
   int c,  h , cpt,l;       nstepm is the number of stepm from age to agelin. 
   int ju,jl, mi;       Look at function hpijx to understand why (it is linked to memory size questions) */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;       survival function given by stepm (the optimization length). Unfortunately it
   int mobilav=0,popforecast=0;       means that if the survival funtion is printed every two years of age and if
   int hstepm, nhstepm;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;       results. So we changed our mind and took the option of the best precision.
     */
   double bage, fage, age, agelim, agebase;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double ftolpl=FTOL;    agelim = AGESUP;
   double **prlim;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double *severity;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   double ***param; /* Matrix of parameters */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double  *p;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double **matcov; /* Matrix of covariance */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   double ***delti3; /* Scale */      gp=matrix(0,nhstepm,1,nlstate);
   double *delti; /* Scale */      gm=matrix(0,nhstepm,1,nlstate);
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;      for(theta=1; theta <=npar; theta++){
   double kk1, kk2;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   char *alph[]={"a","a","b","c","d","e"}, str[4];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
   char z[1]="c", occ;          if(mobilav ==0){
 #include <sys/time.h>            for(i=1; i<=nlstate;i++)
 #include <time.h>              prlim[i][i]=probs[(int)age][i][ij];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
   /* long total_usecs;              prlim[i][i]=mobaverage[(int)age][i][ij];
   struct timeval start_time, end_time;          }
          }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    
   getcwd(pathcd, size);        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   printf("\n%s",version);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   if(argc <=1){              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     printf("\nEnter the parameter file name: ");          }
     scanf("%s",pathtot);        }
   }        /* This for computing probability of death (h=1 means
   else{           computed over hstepm matrices product = hstepm*stepm months) 
     strcpy(pathtot,argv[1]);           as a weighted average of prlim.
   }        */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   /*cygwin_split_path(pathtot,path,optionfile);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   /* cutv(path,optionfile,pathtot,'\\');*/        }    
         /* end probability of death */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   chdir(path);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   replace(pathc,path);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 /*-------- arguments in the command line --------*/   
         if (popbased==1) {
   /* Log file */          if(mobilav ==0){
   strcat(filelog, optionfilefiname);            for(i=1; i<=nlstate;i++)
   strcat(filelog,".log");    /* */              prlim[i][i]=probs[(int)age][i][ij];
   if((ficlog=fopen(filelog,"w"))==NULL)    {          }else{ /* mobilav */ 
     printf("Problem with logfile %s\n",filelog);            for(i=1; i<=nlstate;i++)
     goto end;              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   fprintf(ficlog,"Log filename:%s\n",filelog);        }
   fprintf(ficlog,"\n%s",version);  
   fprintf(ficlog,"\nEnter the parameter file name: ");        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          for(h=0; h<=nhstepm; h++){
   fflush(ficlog);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   /* */          }
   strcpy(fileres,"r");        }
   strcat(fileres, optionfilefiname);        /* This for computing probability of death (h=1 means
   strcat(fileres,".txt");    /* Other files have txt extension */           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   /*---------arguments file --------*/        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     printf("Problem with optionfile %s\n",optionfile);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);        }    
     goto end;        /* end probability of death */
   }  
         for(j=1; j<= nlstate; j++) /* vareij */
   strcpy(filereso,"o");          for(h=0; h<=nhstepm; h++){
   strcat(filereso,fileres);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   if((ficparo=fopen(filereso,"w"))==NULL) {          }
     printf("Problem with Output resultfile: %s\n", filereso);  
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     goto end;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   }        }
   
   /* Reads comments: lines beginning with '#' */      } /* End theta */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for(h=0; h<=nhstepm; h++) /* veij */
     fputs(line,ficparo);        for(j=1; j<=nlstate;j++)
   }          for(theta=1; theta <=npar; theta++)
   ungetc(c,ficpar);            trgradg[h][j][theta]=gradg[h][theta][j];
   
   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);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   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);        for(theta=1; theta <=npar; theta++)
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);          trgradgp[j][theta]=gradgp[theta][j];
 while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     puts(line);      for(i=1;i<=nlstate;i++)
     fputs(line,ficparo);        for(j=1;j<=nlstate;j++)
   }          vareij[i][j][(int)age] =0.;
   ungetc(c,ficpar);  
        for(h=0;h<=nhstepm;h++){
            for(k=0;k<=nhstepm;k++){
   covar=matrix(0,NCOVMAX,1,n);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   cptcovn=0;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
   ncovmodel=2+cptcovn;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        }
        }
   /* Read guess parameters */    
   /* 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);  
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     for(i=1; i <=nlstate; i++)   
     for(j=1; j <=nlstate+ndeath-1; j++){      if (popbased==1) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);        if(mobilav ==0){
       fprintf(ficparo,"%1d%1d",i1,j1);          for(i=1; i<=nlstate;i++)
       if(mle==1)            prlim[i][i]=probs[(int)age][i][ij];
         printf("%1d%1d",i,j);        }else{ /* mobilav */ 
       fprintf(ficlog,"%1d%1d",i,j);          for(i=1; i<=nlstate;i++)
       for(k=1; k<=ncovmodel;k++){            prlim[i][i]=mobaverage[(int)age][i][ij];
         fscanf(ficpar," %lf",&param[i][j][k]);        }
         if(mle==1){      }
           printf(" %lf",param[i][j][k]);               
           fprintf(ficlog," %lf",param[i][j][k]);      /* This for computing probability of death (h=1 means
         }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         else         as a weighted average of prlim.
           fprintf(ficlog," %lf",param[i][j][k]);      */
         fprintf(ficparo," %lf",param[i][j][k]);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       fscanf(ficpar,"\n");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       if(mle==1)      }    
         printf("\n");      /* end probability of death */
       fprintf(ficlog,"\n");  
       fprintf(ficparo,"\n");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   p=param[1][1];        }
        } 
   /* Reads comments: lines beginning with '#' */      fprintf(ficresprobmorprev,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      fprintf(ficresvij,"%.0f ",age );
     fgets(line, MAXLINE, ficpar);      for(i=1; i<=nlstate;i++)
     puts(line);        for(j=1; j<=nlstate;j++){
     fputs(line,ficparo);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   }        }
   ungetc(c,ficpar);      fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      free_matrix(gm,0,nhstepm,1,nlstate);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   for(i=1; i <=nlstate; i++){      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    } /* End age */
       printf("%1d%1d",i,j);    free_vector(gpp,nlstate+1,nlstate+ndeath);
       fprintf(ficparo,"%1d%1d",i1,j1);    free_vector(gmp,nlstate+1,nlstate+ndeath);
       for(k=1; k<=ncovmodel;k++){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         fscanf(ficpar,"%le",&delti3[i][j][k]);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         printf(" %le",delti3[i][j][k]);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
         fprintf(ficparo," %le",delti3[i][j][k]);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       }    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       fscanf(ficpar,"\n");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       printf("\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficparo,"\n");  /*   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 lt 2 ",subdirf(fileresprobmorprev));
   }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 3 ",subdirf(fileresprobmorprev));
   delti=delti3[1][1];    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 3 ",subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   /* Reads comments: lines beginning with '#' */    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);
   while((c=getc(ficpar))=='#' && c!= EOF){    /*  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);
     ungetc(c,ficpar);  */
     fgets(line, MAXLINE, ficpar);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     puts(line);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     fputs(line,ficparo);  
   }    free_vector(xp,1,npar);
   ungetc(c,ficpar);    free_matrix(doldm,1,nlstate,1,nlstate);
      free_matrix(dnewm,1,nlstate,1,npar);
   matcov=matrix(1,npar,1,npar);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   for(i=1; i <=npar; i++){    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     fscanf(ficpar,"%s",&str);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if(mle==1)    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       printf("%s",str);    fclose(ficresprobmorprev);
     fprintf(ficlog,"%s",str);    fflush(ficgp);
     fprintf(ficparo,"%s",str);    fflush(fichtm); 
     for(j=1; j <=i; j++){  }  /* end varevsij */
       fscanf(ficpar," %le",&matcov[i][j]);  
       if(mle==1){  /************ Variance of prevlim ******************/
         printf(" %.5le",matcov[i][j]);  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(ficlog," %.5le",matcov[i][j]);  {
       }    /* Variance of prevalence limit */
       else    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         fprintf(ficlog," %.5le",matcov[i][j]);    double **newm;
       fprintf(ficparo," %.5le",matcov[i][j]);    double **dnewm,**doldm;
     }    int i, j, nhstepm, hstepm;
     fscanf(ficpar,"\n");    int k, cptcode;
     if(mle==1)    double *xp;
       printf("\n");    double *gp, *gm;
     fprintf(ficlog,"\n");    double **gradg, **trgradg;
     fprintf(ficparo,"\n");    double age,agelim;
   }    int theta;
   for(i=1; i <=npar; i++)    
     for(j=i+1;j<=npar;j++)    pstamp(ficresvpl);
       matcov[i][j]=matcov[j][i];    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
        fprintf(ficresvpl,"# Age");
   if(mle==1)    for(i=1; i<=nlstate;i++)
     printf("\n");        fprintf(ficresvpl," %1d-%1d",i,i);
   fprintf(ficlog,"\n");    fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     /*-------- Rewriting paramater file ----------*/    dnewm=matrix(1,nlstate,1,npar);
      strcpy(rfileres,"r");    /* "Rparameterfile */    doldm=matrix(1,nlstate,1,nlstate);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    
      strcat(rfileres,".");    /* */    hstepm=1*YEARM; /* Every year of age */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     if((ficres =fopen(rfileres,"w"))==NULL) {    agelim = AGESUP;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     }      if (stepm >= YEARM) hstepm=1;
     fprintf(ficres,"#%s\n",version);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
          gradg=matrix(1,npar,1,nlstate);
     /*-------- data file ----------*/      gp=vector(1,nlstate);
     if((fic=fopen(datafile,"r"))==NULL)    {      gm=vector(1,nlstate);
       printf("Problem with datafile: %s\n", datafile);goto end;  
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;      for(theta=1; theta <=npar; theta++){
     }        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
     n= lastobs;        }
     severity = vector(1,maxwav);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     outcome=imatrix(1,maxwav+1,1,n);        for(i=1;i<=nlstate;i++)
     num=ivector(1,n);          gp[i] = prlim[i][i];
     moisnais=vector(1,n);      
     annais=vector(1,n);        for(i=1; i<=npar; i++) /* Computes gradient */
     moisdc=vector(1,n);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     andc=vector(1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     agedc=vector(1,n);        for(i=1;i<=nlstate;i++)
     cod=ivector(1,n);          gm[i] = prlim[i][i];
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for(i=1;i<=nlstate;i++)
     mint=matrix(1,maxwav,1,n);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     anint=matrix(1,maxwav,1,n);      } /* End theta */
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);          trgradg =matrix(1,nlstate,1,npar);
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
     i=1;          trgradg[j][theta]=gradg[theta][j];
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {      for(i=1;i<=nlstate;i++)
                varpl[i][(int)age] =0.;
         for (j=maxwav;j>=1;j--){      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           strcpy(line,stra);      for(i=1;i<=nlstate;i++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }      fprintf(ficresvpl,"%.0f ",age );
              for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      free_vector(gm,1,nlstate);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    } /* End age */
         for (j=ncovcol;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(xp,1,npar);
         }    free_matrix(doldm,1,nlstate,1,npar);
         num[i]=atol(stra);    free_matrix(dnewm,1,nlstate,1,nlstate);
          
         /*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;}*/  
   /************ Variance of one-step probabilities  ******************/
         i=i+1;  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
       }  {
     }    int i, j=0,  i1, k1, l1, t, tj;
     /* printf("ii=%d", ij);    int k2, l2, j1,  z1;
        scanf("%d",i);*/    int k=0,l, cptcode;
   imx=i-1; /* Number of individuals */    int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   /* for (i=1; i<=imx; i++){    double **dnewm,**doldm;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    double *xp;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    double *gp, *gm;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    double **gradg, **trgradg;
     }*/    double **mu;
    /*  for (i=1; i<=imx; i++){    double age,agelim, cov[NCOVMAX];
      if (s[4][i]==9)  s[4][i]=-1;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
      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]));}*/    int theta;
      char fileresprob[FILENAMELENGTH];
      char fileresprobcov[FILENAMELENGTH];
   /* Calculation of the number of parameter from char model*/    char fileresprobcor[FILENAMELENGTH];
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */  
   Tprod=ivector(1,15);    double ***varpij;
   Tvaraff=ivector(1,15);  
   Tvard=imatrix(1,15,1,2);    strcpy(fileresprob,"prob"); 
   Tage=ivector(1,15);          strcat(fileresprob,fileres);
        if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   if (strlen(model) >1){      printf("Problem with resultfile: %s\n", fileresprob);
     j=0, j1=0, k1=1, k2=1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     j=nbocc(model,'+');    }
     j1=nbocc(model,'*');    strcpy(fileresprobcov,"probcov"); 
     cptcovn=j+1;    strcat(fileresprobcov,fileres);
     cptcovprod=j1;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresprobcov);
     strcpy(modelsav,model);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    }
       printf("Error. Non available option model=%s ",model);    strcpy(fileresprobcor,"probcor"); 
       fprintf(ficlog,"Error. Non available option model=%s ",model);    strcat(fileresprobcor,fileres);
       goto end;    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobcor);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     for(i=(j+1); i>=1;i--){    }
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       /*scanf("%d",i);*/    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       if (strchr(strb,'*')) {  /* Model includes a product */    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         if (strcmp(strc,"age")==0) { /* Vn*age */    pstamp(ficresprob);
           cptcovprod--;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           cutv(strb,stre,strd,'V');    fprintf(ficresprob,"# Age");
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/    pstamp(ficresprobcov);
           cptcovage++;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
             Tage[cptcovage]=i;    fprintf(ficresprobcov,"# Age");
             /*printf("stre=%s ", stre);*/    pstamp(ficresprobcor);
         }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
         else if (strcmp(strd,"age")==0) { /* or age*Vn */    fprintf(ficresprobcor,"# Age");
           cptcovprod--;  
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);    for(i=1; i<=nlstate;i++)
           cptcovage++;      for(j=1; j<=(nlstate+ndeath);j++){
           Tage[cptcovage]=i;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         else {  /* Age is not in the model */        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/      }  
           Tvar[i]=ncovcol+k1;   /* fprintf(ficresprob,"\n");
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */    fprintf(ficresprobcov,"\n");
           Tprod[k1]=i;    fprintf(ficresprobcor,"\n");
           Tvard[k1][1]=atoi(strc); /* m*/   */
           Tvard[k1][2]=atoi(stre); /* n */    xp=vector(1,npar);
           Tvar[cptcovn+k2]=Tvard[k1][1];    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           for (k=1; k<=lastobs;k++)    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           k1++;    first=1;
           k2=k2+2;    fprintf(ficgp,"\n# Routine varprob");
         }    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       }    fprintf(fichtm,"\n");
       else { /* no more sum */  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
        /*  scanf("%d",i);*/    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
       cutv(strd,strc,strb,'V');    file %s<br>\n",optionfilehtmcov);
       Tvar[i]=atoi(strc);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
       }  and drawn. It helps understanding how is the covariance between two incidences.\
       strcpy(modelsav,stra);     They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    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. \
         scanf("%d",i);*/  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     } /* end of loop + */  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   } /* end model */  standard deviations wide on each axis. <br>\
     Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   printf("cptcovprod=%d ", cptcovprod);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/    cov[1]=1;
     fclose(fic);    tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     /*  if(mle==1){*/    j1=0;
     if (weightopt != 1) { /* Maximisation without weights*/    for(t=1; t<=tj;t++){
       for(i=1;i<=n;i++) weight[i]=1.0;      for(i1=1; i1<=ncodemax[t];i1++){ 
     }        j1++;
     /*-calculation of age at interview from date of interview and age at death -*/        if  (cptcovn>0) {
     agev=matrix(1,maxwav,1,imx);          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for (i=1; i<=imx; i++) {          fprintf(ficresprob, "**********\n#\n");
       for(m=2; (m<= maxwav); m++) {          fprintf(ficresprobcov, "\n#********** Variable "); 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          anint[m][i]=9999;          fprintf(ficresprobcov, "**********\n#\n");
          s[m][i]=-1;          
        }          fprintf(ficgp, "\n#********** Variable "); 
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficgp, "**********\n#\n");
     }          
           
     for (i=1; i<=imx; i++)  {          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for(m=1; (m<= maxwav); m++){          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         if(s[m][i] >0){          
           if (s[m][i] >= nlstate+1) {          fprintf(ficresprobcor, "\n#********** Variable ");    
             if(agedc[i]>0)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               if(moisdc[i]!=99 && andc[i]!=9999)          fprintf(ficresprobcor, "**********\n#");    
                 agev[m][i]=agedc[i];        }
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/        
            else {        for (age=bage; age<=fage; age ++){ 
               if (andc[i]!=9999){          cov[2]=age;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          for (k=1; k<=cptcovn;k++) {
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
               agev[m][i]=-1;          }
               }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
             }          for (k=1; k<=cptcovprod;k++)
           }            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           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]);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
             if(mint[m][i]==99 || anint[m][i]==9999)          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               agev[m][i]=1;          gp=vector(1,(nlstate)*(nlstate+ndeath));
             else if(agev[m][i] <agemin){          gm=vector(1,(nlstate)*(nlstate+ndeath));
               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(theta=1; theta <=npar; theta++){
             }            for(i=1; i<=npar; i++)
             else if(agev[m][i] >agemax){              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
               agemax=agev[m][i];            
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             }            
             /*agev[m][i]=anint[m][i]-annais[i];*/            k=0;
             /*   agev[m][i] = age[i]+2*m;*/            for(i=1; i<= (nlstate); i++){
           }              for(j=1; j<=(nlstate+ndeath);j++){
           else { /* =9 */                k=k+1;
             agev[m][i]=1;                gp[k]=pmmij[i][j];
             s[m][i]=-1;              }
           }            }
         }            
         else /*= 0 Unknown */            for(i=1; i<=npar; i++)
           agev[m][i]=1;              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       }      
                pmij(pmmij,cov,ncovmodel,xp,nlstate);
     }            k=0;
     for (i=1; i<=imx; i++)  {            for(i=1; i<=(nlstate); i++){
       for(m=1; (m<= maxwav); m++){              for(j=1; j<=(nlstate+ndeath);j++){
         if (s[m][i] > (nlstate+ndeath)) {                k=k+1;
           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);                  gm[k]=pmmij[i][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);                }
           goto end;            }
         }       
       }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
 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);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
     free_vector(severity,1,maxwav);              trgradg[j][theta]=gradg[theta][j];
     free_imatrix(outcome,1,maxwav+1,1,n);          
     free_vector(moisnais,1,n);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     free_vector(annais,1,n);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     /* free_matrix(mint,1,maxwav,1,n);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
        free_matrix(anint,1,maxwav,1,n);*/          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     free_vector(moisdc,1,n);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     free_vector(andc,1,n);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
              pmij(pmmij,cov,ncovmodel,x,nlstate);
     wav=ivector(1,imx);          
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          k=0;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          for(i=1; i<=(nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
     /* Concatenates waves */              k=k+1;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              mu[k][(int) age]=pmmij[i][j];
             }
           }
       Tcode=ivector(1,100);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       ncodemax[1]=1;              varpij[i][j][(int)age] = doldm[i][j];
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
                /*printf("\n%d ",(int)age);
    codtab=imatrix(1,100,1,10);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
    h=0;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
    m=pow(2,cptcoveff);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              }*/
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){          fprintf(ficresprob,"\n%d ",(int)age);
        for(j=1; j <= ncodemax[k]; j++){          fprintf(ficresprobcov,"\n%d ",(int)age);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          fprintf(ficresprobcor,"\n%d ",(int)age);
            h++;  
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
          }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
        }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
      }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
    }          }
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);          i=0;
       codtab[1][2]=1;codtab[2][2]=2; */          for (k=1; k<=(nlstate);k++){
    /* for(i=1; i <=m ;i++){            for (l=1; l<=(nlstate+ndeath);l++){ 
       for(k=1; k <=cptcovn; k++){              i=i++;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
       }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       printf("\n");              for (j=1; j<=i;j++){
       }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       scanf("%d",i);*/                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                  }
    /* Calculates basic frequencies. Computes observed prevalence at single age            }
        and prints on file fileres'p'. */          }/* end of loop for state */
         } /* end of loop for age */
      
            /* Confidence intervalle of pij  */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        /*
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp,"\nunset parametric;unset label");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          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);
     /* For Powell, parameters are in a vector p[] starting at p[1]          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        */
   
     if(mle==1){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        first1=1;
     }        for (k2=1; k2<=(nlstate);k2++){
              for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     /*--------- results files --------------*/            if(l2==k2) continue;
     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);            j=(k2-1)*(nlstate+ndeath)+l2;
              for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
    jk=1;                if(l1==k1) continue;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                i=(k1-1)*(nlstate+ndeath)+l1;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                if(i<=j) continue;
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");                for (age=bage; age<=fage; age ++){ 
    for(i=1,jk=1; i <=nlstate; i++){                  if ((int)age %5==0){
      for(k=1; k <=(nlstate+ndeath); k++){                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
        if (k != i)                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
          {                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
            printf("%d%d ",i,k);                    mu1=mu[i][(int) age]/stepm*YEARM ;
            fprintf(ficlog,"%d%d ",i,k);                    mu2=mu[j][(int) age]/stepm*YEARM;
            fprintf(ficres,"%1d%1d ",i,k);                    c12=cv12/sqrt(v1*v2);
            for(j=1; j <=ncovmodel; j++){                    /* Computing eigen value of matrix of covariance */
              printf("%f ",p[jk]);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
              fprintf(ficlog,"%f ",p[jk]);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
              fprintf(ficres,"%f ",p[jk]);                    if ((lc2 <0) || (lc1 <0) ){
              jk++;                      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);
            printf("\n");                      lc1=fabs(lc1);
            fprintf(ficlog,"\n");                      lc2=fabs(lc2);
            fprintf(ficres,"\n");                    }
          }  
      }                    /* Eigen vectors */
    }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
    if(mle==1){                    /*v21=sqrt(1.-v11*v11); *//* error */
      /* Computing hessian and covariance matrix */                    v21=(lc1-v1)/cv12*v11;
      ftolhess=ftol; /* Usually correct */                    v12=-v21;
      hesscov(matcov, p, npar, delti, ftolhess, func);                    v22=v11;
    }                    tnalp=v21/v11;
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");                    if(first1==1){
    printf("# Scales (for hessian or gradient estimation)\n");                      first1=0;
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\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);
    for(i=1,jk=1; i <=nlstate; i++){                    }
      for(j=1; j <=nlstate+ndeath; j++){                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
        if (j!=i) {                    /*printf(fignu*/
          fprintf(ficres,"%1d%1d",i,j);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
          printf("%1d%1d",i,j);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
          fprintf(ficlog,"%1d%1d",i,j);                    if(first==1){
          for(k=1; k<=ncovmodel;k++){                      first=0;
            printf(" %.5e",delti[jk]);                      fprintf(ficgp,"\nset parametric;unset label");
            fprintf(ficlog," %.5e",delti[jk]);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
            fprintf(ficres," %.5e",delti[jk]);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
            jk++;                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
          }   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
          printf("\n");  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
          fprintf(ficlog,"\n");                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
          fprintf(ficres,"\n");                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
        }                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
      }                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
    }                      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);
    k=1;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");                      fprintf(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),\
      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");                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
    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");                    }else{
    for(i=1;i<=npar;i++){                      first=0;
      /*  if (k>nlstate) k=1;                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
          i1=(i-1)/(ncovmodel*nlstate)+1;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
          printf("%s%d%d",alph[k],i1,tab[i]);*/                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
      fprintf(ficres,"%3d",i);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
      if(mle==1)                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
        printf("%3d",i);                    }/* if first */
      fprintf(ficlog,"%3d",i);                  } /* age mod 5 */
      for(j=1; j<=i;j++){                } /* end loop age */
        fprintf(ficres," %.5e",matcov[i][j]);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
        if(mle==1)                first=1;
          printf(" %.5e",matcov[i][j]);              } /*l12 */
        fprintf(ficlog," %.5e",matcov[i][j]);            } /* k12 */
      }          } /*l1 */
      fprintf(ficres,"\n");        }/* k1 */
      if(mle==1)      } /* loop covariates */
        printf("\n");    }
      fprintf(ficlog,"\n");    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
      k++;    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);
    while((c=getc(ficpar))=='#' && c!= EOF){    free_vector(xp,1,npar);
      ungetc(c,ficpar);    fclose(ficresprob);
      fgets(line, MAXLINE, ficpar);    fclose(ficresprobcov);
      puts(line);    fclose(ficresprobcor);
      fputs(line,ficparo);    fflush(ficgp);
    }    fflush(fichtmcov);
    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;  /******************* Printing html file ***********/
    if (fage <= 2) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
      bage = ageminpar;                    int lastpass, int stepm, int weightopt, char model[],\
      fage = agemaxpar;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
    }                    int popforecast, int estepm ,\
                        double jprev1, double mprev1,double anprev1, \
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                    double jprev2, double mprev2,double anprev2){
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    int jj1, k1, i1, cpt;
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  
         fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
    while((c=getc(ficpar))=='#' && c!= EOF){     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
      ungetc(c,ficpar);  </ul>");
      fgets(line, MAXLINE, ficpar);     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
      puts(line);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
      fputs(line,ficparo);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
    }     fprintf(fichtm,"\
    ungetc(c,ficpar);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
               stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);     fprintf(fichtm,"\
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
         fprintf(fichtm,"\
    while((c=getc(ficpar))=='#' && c!= EOF){   - (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): \
      ungetc(c,ficpar);     <a href=\"%s\">%s</a> <br>\n",
      fgets(line, MAXLINE, ficpar);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      puts(line);     fprintf(fichtm,"\
      fputs(line,ficparo);   - Population projections by age and states: \
    }     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
    ungetc(c,ficpar);  
    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;   m=cptcoveff;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);   jj1=0;
   fprintf(ficparo,"pop_based=%d\n",popbased);     for(k1=1; k1<=m;k1++){
   fprintf(ficres,"pop_based=%d\n",popbased);       for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
   while((c=getc(ficpar))=='#' && c!= EOF){       if (cptcovn > 0) {
     ungetc(c,ficpar);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fgets(line, MAXLINE, ficpar);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     puts(line);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     fputs(line,ficparo);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   }       }
   ungetc(c,ficpar);       /* Pij */
        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> \
   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);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
 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);       /* Quasi-incidences */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <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);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);       }
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);     } /* end i1 */
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);   }/* End k1 */
    fprintf(fichtm,"</ul>");
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
   
 /*------------ gnuplot -------------*/   fprintf(fichtm,"\
   strcpy(optionfilegnuplot,optionfilefiname);  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
   strcat(optionfilegnuplot,".gp");   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   }           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
   fclose(ficgp);   fprintf(fichtm,"\
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
 /*--------- index.htm --------*/           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
   strcpy(optionfilehtm,optionfile);   fprintf(fichtm,"\
   strcat(optionfilehtm,".htm");   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
     printf("Problem with %s \n",optionfilehtm), exit(0);   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): \
      <a href=\"%s\">%s</a> <br>\n</li>",
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n   fprintf(fichtm,"\
 \n   - (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): \
 Total number of observations=%d <br>\n     <a href=\"%s\">%s</a> <br>\n</li>",
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
 <hr  size=\"2\" color=\"#EC5E5E\">   fprintf(fichtm,"\
  <ul><li><h4>Parameter files</h4>\n   - 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",
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
  - Log file of the run: <a href=\"%s\">%s</a><br>\n   fprintf(fichtm,"\
  - 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);   - 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",
   fclose(fichtm);           estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
             subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
 /*------------ free_vector  -------------*/  
  chdir(path);  /*  if(popforecast==1) fprintf(fichtm,"\n */
    /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
  free_ivector(wav,1,imx);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  /*      <br>",fileres,fileres,fileres,fileres); */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    /*  else  */
  free_ivector(num,1,n);  /*    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); */
  free_vector(agedc,1,n);   fflush(fichtm);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
  fclose(ficparo);  
  fclose(ficres);   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
   /*--------------- Prevalence limit --------------*/   jj1=0;
     for(k1=1; k1<=m;k1++){
   strcpy(filerespl,"pl");     for(i1=1; i1<=ncodemax[k1];i1++){
   strcat(filerespl,fileres);       jj1++;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       if (cptcovn > 0) {
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);       }
   fprintf(ficrespl,"#Prevalence limit\n");       for(cpt=1; cpt<=nlstate;cpt++) {
   fprintf(ficrespl,"#Age ");         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   fprintf(ficrespl,"\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
         }
   prlim=matrix(1,nlstate,1,nlstate);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  true period expectancies (those weighted with period prevalences are also\
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   drawn in addition to the population based expectancies computed using\
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   observed and cahotic prevalences: %s%d.png<br>\
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   k=0;     } /* end i1 */
   agebase=ageminpar;   }/* End k1 */
   agelim=agemaxpar;   fprintf(fichtm,"</ul>");
   ftolpl=1.e-10;   fflush(fichtm);
   i1=cptcoveff;  }
   if (cptcovn < 1){i1=1;}  
   /******************* Gnuplot file **************/
   for(cptcov=1;cptcov<=i1;cptcov++){  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;    char dirfileres[132],optfileres[132];
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
         fprintf(ficrespl,"\n#******");    int ng=0;
         printf("\n#******");  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
         fprintf(ficlog,"\n#******");  /*     printf("Problem with file %s",optionfilegnuplot); */
         for(j=1;j<=cptcoveff;j++) {  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
           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]]);    /*#ifdef windows */
         }    fprintf(ficgp,"cd \"%s\" \n",pathc);
         fprintf(ficrespl,"******\n");      /*#endif */
         printf("******\n");    m=pow(2,cptcoveff);
         fprintf(ficlog,"******\n");  
            strcpy(dirfileres,optionfilefiname);
         for (age=agebase; age<=agelim; age++){    strcpy(optfileres,"vpl");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   /* 1eme*/
           fprintf(ficrespl,"%.0f",age );    for (cpt=1; cpt<= nlstate ; cpt ++) {
           for(i=1; i<=nlstate;i++)     for (k1=1; k1<= m ; k1 ++) {
           fprintf(ficrespl," %.5f", prlim[i][i]);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
           fprintf(ficrespl,"\n");       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
         }       fprintf(ficgp,"set xlabel \"Age\" \n\
       }  set ylabel \"Probability\" \n\
     }  set ter png small\n\
   fclose(ficrespl);  set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   /*------------- h Pij x at various ages ------------*/  
         for (i=1; i<= nlstate ; i ++) {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   if((ficrespij=fopen(filerespij,"w"))==NULL) {         else        fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;       }
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 1,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
   }       for (i=1; i<= nlstate ; i ++) {
   printf("Computing pij: result on file '%s' \n", filerespij);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         } 
   stepsize=(int) (stepm+YEARM-1)/YEARM;       fprintf(ficgp,"\" t\"95\%% CI\" w l lt 2,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
   /*if (stepm<=24) stepsize=2;*/       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   agelim=AGESUP;         else fprintf(ficgp," \%%*lf (\%%*lf)");
   hstepm=stepsize*YEARM; /* Every year of age */       }  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
   /* hstepm=1;   aff par mois*/    }
     /*2 eme*/
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    for (k1=1; k1<= m ; k1 ++) { 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       k=k+1;      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
         fprintf(ficrespij,"\n#****** ");      
         for(j=1;j<=cptcoveff;j++)      for (i=1; i<= nlstate+1 ; i ++) {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        k=2*i;
         fprintf(ficrespij,"******\n");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
                for (j=1; j<= nlstate+1 ; j ++) {
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          else fprintf(ficgp," \%%*lf (\%%*lf)");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
           /*      nhstepm=nhstepm*YEARM; aff par mois*/        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (j=1; j<= nlstate+1 ; j ++) {
           oldm=oldms;savm=savms;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            else fprintf(ficgp," \%%*lf (\%%*lf)");
           fprintf(ficrespij,"# Age");        }   
           for(i=1; i<=nlstate;i++)        fprintf(ficgp,"\" t\"\" w l lt 1,");
             for(j=1; j<=nlstate+ndeath;j++)        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
               fprintf(ficrespij," %1d-%1d",i,j);        for (j=1; j<= nlstate+1 ; j ++) {
           fprintf(ficrespij,"\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
            for (h=0; h<=nhstepm; h++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        }   
             for(i=1; i<=nlstate;i++)        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");
               for(j=1; j<=nlstate+ndeath;j++)        else fprintf(ficgp,"\" t\"\" w l lt 1,");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      }
             fprintf(ficrespij,"\n");    }
              }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*3eme*/
           fprintf(ficrespij,"\n");    
         }    for (k1=1; k1<= m ; k1 ++) { 
     }      for (cpt=1; cpt<= nlstate ; cpt ++) {
   }        /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   fclose(ficrespij);  set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   /*---------- Forecasting ------------------*/          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   if((stepm == 1) && (strcmp(model,".")==0)){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+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*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   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);        for (i=1; i< nlstate ; i ++) {
     fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
   }          /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
            
         } 
   /*---------- Health expectancies and variances ------------*/        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
   strcpy(filerest,"t");    }
   strcat(filerest,fileres);    
   if((ficrest=fopen(filerest,"w"))==NULL) {    /* CV preval stable (period) */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;      for (cpt=1; cpt<=nlstate ; cpt ++) {
   }        k=3;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   strcpy(filerese,"e");  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   strcat(filerese,fileres);        
   if((ficreseij=fopen(filerese,"w"))==NULL) {        for (i=1; i< nlstate ; i ++)
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          fprintf(ficgp,"+$%d",k+i+1);
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   }        
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        l=3+(nlstate+ndeath)*cpt;
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
   strcpy(fileresv,"v");          l=3+(nlstate+ndeath)*cpt;
   strcat(fileresv,fileres);          fprintf(ficgp,"+$%d",l+i+1);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     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);    /* proba elementaires */
   calagedate=-1;    for(i=1,jk=1; i <=nlstate; i++){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
   k=0;          for(j=1; j <=ncovmodel; j++){
   for(cptcov=1;cptcov<=i1;cptcov++){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            jk++; 
       k=k+1;            fprintf(ficgp,"\n");
       fprintf(ficrest,"\n#****** ");          }
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }
       fprintf(ficrest,"******\n");     }
   
       fprintf(ficreseij,"\n#****** ");     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       for(j=1;j<=cptcoveff;j++)       for(jk=1; jk <=m; jk++) {
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
       fprintf(ficreseij,"******\n");         if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
       fprintf(ficresvij,"\n#****** ");         else
       for(j=1;j<=cptcoveff;j++)           fprintf(ficgp,"\nset title \"Probability\"\n");
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
       fprintf(ficresvij,"******\n");         i=1;
          for(k2=1; k2<=nlstate; k2++) {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);           k3=i;
       oldm=oldms;savm=savms;           for(k=1; k<=(nlstate+ndeath); k++) {
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);               if (k != k2){
                 if(ng==2)
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
       oldm=oldms;savm=savms;               else
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
       if(popbased==1){               ij=1;/* To be checked else nbcode[0][0] wrong */
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);               for(j=3; j <=ncovmodel; j++) {
        }                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                     ij++;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                 }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                 else
       fprintf(ficrest,"\n");                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
       epj=vector(1,nlstate+1);               fprintf(ficgp,")/(1");
       for(age=bage; age <=fage ;age++){               
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);               for(k1=1; k1 <=nlstate; k1++){   
         if (popbased==1) {                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
           for(i=1; i<=nlstate;i++)                 ij=1;
             prlim[i][i]=probs[(int)age][i][k];                 for(j=3; j <=ncovmodel; j++){
         }                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
         fprintf(ficrest," %4.0f",age);                     ij++;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                   }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                   else
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                 }
           }                 fprintf(ficgp,")");
           epj[nlstate+1] +=epj[j];               }
         }               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
         for(i=1, vepp=0.;i <=nlstate;i++)               i=i+ncovmodel;
           for(j=1;j <=nlstate;j++)             }
             vepp += vareij[i][j][(int)age];           } /* end k */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));         } /* end k2 */
         for(j=1;j <=nlstate;j++){       } /* end jk */
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));     } /* end ng */
         }     fflush(ficgp); 
         fprintf(ficrest,"\n");  }  /* end gnuplot */
       }  
     }  
   }  /*************** Moving average **************/
 free_matrix(mint,1,maxwav,1,n);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);    int i, cpt, cptcod;
   fclose(ficreseij);    int modcovmax =1;
   fclose(ficresvij);    int mobilavrange, mob;
   fclose(ficrest);    double age;
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                               a covariate has 2 modalities */
   /*------- Variance limit prevalence------*/      if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   strcpy(fileresvpl,"vpl");    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   strcat(fileresvpl,fileres);      if(mobilav==1) mobilavrange=5; /* default */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      else mobilavrange=mobilav;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      for (age=bage; age<=fage; age++)
     exit(0);        for (i=1; i<=nlstate;i++)
   }          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
   k=0;         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   for(cptcov=1;cptcov<=i1;cptcov++){         we use a 5 terms etc. until the borders are no more concerned. 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      */ 
       k=k+1;      for (mob=3;mob <=mobilavrange;mob=mob+2){
       fprintf(ficresvpl,"\n#****** ");        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
       for(j=1;j<=cptcoveff;j++)          for (i=1; i<=nlstate;i++){
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
       fprintf(ficresvpl,"******\n");              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                      for (cpt=1;cpt<=(mob-1)/2;cpt++){
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       oldm=oldms;savm=savms;                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                }
     }              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
  }            }
           }
   fclose(ficresvpl);        }/* end age */
       }/* end mob */
   /*---------- End : free ----------------*/    }else return -1;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    return 0;
    }/* End movingaverage */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
    /************** Forecasting ******************/
    prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    /* proj1, year, month, day of starting projection 
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);       agemin, agemax range of age
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       dateprev1 dateprev2 range of dates during which prevalence is computed
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       anproj2 year of en of projection (same day and month as proj1).
      */
   free_matrix(matcov,1,npar,1,npar);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   free_vector(delti,1,npar);    int *popage;
   free_matrix(agev,1,maxwav,1,imx);    double agec; /* generic age */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
   fprintf(fichtm,"\n</body>");    double ***p3mat;
   fclose(fichtm);    double ***mobaverage;
   fclose(ficgp);    char fileresf[FILENAMELENGTH];
    
     agelim=AGESUP;
   if(erreur >0){    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     printf("End of Imach with error or warning %d\n",erreur);   
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);    strcpy(fileresf,"f"); 
   }else{    strcat(fileresf,fileres);
    printf("End of Imach\n");    if((ficresf=fopen(fileresf,"w"))==NULL) {
    fprintf(ficlog,"End of Imach\n");      printf("Problem with forecast resultfile: %s\n", fileresf);
   }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   printf("See log file on %s\n",filelog);    }
   fclose(ficlog);    printf("Computing forecasting: result on file '%s' \n", fileresf);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
    
   /* 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 (cptcoveff==0) ncodemax[cptcoveff]=1;
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
  end:        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 #ifdef windows        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   /* chdir(pathcd);*/      }
 #endif    }
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/    stepsize=(int) (stepm+YEARM-1)/YEARM;
  /*system("cd ../gp37mgw");*/    if (stepm<=12) stepsize=1;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    if(estepm < stepm){
  strcpy(plotcmd,GNUPLOTPROGRAM);      printf ("Problem %d lower than %d\n",estepm, stepm);
  strcat(plotcmd," ");    }
  strcat(plotcmd,optionfilegnuplot);    else  hstepm=estepm;   
  system(plotcmd);  
     hstepm=hstepm/stepm; 
 #ifdef windows    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   while (z[0] != 'q') {                                 fractional in yp1 */
     /* chdir(path); */    anprojmean=yp;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    yp2=modf((yp1*12),&yp);
     scanf("%s",z);    mprojmean=yp;
     if (z[0] == 'c') system("./imach");    yp1=modf((yp2*30.5),&yp);
     else if (z[0] == 'e') system(optionfilehtm);    jprojmean=yp;
     else if (z[0] == 'g') system(plotcmd);    if(jprojmean==0) jprojmean=1;
     else if (z[0] == 'q') exit(0);    if(mprojmean==0) jprojmean=1;
   }  
 #endif    i1=cptcoveff;
 }    if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   
   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;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /* 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++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     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++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8); /* 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); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,15); /* 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 <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             codtab[h][Tvar[k]]=j;
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       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=pow(2,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\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
       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); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       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 %ld 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 %ld 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.1.143


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