Diff for /imach/src/imach.c between versions 1.48 and 1.138

version 1.48, 2002/06/10 13:12:49 version 1.138, 2010/04/30 18:19:40
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.138  2010/04/30 18:19:40  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.137  2010/04/29 18:11:38  brouard
   first survey ("cross") where individuals from different ages are    (Module): Checking covariates for more complex models
   interviewed on their health status or degree of disability (in the    than V1+V2. A lot of change to be done. Unstable.
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.136  2010/04/26 20:30:53  brouard
   (if any) in individual health status.  Health expectancies are    (Module): merging some libgsl code. Fixing computation
   computed from the time spent in each health state according to a    of likelione (using inter/intrapolation if mle = 0) in order to
   model. More health states you consider, more time is necessary to reach the    get same likelihood as if mle=1.
   Maximum Likelihood of the parameters involved in the model.  The    Some cleaning of code and comments added.
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Revision 1.135  2009/10/29 15:33:14  brouard
   conditional to be observed in state i at the first wave. Therefore    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.134  2009/10/29 13:18:53  brouard
   complex model than "constant and age", you should modify the program    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.133  2009/07/06 10:21:25  brouard
   convergence.    just nforces
   
   The advantage of this computer programme, compared to a simple    Revision 1.132  2009/07/06 08:22:05  brouard
   multinomial logistic model, is clear when the delay between waves is not    Many tings
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.131  2009/06/20 16:22:47  brouard
   account using an interpolation or extrapolation.      Some dimensions resccaled
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.130  2009/05/26 06:44:34  brouard
   conditional to the observed state i at age x. The delay 'h' can be    (Module): Max Covariate is now set to 20 instead of 8. A
   split into an exact number (nh*stepm) of unobserved intermediate    lot of cleaning with variables initialized to 0. Trying to make
   states. This elementary transition (by month or quarter trimester,    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.129  2007/08/31 13:49:27  lievre
   and the contribution of each individual to the likelihood is simply    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   hPijx.  
     Revision 1.128  2006/06/30 13:02:05  brouard
   Also this programme outputs the covariance matrix of the parameters but also    (Module): Clarifications on computing e.j
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.127  2006/04/28 18:11:50  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): Yes the sum of survivors was wrong since
            Institut national d'études démographiques, Paris.    imach-114 because nhstepm was no more computed in the age
   This software have been partly granted by Euro-REVES, a concerted action    loop. Now we define nhstepma in the age loop.
   from the European Union.    (Module): In order to speed up (in case of numerous covariates) we
   It is copyrighted identically to a GNU software product, ie programme and    compute health expectancies (without variances) in a first step
   software can be distributed freely for non commercial use. Latest version    and then all the health expectancies with variances or standard
   can be accessed at http://euroreves.ined.fr/imach .    deviation (needs data from the Hessian matrices) which slows the
   **********************************************************************/    computation.
      In the future we should be able to stop the program is only health
 #include <math.h>    expectancies and graph are needed without standard deviations.
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.126  2006/04/28 17:23:28  brouard
 #include <unistd.h>    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 #define MAXLINE 256    loop. Now we define nhstepma in the age loop.
 #define GNUPLOTPROGRAM "gnuplot"    Version 0.98h
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.125  2006/04/04 15:20:31  lievre
 /*#define DEBUG*/    Errors in calculation of health expectancies. Age was not initialized.
 #define windows    Forecasting file added.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    The log-likelihood is printed in the log file
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.123  2006/03/20 10:52:43  brouard
 #define NINTERVMAX 8    * imach.c (Module): <title> changed, corresponds to .htm file
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    name. <head> headers where missing.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    * imach.c (Module): Weights can have a decimal point as for
 #define MAXN 20000    English (a comma might work with a correct LC_NUMERIC environment,
 #define YEARM 12. /* Number of months per year */    otherwise the weight is truncated).
 #define AGESUP 130    Modification of warning when the covariates values are not 0 or
 #define AGEBASE 40    1.
 #ifdef windows    Version 0.98g
 #define DIRSEPARATOR '\\'  
 #else    Revision 1.122  2006/03/20 09:45:41  brouard
 #define DIRSEPARATOR '/'    (Module): Weights can have a decimal point as for
 #endif    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";    Modification of warning when the covariates values are not 0 or
 int erreur; /* Error number */    1.
 int nvar;    Version 0.98g
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.121  2006/03/16 17:45:01  lievre
 int nlstate=2; /* Number of live states */    * imach.c (Module): Comments concerning covariates added
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    * imach.c (Module): refinements in the computation of lli if
 int popbased=0;    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.120  2006/03/16 15:10:38  lievre
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): refinements in the computation of lli if
 int mle, weightopt;    status=-2 in order to have more reliable computation if stepm is
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    not 1 month. Version 0.98f
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.119  2006/03/15 17:42:26  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Bug if status = -2, the loglikelihood was
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    computed as likelihood omitting the logarithm. Version O.98e
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    Revision 1.118  2006/03/14 18:20:07  brouard
 FILE *fichtm; /* Html File */    (Module): varevsij Comments added explaining the second
 FILE *ficreseij;    table of variances if popbased=1 .
 char filerese[FILENAMELENGTH];    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 FILE  *ficresvij;    (Module): Function pstamp added
 char fileresv[FILENAMELENGTH];    (Module): Version 0.98d
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    Revision 1.117  2006/03/14 17:16:22  brouard
 char title[MAXLINE];    (Module): varevsij Comments added explaining the second
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    table of variances if popbased=1 .
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    (Module): Version 0.98d
   
 char filerest[FILENAMELENGTH];    Revision 1.116  2006/03/06 10:29:27  brouard
 char fileregp[FILENAMELENGTH];    (Module): Variance-covariance wrong links and
 char popfile[FILENAMELENGTH];    varian-covariance of ej. is needed (Saito).
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.114  2006/02/26 12:57:58  brouard
 #define FTOL 1.0e-10    (Module): Some improvements in processing parameter
     filename with strsep.
 #define NRANSI  
 #define ITMAX 200    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 #define TOL 2.0e-4    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.112  2006/01/30 09:55:26  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
 #define GOLD 1.618034    Revision 1.111  2006/01/25 20:38:18  brouard
 #define GLIMIT 100.0    (Module): Lots of cleaning and bugs added (Gompertz)
 #define TINY 1.0e-20    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.110  2006/01/25 00:51:50  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Lots of cleaning and bugs added (Gompertz)
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.109  2006/01/24 19:37:15  brouard
 #define rint(a) floor(a+0.5)    (Module): Comments (lines starting with a #) are allowed in data.
   
 static double sqrarg;    Revision 1.108  2006/01/19 18:05:42  lievre
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Gnuplot problem appeared...
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    To be fixed
   
 int imx;    Revision 1.107  2006/01/19 16:20:37  brouard
 int stepm;    Test existence of gnuplot in imach path
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.106  2006/01/19 13:24:36  brouard
 int estepm;    Some cleaning and links added in html output
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Revision 1.105  2006/01/05 20:23:19  lievre
 int m,nb;    *** empty log message ***
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.104  2005/09/30 16:11:43  lievre
 double **pmmij, ***probs, ***mobaverage;    (Module): sump fixed, loop imx fixed, and simplifications.
 double dateintmean=0;    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
 double *weight;    (instead of missing=-1 in earlier versions) and his/her
 int **s; /* Status */    contributions to the likelihood is 1 - Prob of dying from last
 double *agedc, **covar, idx;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    the healthy state at last known wave). Version is 0.98
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.103  2005/09/30 15:54:49  lievre
 double ftolhess; /* Tolerance for computing hessian */    (Module): sump fixed, loop imx fixed, and simplifications.
   
 /**************** split *************************/    Revision 1.102  2004/09/15 17:31:30  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Add the possibility to read data file including tab characters.
 {  
    char *s;                             /* pointer */    Revision 1.101  2004/09/15 10:38:38  brouard
    int  l1, l2;                         /* length counters */    Fix on curr_time
   
    l1 = strlen( path );                 /* length of path */    Revision 1.100  2004/07/12 18:29:06  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Add version for Mac OS X. Just define UNIX in Makefile
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.99  2004/06/05 08:57:40  brouard
 #if     defined(__bsd__)                /* get current working directory */    *** empty log message ***
       extern char       *getwd( );  
     Revision 1.98  2004/05/16 15:05:56  brouard
       if ( getwd( dirc ) == NULL ) {    New version 0.97 . First attempt to estimate force of mortality
 #else    directly from the data i.e. without the need of knowing the health
       extern char       *getcwd( );    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    other analysis, in order to test if the mortality estimated from the
 #endif    cross-longitudinal survey is different from the mortality estimated
          return( GLOCK_ERROR_GETCWD );    from other sources like vital statistic data.
       }  
       strcpy( name, path );             /* we've got it */    The same imach parameter file can be used but the option for mle should be -3.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Agnès, who wrote this part of the code, tried to keep most of the
       l2 = strlen( s );                 /* length of filename */    former routines in order to include the new code within the former code.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    The output is very simple: only an estimate of the intercept and of
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    the slope with 95% confident intervals.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Current limitations:
    l1 = strlen( dirc );                 /* length of directory */    A) Even if you enter covariates, i.e. with the
 #ifdef windows    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    B) There is no computation of Life Expectancy nor Life Table.
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.97  2004/02/20 13:25:42  lievre
 #endif    Version 0.96d. Population forecasting command line is (temporarily)
    s = strrchr( name, '.' );            /* find last / */    suppressed.
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.96  2003/07/15 15:38:55  brouard
    l1= strlen( name);    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
    l2= strlen( s)+1;    rewritten within the same printf. Workaround: many printfs.
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.95  2003/07/08 07:54:34  brouard
    return( 0 );                         /* we're done */    * imach.c (Repository):
 }    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
   
 /******************************************/    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 void replace(char *s, char*t)  
 {    Revision 1.93  2003/06/25 16:33:55  brouard
   int i;    (Module): On windows (cygwin) function asctime_r doesn't
   int lg=20;    exist so I changed back to asctime which exists.
   i=0;    (Module): Version 0.96b
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.92  2003/06/25 16:30:45  brouard
     (s[i] = t[i]);    (Module): On windows (cygwin) function asctime_r doesn't
     if (t[i]== '\\') s[i]='/';    exist so I changed back to asctime which exists.
   }  
 }    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
 int nbocc(char *s, char occ)    (Repository): Elapsed time after each iteration is now output. It
 {    helps to forecast when convergence will be reached. Elapsed time
   int i,j=0;    is stamped in powell.  We created a new html file for the graphs
   int lg=20;    concerning matrix of covariance. It has extension -cov.htm.
   i=0;  
   lg=strlen(s);    Revision 1.90  2003/06/24 12:34:15  brouard
   for(i=0; i<= lg; i++) {    (Module): Some bugs corrected for windows. Also, when
   if  (s[i] == occ ) j++;    mle=-1 a template is output in file "or"mypar.txt with the design
   }    of the covariance matrix to be input.
   return j;  
 }    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 void cutv(char *u,char *v, char*t, char occ)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   int i,lg,j,p=0;  
   i=0;    Revision 1.88  2003/06/23 17:54:56  brouard
   for(j=0; j<=strlen(t)-1; j++) {    * 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.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.86  2003/06/17 20:04:08  brouard
     (u[j] = t[j]);    (Module): Change position of html and gnuplot routines and added
   }    routine fileappend.
      u[p]='\0';  
     Revision 1.85  2003/06/17 13:12:43  brouard
    for(j=0; j<= lg; j++) {    * imach.c (Repository): Check when date of death was earlier that
     if (j>=(p+1))(v[j-p-1] = t[j]);    current date of interview. It may happen when the death was just
   }    prior to the death. In this case, dh was negative and likelihood
 }    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 /********************** nrerror ********************/    interview.
     (Repository): Because some people have very long ID (first column)
 void nrerror(char error_text[])    we changed int to long in num[] and we added a new lvector for
 {    memory allocation. But we also truncated to 8 characters (left
   fprintf(stderr,"ERREUR ...\n");    truncation)
   fprintf(stderr,"%s\n",error_text);    (Repository): No more line truncation errors.
   exit(1);  
 }    Revision 1.84  2003/06/13 21:44:43  brouard
 /*********************** vector *******************/    * imach.c (Repository): Replace "freqsummary" at a correct
 double *vector(int nl, int nh)    place. It differs from routine "prevalence" which may be called
 {    many times. Probs is memory consuming and must be used with
   double *v;    parcimony.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.83  2003/06/10 13:39:11  lievre
 }    *** empty log message ***
   
 /************************ free vector ******************/    Revision 1.82  2003/06/05 15:57:20  brouard
 void free_vector(double*v, int nl, int nh)    Add log in  imach.c and  fullversion number is now printed.
 {  
   free((FREE_ARG)(v+nl-NR_END));  */
 }  /*
      Interpolated Markov Chain
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Short summary of the programme:
 {    
   int *v;    This program computes Healthy Life Expectancies from
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   if (!v) nrerror("allocation failure in ivector");    first survey ("cross") where individuals from different ages are
   return v-nl+NR_END;    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
     second wave of interviews ("longitudinal") which measure each change
 /******************free ivector **************************/    (if any) in individual health status.  Health expectancies are
 void free_ivector(int *v, long nl, long nh)    computed from the time spent in each health state according to a
 {    model. More health states you consider, more time is necessary to reach the
   free((FREE_ARG)(v+nl-NR_END));    Maximum Likelihood of the parameters involved in the model.  The
 }    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 /******************* imatrix *******************************/    conditional to be observed in state i at the first wave. Therefore
 int **imatrix(long nrl, long nrh, long ncl, long nch)    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    '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
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    where the markup *Covariates have to be included here again* invites
   int **m;    you to do it.  More covariates you add, slower the
      convergence.
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    The advantage of this computer programme, compared to a simple
   if (!m) nrerror("allocation failure 1 in matrix()");    multinomial logistic model, is clear when the delay between waves is not
   m += NR_END;    identical for each individual. Also, if a individual missed an
   m -= nrl;    intermediate interview, the information is lost, but taken into
      account using an interpolation or extrapolation.  
    
   /* allocate rows and set pointers to them */    hPijx is the probability to be observed in state i at age x+h
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    conditional to the observed state i at age x. The delay 'h' can be
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    split into an exact number (nh*stepm) of unobserved intermediate
   m[nrl] += NR_END;    states. This elementary transition (by month, quarter,
   m[nrl] -= ncl;    semester or year) is modelled as a multinomial logistic.  The hPx
      matrix is simply the matrix product of nh*stepm elementary matrices
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    and the contribution of each individual to the likelihood is simply
      hPijx.
   /* return pointer to array of pointers to rows */  
   return m;    Also this programme outputs the covariance matrix of the parameters but also
 }    of the life expectancies. It also computes the period (stable) prevalence. 
     
 /****************** free_imatrix *************************/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 void free_imatrix(m,nrl,nrh,ncl,nch)             Institut national d'études démographiques, Paris.
       int **m;    This software have been partly granted by Euro-REVES, a concerted action
       long nch,ncl,nrh,nrl;    from the European Union.
      /* free an int matrix allocated by imatrix() */    It is copyrighted identically to a GNU software product, ie programme and
 {    software can be distributed freely for non commercial use. Latest version
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    can be accessed at http://euroreves.ined.fr/imach .
   free((FREE_ARG) (m+nrl-NR_END));  
 }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 /******************* matrix *******************************/    
 double **matrix(long nrl, long nrh, long ncl, long nch)    **********************************************************************/
 {  /*
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    main
   double **m;    read parameterfile
     read datafile
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    concatwav
   if (!m) nrerror("allocation failure 1 in matrix()");    freqsummary
   m += NR_END;    if (mle >= 1)
   m -= nrl;      mlikeli
     print results files
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if mle==1 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");       computes hessian
   m[nrl] += NR_END;    read end of parameter file: agemin, agemax, bage, fage, estepm
   m[nrl] -= ncl;        begin-prev-date,...
     open gnuplot file
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    open html file
   return m;    period (stable) prevalence
 }     for age prevalim()
     h Pij x
 /*************************free matrix ************************/    variance of p varprob
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    forecasting if prevfcast==1 prevforecast call prevalence()
 {    health expectancies
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Variance-covariance of DFLE
   free((FREE_ARG)(m+nrl-NR_END));    prevalence()
 }     movingaverage()
     varevsij() 
 /******************* ma3x *******************************/    if popbased==1 varevsij(,popbased)
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    total life expectancies
 {    Variance of period (stable) prevalence
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;   end
   double ***m;  */
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;   
   m -= nrl;  #include <math.h>
   #include <stdio.h>
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <stdlib.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <string.h>
   m[nrl] += NR_END;  #include <unistd.h>
   m[nrl] -= ncl;  
   #include <limits.h>
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <sys/types.h>
   #include <sys/stat.h>
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #include <errno.h>
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  extern int errno;
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  /* #include <sys/time.h> */
   for (j=ncl+1; j<=nch; j++)  #include <time.h>
     m[nrl][j]=m[nrl][j-1]+nlay;  #include "timeval.h"
    
   for (i=nrl+1; i<=nrh; i++) {  #ifdef GSL
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #include <gsl/gsl_errno.h>
     for (j=ncl+1; j<=nch; j++)  #include <gsl/gsl_multimin.h>
       m[i][j]=m[i][j-1]+nlay;  #endif
   }  
   return m;  /* #include <libintl.h> */
 }  /* #define _(String) gettext (String) */
   
 /*************************free ma3x ************************/  #define MAXLINE 256
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  #define GNUPLOTPROGRAM "gnuplot"
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define FILENAMELENGTH 132
   free((FREE_ARG)(m+nrl-NR_END));  
 }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 /***************** f1dim *************************/  
 extern int ncom;  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
 extern double *pcom,*xicom;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 extern double (*nrfunc)(double []);  
    #define NINTERVMAX 8
 double f1dim(double x)  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   int j;  #define NCOVMAX 20 /* Maximum number of covariates */
   double f;  #define MAXN 20000
   double *xt;  #define YEARM 12. /* Number of months per year */
    #define AGESUP 130
   xt=vector(1,ncom);  #define AGEBASE 40
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   f=(*nrfunc)(xt);  #ifdef UNIX
   free_vector(xt,1,ncom);  #define DIRSEPARATOR '/'
   return f;  #define CHARSEPARATOR "/"
 }  #define ODIRSEPARATOR '\\'
   #else
 /*****************brent *************************/  #define DIRSEPARATOR '\\'
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define CHARSEPARATOR "\\"
 {  #define ODIRSEPARATOR '/'
   int iter;  #endif
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  /* $Id$ */
   double ftemp;  /* $State$ */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
    char fullversion[]="$Revision$ $Date$"; 
   a=(ax < cx ? ax : cx);  char strstart[80];
   b=(ax > cx ? ax : cx);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   x=w=v=bx;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   fw=fv=fx=(*f)(x);  int nvar=0, nforce=0; /* Number of variables, number of forces */
   for (iter=1;iter<=ITMAX;iter++) {  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
     xm=0.5*(a+b);  int npar=NPARMAX;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int nlstate=2; /* Number of live states */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int ndeath=1; /* Number of dead states */
     printf(".");fflush(stdout);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #ifdef DEBUG  int popbased=0;
     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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  int *wav; /* Number of waves for this individuual 0 is possible */
 #endif  int maxwav=0; /* Maxim number of waves */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       *xmin=x;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       return fx;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     }                     to the likelihood and the sum of weights (done by funcone)*/
     ftemp=fu;  int mle=1, weightopt=0;
     if (fabs(e) > tol1) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       r=(x-w)*(fx-fv);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       q=(x-v)*(fx-fw);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       p=(x-v)*q-(x-w)*r;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       q=2.0*(q-r);  double jmean=1; /* Mean space between 2 waves */
       if (q > 0.0) p = -p;  double **oldm, **newm, **savm; /* Working pointers to matrices */
       q=fabs(q);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       etemp=e;  /*FILE *fic ; */ /* Used in readdata only */
       e=d;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  FILE *ficlog, *ficrespow;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  int globpr=0; /* Global variable for printing or not */
       else {  double fretone; /* Only one call to likelihood */
         d=p/q;  long ipmx=0; /* Number of contributions */
         u=x+d;  double sw; /* Sum of weights */
         if (u-a < tol2 || b-u < tol2)  char filerespow[FILENAMELENGTH];
           d=SIGN(tol1,xm-x);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       }  FILE *ficresilk;
     } else {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficresprobmorprev;
     }  FILE *fichtm, *fichtmcov; /* Html File */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  FILE *ficreseij;
     fu=(*f)(u);  char filerese[FILENAMELENGTH];
     if (fu <= fx) {  FILE *ficresstdeij;
       if (u >= x) a=x; else b=x;  char fileresstde[FILENAMELENGTH];
       SHFT(v,w,x,u)  FILE *ficrescveij;
         SHFT(fv,fw,fx,fu)  char filerescve[FILENAMELENGTH];
         } else {  FILE  *ficresvij;
           if (u < x) a=u; else b=u;  char fileresv[FILENAMELENGTH];
           if (fu <= fw || w == x) {  FILE  *ficresvpl;
             v=w;  char fileresvpl[FILENAMELENGTH];
             w=u;  char title[MAXLINE];
             fv=fw;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
             fw=fu;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
           } else if (fu <= fv || v == x || v == w) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
             v=u;  char command[FILENAMELENGTH];
             fv=fu;  int  outcmd=0;
           }  
         }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   }  
   nrerror("Too many iterations in brent");  char filelog[FILENAMELENGTH]; /* Log file */
   *xmin=x;  char filerest[FILENAMELENGTH];
   return fx;  char fileregp[FILENAMELENGTH];
 }  char popfile[FILENAMELENGTH];
   
 /****************** mnbrak ***********************/  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
             double (*func)(double))  struct timezone tzp;
 {  extern int gettimeofday();
   double ulim,u,r,q, dum;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   double fu;  long time_value;
    extern long time();
   *fa=(*func)(*ax);  char strcurr[80], strfor[80];
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  char *endptr;
     SHFT(dum,*ax,*bx,dum)  long lval;
       SHFT(dum,*fb,*fa,dum)  double dval;
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  #define NR_END 1
   *fc=(*func)(*cx);  #define FREE_ARG char*
   while (*fb > *fc) {  #define FTOL 1.0e-10
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  #define NRANSI 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #define ITMAX 200 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define TOL 2.0e-4 
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  #define CGOLD 0.3819660 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define ZEPS 1.0e-10 
       fu=(*func)(u);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define GOLD 1.618034 
           SHFT(*fb,*fc,fu,(*func)(u))  #define GLIMIT 100.0 
           }  #define TINY 1.0e-20 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  static double maxarg1,maxarg2;
       fu=(*func)(u);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     } else {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       u=(*cx)+GOLD*(*cx-*bx);    
       fu=(*func)(u);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     }  #define rint(a) floor(a+0.5)
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  static double sqrarg;
       }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
 /*************** linmin ************************/  
   int imx; 
 int ncom;  int stepm=1;
 double *pcom,*xicom;  /* Stepm, step in month: minimum step interpolation*/
 double (*nrfunc)(double []);  
    int estepm;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 {  
   double brent(double ax, double bx, double cx,  int m,nb;
                double (*f)(double), double tol, double *xmin);  long *num;
   double f1dim(double x);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
               double *fc, double (*func)(double));  double **pmmij, ***probs;
   int j;  double *ageexmed,*agecens;
   double xx,xmin,bx,ax;  double dateintmean=0;
   double fx,fb,fa;  
    double *weight;
   ncom=n;  int **s; /* Status */
   pcom=vector(1,n);  double *agedc, **covar, idx;
   xicom=vector(1,n);  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   nrfunc=func;  double *lsurv, *lpop, *tpop;
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     xicom[j]=xi[j];  double ftolhess; /* Tolerance for computing hessian */
   }  
   ax=0.0;  /**************** split *************************/
   xx=1.0;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  {
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 #ifdef DEBUG       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    */ 
 #endif    char  *ss;                            /* pointer */
   for (j=1;j<=n;j++) {    int   l1, l2;                         /* length counters */
     xi[j] *= xmin;  
     p[j] += xi[j];    l1 = strlen(path );                   /* length of path */
   }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   free_vector(xicom,1,n);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   free_vector(pcom,1,n);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
 }      strcpy( name, path );               /* we got the fullname name because no directory */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 /*************** powell ************************/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      /* get current working directory */
             double (*func)(double []))      /*    extern  char* getcwd ( char *buf , int len);*/
 {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   void linmin(double p[], double xi[], int n, double *fret,        return( GLOCK_ERROR_GETCWD );
               double (*func)(double []));      }
   int i,ibig,j;      /* got dirc from getcwd*/
   double del,t,*pt,*ptt,*xit;      printf(" DIRC = %s \n",dirc);
   double fp,fptt;    } else {                              /* strip direcotry from path */
   double *xits;      ss++;                               /* after this, the filename */
   pt=vector(1,n);      l2 = strlen( ss );                  /* length of filename */
   ptt=vector(1,n);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   xit=vector(1,n);      strcpy( name, ss );         /* save file name */
   xits=vector(1,n);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   *fret=(*func)(p);      dirc[l1-l2] = 0;                    /* add zero */
   for (j=1;j<=n;j++) pt[j]=p[j];      printf(" DIRC2 = %s \n",dirc);
   for (*iter=1;;++(*iter)) {    }
     fp=(*fret);    /* We add a separator at the end of dirc if not exists */
     ibig=0;    l1 = strlen( dirc );                  /* length of directory */
     del=0.0;    if( dirc[l1-1] != DIRSEPARATOR ){
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      dirc[l1] =  DIRSEPARATOR;
     for (i=1;i<=n;i++)      dirc[l1+1] = 0; 
       printf(" %d %.12f",i, p[i]);      printf(" DIRC3 = %s \n",dirc);
     printf("\n");    }
     for (i=1;i<=n;i++) {    ss = strrchr( name, '.' );            /* find last / */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    if (ss >0){
       fptt=(*fret);      ss++;
 #ifdef DEBUG      strcpy(ext,ss);                     /* save extension */
       printf("fret=%lf \n",*fret);      l1= strlen( name);
 #endif      l2= strlen(ss)+1;
       printf("%d",i);fflush(stdout);      strncpy( finame, name, l1-l2);
       linmin(p,xit,n,fret,func);      finame[l1-l2]= 0;
       if (fabs(fptt-(*fret)) > del) {    }
         del=fabs(fptt-(*fret));  
         ibig=i;    return( 0 );                          /* we're done */
       }  }
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  /******************************************/
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  void replace_back_to_slash(char *s, char*t)
       }  {
       for(j=1;j<=n;j++)    int i;
         printf(" p=%.12e",p[j]);    int lg=0;
       printf("\n");    i=0;
 #endif    lg=strlen(t);
     }    for(i=0; i<= lg; i++) {
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      (s[i] = t[i]);
 #ifdef DEBUG      if (t[i]== '\\') s[i]='/';
       int k[2],l;    }
       k[0]=1;  }
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  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 */
         printf(" %.12e",p[j]);    char *s;
       printf("\n");    s=out;
       for(l=0;l<=1;l++) {    while (*in != '\0'){
         for (j=1;j<=n;j++) {      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        in++;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      }
         }      *out++ = *in++;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    }
       }    *out='\0';
 #endif    return s;
   }
   
       free_vector(xit,1,n);  char *cutv(char *blocc, char *alocc, char *in, char occ)
       free_vector(xits,1,n);  {
       free_vector(ptt,1,n);    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       free_vector(pt,1,n);       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       return;       gives blocc="abcdef2ghi" and alocc="j".
     }       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    */
     for (j=1;j<=n;j++) {    char *s, *t;
       ptt[j]=2.0*p[j]-pt[j];    t=in;s=in;
       xit[j]=p[j]-pt[j];    while (*in != '\0'){
       pt[j]=p[j];      while( *in == occ){
     }        *blocc++ = *in++;
     fptt=(*func)(ptt);        s=in;
     if (fptt < fp) {      }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      *blocc++ = *in++;
       if (t < 0.0) {    }
         linmin(p,xit,n,fret,func);    if (s == t) /* occ not found */
         for (j=1;j<=n;j++) {      *(blocc-(in-s))='\0';
           xi[j][ibig]=xi[j][n];    else
           xi[j][n]=xit[j];      *(blocc-(in-s)-1)='\0';
         }    in=s;
 #ifdef DEBUG    while ( *in != '\0'){
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      *alocc++ = *in++;
         for(j=1;j<=n;j++)    }
           printf(" %.12e",xit[j]);  
         printf("\n");    *alocc='\0';
 #endif    return s;
       }  }
     }  
   }  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /**** Prevalence limit ****************/    int lg=20;
     i=0;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    lg=strlen(s);
 {    for(i=0; i<= lg; i++) {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    if  (s[i] == occ ) j++;
      matrix by transitions matrix until convergence is reached */    }
     return j;
   int i, ii,j,k;  }
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  /* void cutv(char *u,char *v, char*t, char occ) */
   double **out, cov[NCOVMAX], **pmij();  /* { */
   double **newm;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   double agefin, delaymax=50 ; /* Max number of years to converge */  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   /*      gives u="abcdef2ghi" and v="j" *\/ */
   for (ii=1;ii<=nlstate+ndeath;ii++)  /*   int i,lg,j,p=0; */
     for (j=1;j<=nlstate+ndeath;j++){  /*   i=0; */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*   lg=strlen(t); */
     }  /*   for(j=0; j<=lg-1; j++) { */
   /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
    cov[1]=1.;  /*   } */
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*   for(j=0; j<p; j++) { */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  /*     (u[j] = t[j]); */
     newm=savm;  /*   } */
     /* Covariates have to be included here again */  /*      u[p]='\0'; */
      cov[2]=agefin;  
    /*    for(j=0; j<= lg; j++) { */
       for (k=1; k<=cptcovn;k++) {  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
         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]]);*/  /* } */
       }  
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /********************** nrerror ********************/
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  void nrerror(char error_text[])
   {
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    fprintf(stderr,"ERREUR ...\n");
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    fprintf(stderr,"%s\n",error_text);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    exit(EXIT_FAILURE);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  }
   /*********************** vector *******************/
     savm=oldm;  double *vector(int nl, int nh)
     oldm=newm;  {
     maxmax=0.;    double *v;
     for(j=1;j<=nlstate;j++){    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       min=1.;    if (!v) nrerror("allocation failure in vector");
       max=0.;    return v-nl+NR_END;
       for(i=1; i<=nlstate; i++) {  }
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /************************ free vector ******************/
         prlim[i][j]= newm[i][j]/(1-sumnew);  void free_vector(double*v, int nl, int nh)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    free((FREE_ARG)(v+nl-NR_END));
       }  }
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);  /************************ivector *******************************/
     }  int *ivector(long nl,long nh)
     if(maxmax < ftolpl){  {
       return prlim;    int *v;
     }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   }    if (!v) nrerror("allocation failure in ivector");
 }    return v-nl+NR_END;
   }
 /*************** transition probabilities ***************/  
   /******************free ivector **************************/
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  void free_ivector(int *v, long nl, long nh)
 {  {
   double s1, s2;    free((FREE_ARG)(v+nl-NR_END));
   /*double t34;*/  }
   int i,j,j1, nc, ii, jj;  
   /************************lvector *******************************/
     for(i=1; i<= nlstate; i++){  long *lvector(long nl,long nh)
     for(j=1; j<i;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    long *v;
         /*s2 += param[i][j][nc]*cov[nc];*/    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    if (!v) nrerror("allocation failure in ivector");
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    return v-nl+NR_END;
       }  }
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /******************free lvector **************************/
     }  void free_lvector(long *v, long nl, long nh)
     for(j=i+1; j<=nlstate+ndeath;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free((FREE_ARG)(v+nl-NR_END));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  }
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }  /******************* imatrix *******************************/
       ps[i][j]=s2;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   }  { 
     /*ps[3][2]=1;*/    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
   for(i=1; i<= nlstate; i++){    
      s1=0;    /* allocate pointers to rows */ 
     for(j=1; j<i; j++)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       s1+=exp(ps[i][j]);    if (!m) nrerror("allocation failure 1 in matrix()"); 
     for(j=i+1; j<=nlstate+ndeath; j++)    m += NR_END; 
       s1+=exp(ps[i][j]);    m -= nrl; 
     ps[i][i]=1./(s1+1.);    
     for(j=1; j<i; j++)    
       ps[i][j]= exp(ps[i][j])*ps[i][i];    /* allocate rows and set pointers to them */ 
     for(j=i+1; j<=nlstate+ndeath; 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()"); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    m[nrl] += NR_END; 
   } /* end i */    m[nrl] -= ncl; 
     
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    
       ps[ii][jj]=0;    /* return pointer to array of pointers to rows */ 
       ps[ii][ii]=1;    return m; 
     }  } 
   }  
   /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        int **m;
     for(jj=1; jj<= nlstate+ndeath; jj++){        long nch,ncl,nrh,nrl; 
      printf("%lf ",ps[ii][jj]);       /* free an int matrix allocated by imatrix() */ 
    }  { 
     printf("\n ");    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     }    free((FREE_ARG) (m+nrl-NR_END)); 
     printf("\n ");printf("%lf ",cov[2]);*/  } 
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  /******************* matrix *******************************/
   goto end;*/  double **matrix(long nrl, long nrh, long ncl, long nch)
     return ps;  {
 }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
 /**************** Product of 2 matrices ******************/  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    m -= nrl;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      before: only the contents of out is modified. The function returns    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      a pointer to pointers identical to out */    m[nrl] += NR_END;
   long i, j, k;    m[nrl] -= ncl;
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    return m;
         out[i][k] +=in[i][j]*b[j][k];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
      */
   return out;  }
 }  
   /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 /************* Higher Matrix Product ***************/  {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    free((FREE_ARG)(m+nrl-NR_END));
 {  }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until  /******************* ma3x *******************************/
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  {
      (typically every 2 years instead of every month which is too big).    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
      Model is determined by parameters x and covariates have to be    double ***m;
      included manually here.  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      */    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   int i, j, d, h, k;    m -= nrl;
   double **out, cov[NCOVMAX];  
   double **newm;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   /* Hstepm could be zero and should return the unit matrix */    m[nrl] += NR_END;
   for (i=1;i<=nlstate+ndeath;i++)    m[nrl] -= ncl;
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   for(h=1; h <=nhstepm; h++){    m[nrl][ncl] += NR_END;
     for(d=1; d <=hstepm; d++){    m[nrl][ncl] -= nll;
       newm=savm;    for (j=ncl+1; j<=nch; j++) 
       /* Covariates have to be included here again */      m[nrl][j]=m[nrl][j-1]+nlay;
       cov[1]=1.;    
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    for (i=nrl+1; i<=nrh; i++) {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (k=1; k<=cptcovage;k++)      for (j=ncl+1; j<=nch; j++) 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        m[i][j]=m[i][j-1]+nlay;
       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]]];    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
              &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    */
       /*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 ************************/
       savm=oldm;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       oldm=newm;  {
     }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for(i=1; i<=nlstate+ndeath; i++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       for(j=1;j<=nlstate+ndeath;j++) {    free((FREE_ARG)(m+nrl-NR_END));
         po[i][j][h]=newm[i][j];  }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  /*************** function subdirf ***********/
       }  char *subdirf(char fileres[])
   } /* end h */  {
   return po;    /* Caution optionfilefiname is hidden */
 }    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
 /*************** log-likelihood *************/    return tmpout;
 double func( double *x)  }
 {  
   int i, ii, j, k, mi, d, kk;  /*************** function subdirf2 ***********/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  char *subdirf2(char fileres[], char *preop)
   double **out;  {
   double sw; /* Sum of weights */    
   double lli; /* Individual log likelihood */    /* Caution optionfilefiname is hidden */
   long ipmx;    strcpy(tmpout,optionfilefiname);
   /*extern weight */    strcat(tmpout,"/");
   /* We are differentiating ll according to initial status */    strcat(tmpout,preop);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    strcat(tmpout,fileres);
   /*for(i=1;i<imx;i++)    return tmpout;
     printf(" %d\n",s[4][i]);  }
   */  
   cov[1]=1.;  /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
   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];    /* Caution optionfilefiname is hidden */
     for(mi=1; mi<= wav[i]-1; mi++){    strcpy(tmpout,optionfilefiname);
       for (ii=1;ii<=nlstate+ndeath;ii++)    strcat(tmpout,"/");
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    strcat(tmpout,preop);
       for(d=0; d<dh[mi][i]; d++){    strcat(tmpout,preop2);
         newm=savm;    strcat(tmpout,fileres);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return tmpout;
         for (kk=1; kk<=cptcovage;kk++) {  }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  /***************** f1dim *************************/
          extern int ncom; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  extern double *pcom,*xicom;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  extern double (*nrfunc)(double []); 
         savm=oldm;   
         oldm=newm;  double f1dim(double x) 
          { 
            int j; 
       } /* end mult */    double f;
          double *xt; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);   
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    xt=vector(1,ncom); 
       ipmx +=1;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       sw += weight[i];    f=(*nrfunc)(xt); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    free_vector(xt,1,ncom); 
     } /* end of wave */    return f; 
   } /* end of individual */  } 
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  /*****************brent *************************/
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  { 
   return -l;    int iter; 
 }    double a,b,d,etemp;
     double fu,fv,fw,fx;
     double ftemp;
 /*********** Maximum Likelihood Estimation ***************/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))   
 {    a=(ax < cx ? ax : cx); 
   int i,j, iter;    b=(ax > cx ? ax : cx); 
   double **xi,*delti;    x=w=v=bx; 
   double fret;    fw=fv=fx=(*f)(x); 
   xi=matrix(1,npar,1,npar);    for (iter=1;iter<=ITMAX;iter++) { 
   for (i=1;i<=npar;i++)      xm=0.5*(a+b); 
     for (j=1;j<=npar;j++)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       xi[i][j]=(i==j ? 1.0 : 0.0);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   printf("Powell\n");      printf(".");fflush(stdout);
   powell(p,xi,npar,ftol,&iter,&fret,func);      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      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(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      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)))) { */
 }  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 /**** Computes Hessian and covariance matrix ***/        *xmin=x; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        return fx; 
 {      } 
   double  **a,**y,*x,pd;      ftemp=fu;
   double **hess;      if (fabs(e) > tol1) { 
   int i, j,jk;        r=(x-w)*(fx-fv); 
   int *indx;        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
   double hessii(double p[], double delta, int theta, double delti[]);        q=2.0*(q-r); 
   double hessij(double p[], double delti[], int i, int j);        if (q > 0.0) p = -p; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;        q=fabs(q); 
   void ludcmp(double **a, int npar, int *indx, double *d) ;        etemp=e; 
         e=d; 
   hess=matrix(1,npar,1,npar);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   printf("\nCalculation of the hessian matrix. Wait...\n");        else { 
   for (i=1;i<=npar;i++){          d=p/q; 
     printf("%d",i);fflush(stdout);          u=x+d; 
     hess[i][i]=hessii(p,ftolhess,i,delti);          if (u-a < tol2 || b-u < tol2) 
     /*printf(" %f ",p[i]);*/            d=SIGN(tol1,xm-x); 
     /*printf(" %lf ",hess[i][i]);*/        } 
   }      } else { 
          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (i=1;i<=npar;i++) {      } 
     for (j=1;j<=npar;j++)  {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       if (j>i) {      fu=(*f)(u); 
         printf(".%d%d",i,j);fflush(stdout);      if (fu <= fx) { 
         hess[i][j]=hessij(p,delti,i,j);        if (u >= x) a=x; else b=x; 
         hess[j][i]=hess[i][j];            SHFT(v,w,x,u) 
         /*printf(" %lf ",hess[i][j]);*/          SHFT(fv,fw,fx,fu) 
       }          } else { 
     }            if (u < x) a=u; else b=u; 
   }            if (fu <= fw || w == x) { 
   printf("\n");              v=w; 
               w=u; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");              fv=fw; 
                fw=fu; 
   a=matrix(1,npar,1,npar);            } else if (fu <= fv || v == x || v == w) { 
   y=matrix(1,npar,1,npar);              v=u; 
   x=vector(1,npar);              fv=fu; 
   indx=ivector(1,npar);            } 
   for (i=1;i<=npar;i++)          } 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    } 
   ludcmp(a,npar,indx,&pd);    nrerror("Too many iterations in brent"); 
     *xmin=x; 
   for (j=1;j<=npar;j++) {    return fx; 
     for (i=1;i<=npar;i++) x[i]=0;  } 
     x[j]=1;  
     lubksb(a,npar,indx,x);  /****************** mnbrak ***********************/
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     }              double (*func)(double)) 
   }  { 
     double ulim,u,r,q, dum;
   printf("\n#Hessian matrix#\n");    double fu; 
   for (i=1;i<=npar;i++) {   
     for (j=1;j<=npar;j++) {    *fa=(*func)(*ax); 
       printf("%.3e ",hess[i][j]);    *fb=(*func)(*bx); 
     }    if (*fb > *fa) { 
     printf("\n");      SHFT(dum,*ax,*bx,dum) 
   }        SHFT(dum,*fb,*fa,dum) 
         } 
   /* Recompute Inverse */    *cx=(*bx)+GOLD*(*bx-*ax); 
   for (i=1;i<=npar;i++)    *fc=(*func)(*cx); 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    while (*fb > *fc) { 
   ludcmp(a,npar,indx,&pd);      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
   /*  printf("\n#Hessian matrix recomputed#\n");      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   for (j=1;j<=npar;j++) {      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     for (i=1;i<=npar;i++) x[i]=0;      if ((*bx-u)*(u-*cx) > 0.0) { 
     x[j]=1;        fu=(*func)(u); 
     lubksb(a,npar,indx,x);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     for (i=1;i<=npar;i++){        fu=(*func)(u); 
       y[i][j]=x[i];        if (fu < *fc) { 
       printf("%.3e ",y[i][j]);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     }            SHFT(*fb,*fc,fu,(*func)(u)) 
     printf("\n");            } 
   }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   */        u=ulim; 
         fu=(*func)(u); 
   free_matrix(a,1,npar,1,npar);      } else { 
   free_matrix(y,1,npar,1,npar);        u=(*cx)+GOLD*(*cx-*bx); 
   free_vector(x,1,npar);        fu=(*func)(u); 
   free_ivector(indx,1,npar);      } 
   free_matrix(hess,1,npar,1,npar);      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
         } 
 }  } 
   
 /*************** hessian matrix ****************/  /*************** linmin ************************/
 double hessii( double x[], double delta, int theta, double delti[])  
 {  int ncom; 
   int i;  double *pcom,*xicom;
   int l=1, lmax=20;  double (*nrfunc)(double []); 
   double k1,k2;   
   double p2[NPARMAX+1];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   double res;  { 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double brent(double ax, double bx, double cx, 
   double fx;                 double (*f)(double), double tol, double *xmin); 
   int k=0,kmax=10;    double f1dim(double x); 
   double l1;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
   fx=func(x);    int j; 
   for (i=1;i<=npar;i++) p2[i]=x[i];    double xx,xmin,bx,ax; 
   for(l=0 ; l <=lmax; l++){    double fx,fb,fa;
     l1=pow(10,l);   
     delts=delt;    ncom=n; 
     for(k=1 ; k <kmax; k=k+1){    pcom=vector(1,n); 
       delt = delta*(l1*k);    xicom=vector(1,n); 
       p2[theta]=x[theta] +delt;    nrfunc=func; 
       k1=func(p2)-fx;    for (j=1;j<=n;j++) { 
       p2[theta]=x[theta]-delt;      pcom[j]=p[j]; 
       k2=func(p2)-fx;      xicom[j]=xi[j]; 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    } 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    ax=0.0; 
          xx=1.0; 
 #ifdef DEBUG    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       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);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 #endif  #ifdef DEBUG
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         k=kmax;  #endif
       }    for (j=1;j<=n;j++) { 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      xi[j] *= xmin; 
         k=kmax; l=lmax*10.;      p[j] += xi[j]; 
       }    } 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    free_vector(xicom,1,n); 
         delts=delt;    free_vector(pcom,1,n); 
       }  } 
     }  
   }  char *asc_diff_time(long time_sec, char ascdiff[])
   delti[theta]=delts;  {
   return res;    long sec_left, days, hours, minutes;
      days = (time_sec) / (60*60*24);
 }    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
 double hessij( double x[], double delti[], int thetai,int thetaj)    sec_left = (sec_left) %(60*60);
 {    minutes = (sec_left) /60;
   int i;    sec_left = (sec_left) % (60);
   int l=1, l1, lmax=20;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   double k1,k2,k3,k4,res,fx;    return ascdiff;
   double p2[NPARMAX+1];  }
   int k;  
   /*************** powell ************************/
   fx=func(x);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   for (k=1; k<=2; k++) {              double (*func)(double [])) 
     for (i=1;i<=npar;i++) p2[i]=x[i];  { 
     p2[thetai]=x[thetai]+delti[thetai]/k;    void linmin(double p[], double xi[], int n, double *fret, 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;                double (*func)(double [])); 
     k1=func(p2)-fx;    int i,ibig,j; 
      double del,t,*pt,*ptt,*xit;
     p2[thetai]=x[thetai]+delti[thetai]/k;    double fp,fptt;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double *xits;
     k2=func(p2)-fx;    int niterf, itmp;
    
     p2[thetai]=x[thetai]-delti[thetai]/k;    pt=vector(1,n); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    ptt=vector(1,n); 
     k3=func(p2)-fx;    xit=vector(1,n); 
      xits=vector(1,n); 
     p2[thetai]=x[thetai]-delti[thetai]/k;    *fret=(*func)(p); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    for (j=1;j<=n;j++) pt[j]=p[j]; 
     k4=func(p2)-fx;    for (*iter=1;;++(*iter)) { 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      fp=(*fret); 
 #ifdef DEBUG      ibig=0; 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      del=0.0; 
 #endif      last_time=curr_time;
   }      (void) gettimeofday(&curr_time,&tzp);
   return res;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
 }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
   /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
 /************** Inverse of matrix **************/     for (i=1;i<=n;i++) {
 void ludcmp(double **a, int n, int *indx, double *d)        printf(" %d %.12f",i, p[i]);
 {        fprintf(ficlog," %d %.12lf",i, p[i]);
   int i,imax,j,k;        fprintf(ficrespow," %.12lf", p[i]);
   double big,dum,sum,temp;      }
   double *vv;      printf("\n");
        fprintf(ficlog,"\n");
   vv=vector(1,n);      fprintf(ficrespow,"\n");fflush(ficrespow);
   *d=1.0;      if(*iter <=3){
   for (i=1;i<=n;i++) {        tm = *localtime(&curr_time.tv_sec);
     big=0.0;        strcpy(strcurr,asctime(&tm));
     for (j=1;j<=n;j++)  /*       asctime_r(&tm,strcurr); */
       if ((temp=fabs(a[i][j])) > big) big=temp;        forecast_time=curr_time; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        itmp = strlen(strcurr);
     vv[i]=1.0/big;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   }          strcurr[itmp-1]='\0';
   for (j=1;j<=n;j++) {        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for (i=1;i<j;i++) {        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       sum=a[i][j];        for(niterf=10;niterf<=30;niterf+=10){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       a[i][j]=sum;          tmf = *localtime(&forecast_time.tv_sec);
     }  /*      asctime_r(&tmf,strfor); */
     big=0.0;          strcpy(strfor,asctime(&tmf));
     for (i=j;i<=n;i++) {          itmp = strlen(strfor);
       sum=a[i][j];          if(strfor[itmp-1]=='\n')
       for (k=1;k<j;k++)          strfor[itmp-1]='\0';
         sum -= a[i][k]*a[k][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);
       a[i][j]=sum;          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 ( (dum=vv[i]*fabs(sum)) >= big) {        }
         big=dum;      }
         imax=i;      for (i=1;i<=n;i++) { 
       }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     }        fptt=(*fret); 
     if (j != imax) {  #ifdef DEBUG
       for (k=1;k<=n;k++) {        printf("fret=%lf \n",*fret);
         dum=a[imax][k];        fprintf(ficlog,"fret=%lf \n",*fret);
         a[imax][k]=a[j][k];  #endif
         a[j][k]=dum;        printf("%d",i);fflush(stdout);
       }        fprintf(ficlog,"%d",i);fflush(ficlog);
       *d = -(*d);        linmin(p,xit,n,fret,func); 
       vv[imax]=vv[j];        if (fabs(fptt-(*fret)) > del) { 
     }          del=fabs(fptt-(*fret)); 
     indx[j]=imax;          ibig=i; 
     if (a[j][j] == 0.0) a[j][j]=TINY;        } 
     if (j != n) {  #ifdef DEBUG
       dum=1.0/(a[j][j]);        printf("%d %.12e",i,(*fret));
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
   }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   free_vector(vv,1,n);  /* Doesn't work */          printf(" x(%d)=%.12e",j,xit[j]);
 ;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
 }        }
         for(j=1;j<=n;j++) {
 void lubksb(double **a, int n, int *indx, double b[])          printf(" p=%.12e",p[j]);
 {          fprintf(ficlog," p=%.12e",p[j]);
   int i,ii=0,ip,j;        }
   double sum;        printf("\n");
          fprintf(ficlog,"\n");
   for (i=1;i<=n;i++) {  #endif
     ip=indx[i];      } 
     sum=b[ip];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     b[ip]=b[i];  #ifdef DEBUG
     if (ii)        int k[2],l;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        k[0]=1;
     else if (sum) ii=i;        k[1]=-1;
     b[i]=sum;        printf("Max: %.12e",(*func)(p));
   }        fprintf(ficlog,"Max: %.12e",(*func)(p));
   for (i=n;i>=1;i--) {        for (j=1;j<=n;j++) {
     sum=b[i];          printf(" %.12e",p[j]);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          fprintf(ficlog," %.12e",p[j]);
     b[i]=sum/a[i][i];        }
   }        printf("\n");
 }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 /************ Frequencies ********************/          for (j=1;j<=n;j++) {
 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)            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 {  /* Some frequencies */            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
              fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          }
   double ***freq; /* Frequencies */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double *pp;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double pos, k2, dateintsum=0,k2cpt=0;        }
   FILE *ficresp;  #endif
   char fileresp[FILENAMELENGTH];  
    
   pp=vector(1,nlstate);        free_vector(xit,1,n); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        free_vector(xits,1,n); 
   strcpy(fileresp,"p");        free_vector(ptt,1,n); 
   strcat(fileresp,fileres);        free_vector(pt,1,n); 
   if((ficresp=fopen(fileresp,"w"))==NULL) {        return; 
     printf("Problem with prevalence resultfile: %s\n", fileresp);      } 
     exit(0);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   }      for (j=1;j<=n;j++) { 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        ptt[j]=2.0*p[j]-pt[j]; 
   j1=0;        xit[j]=p[j]-pt[j]; 
          pt[j]=p[j]; 
   j=cptcoveff;      } 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      fptt=(*func)(ptt); 
        if (fptt < fp) { 
   for(k1=1; k1<=j;k1++){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     for(i1=1; i1<=ncodemax[k1];i1++){        if (t < 0.0) { 
       j1++;          linmin(p,xit,n,fret,func); 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          for (j=1;j<=n;j++) { 
         scanf("%d", i);*/            xi[j][ibig]=xi[j][n]; 
       for (i=-1; i<=nlstate+ndeath; i++)              xi[j][n]=xit[j]; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)            }
           for(m=agemin; m <= agemax+3; m++)  #ifdef DEBUG
             freq[i][jk][m]=0;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       dateintsum=0;          for(j=1;j<=n;j++){
       k2cpt=0;            printf(" %.12e",xit[j]);
       for (i=1; i<=imx; i++) {            fprintf(ficlog," %.12e",xit[j]);
         bool=1;          }
         if  (cptcovn>0) {          printf("\n");
           for (z1=1; z1<=cptcoveff; z1++)          fprintf(ficlog,"\n");
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  #endif
               bool=0;        }
         }      } 
         if (bool==1) {    } 
           for(m=firstpass; m<=lastpass; m++){  } 
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  /**** Prevalence limit (stable or period prevalence)  ****************/
               if(agev[m][i]==0) agev[m][i]=agemax+1;  
               if(agev[m][i]==1) agev[m][i]=agemax+2;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
               if (m<lastpass) {  {
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];       matrix by transitions matrix until convergence is reached */
               }  
                  int i, ii,j,k;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    double min, max, maxmin, maxmax,sumnew=0.;
                 dateintsum=dateintsum+k2;    double **matprod2();
                 k2cpt++;    double **out, cov[NCOVMAX+1], **pmij();
               }    double **newm;
             }    double agefin, delaymax=50 ; /* Max number of years to converge */
           }  
         }    for (ii=1;ii<=nlstate+ndeath;ii++)
       }      for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      }
   
       if  (cptcovn>0) {     cov[1]=1.;
         fprintf(ficresp, "\n#********** Variable ");   
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         fprintf(ficresp, "**********\n#");    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       }      newm=savm;
       for(i=1; i<=nlstate;i++)      /* Covariates have to be included here again */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      cov[2]=agefin;
       fprintf(ficresp, "\n");      
            for (k=1; k<=cptcovn;k++) {
       for(i=(int)agemin; i <= (int)agemax+3; i++){        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         if(i==(int)agemax+3)        /*        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]]);*/
           printf("Total");      }
         else      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           printf("Age %d", i);      for (k=1; k<=cptcovprod;k++)
         for(jk=1; jk <=nlstate ; jk++){        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      
             pp[jk] += freq[jk][m][i];      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         }      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         for(jk=1; jk <=nlstate ; jk++){      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
           for(m=-1, pos=0; m <=0 ; m++)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
             pos += freq[jk][m][i];      
           if(pp[jk]>=1.e-10)      savm=oldm;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      oldm=newm;
           else      maxmax=0.;
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      for(j=1;j<=nlstate;j++){
         }        min=1.;
         max=0.;
         for(jk=1; jk <=nlstate ; jk++){        for(i=1; i<=nlstate; i++) {
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          sumnew=0;
             pp[jk] += freq[jk][m][i];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         }          prlim[i][j]= newm[i][j]/(1-sumnew);
           max=FMAX(max,prlim[i][j]);
         for(jk=1,pos=0; jk <=nlstate ; jk++)          min=FMIN(min,prlim[i][j]);
           pos += pp[jk];        }
         for(jk=1; jk <=nlstate ; jk++){        maxmin=max-min;
           if(pos>=1.e-5)        maxmax=FMAX(maxmax,maxmin);
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      }
           else      if(maxmax < ftolpl){
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        return prlim;
           if( i <= (int) agemax){      }
             if(pos>=1.e-5){    }
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  }
               probs[i][jk][j1]= pp[jk]/pos;  
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  /*************** transition probabilities ***************/ 
             }  
             else  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  {
           }    /* 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
               model to the ncovmodel covariates (including constant and age).
         for(jk=-1; jk <=nlstate+ndeath; jk++)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
           for(m=-1; m <=nlstate+ndeath; m++)       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);       ncth covariate in the global vector x is given by the formula:
         if(i <= (int) agemax)       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           fprintf(ficresp,"\n");       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
         printf("\n");       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.
     }       Outputs ps[i][j] the probability to be observed in j being in j according to
   }       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   dateintmean=dateintsum/k2cpt;    */
      double s1, lnpijopii;
   fclose(ficresp);    /*double t34;*/
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    int i,j,j1, nc, ii, jj;
   free_vector(pp,1,nlstate);  
        for(i=1; i<= nlstate; i++){
   /* End of Freq */        for(j=1; j<i;j++){
 }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += param[i][j][nc]*cov[nc];*/
 /************ Prevalence ********************/            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
 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)  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
 {  /* Some frequencies */          }
            ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   double ***freq; /* Frequencies */        }
   double *pp;        for(j=i+1; j<=nlstate+ndeath;j++){
   double pos, k2;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   pp=vector(1,nlstate);            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
            }
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   j1=0;        }
        }
   j=cptcoveff;      
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for(i=1; i<= nlstate; i++){
          s1=0;
   for(k1=1; k1<=j;k1++){        for(j=1; j<i; j++){
     for(i1=1; i1<=ncodemax[k1];i1++){          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       j1++;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
              }
       for (i=-1; i<=nlstate+ndeath; i++)          for(j=i+1; j<=nlstate+ndeath; j++){
         for (jk=-1; jk<=nlstate+ndeath; jk++)            s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           for(m=agemin; m <= agemax+3; m++)          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
             freq[i][jk][m]=0;        }
              /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       for (i=1; i<=imx; i++) {        ps[i][i]=1./(s1+1.);
         bool=1;        /* Computing other pijs */
         if  (cptcovn>0) {        for(j=1; j<i; j++)
           for (z1=1; z1<=cptcoveff; z1++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        for(j=i+1; j<=nlstate+ndeath; j++)
               bool=0;          ps[i][j]= exp(ps[i][j])*ps[i][i];
         }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         if (bool==1) {      } /* end i */
           for(m=firstpass; m<=lastpass; m++){      
             k2=anint[m][i]+(mint[m][i]/12.);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(jj=1; jj<= nlstate+ndeath; jj++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;          ps[ii][jj]=0;
               if(agev[m][i]==1) agev[m][i]=agemax+2;          ps[ii][ii]=1;
               if (m<lastpass) {        }
                 if (calagedate>0)      }
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      
                 else  
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
               }  /*         printf("ddd %lf ",ps[ii][jj]); */
             }  /*       } */
           }  /*       printf("\n "); */
         }  /*        } */
       }  /*        printf("\n ");printf("%lf ",cov[2]); */
       for(i=(int)agemin; i <= (int)agemax+3; i++){         /*
         for(jk=1; jk <=nlstate ; jk++){        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        goto end;*/
             pp[jk] += freq[jk][m][i];      return ps;
         }  }
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)  /**************** Product of 2 matrices ******************/
             pos += freq[jk][m][i];  
         }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
          {
         for(jk=1; jk <=nlstate ; jk++){    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
             pp[jk] += freq[jk][m][i];    /* in, b, out are matrice of pointers which should have been initialized 
         }       before: only the contents of out is modified. The function returns
               a pointer to pointers identical to out */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    long i, j, k;
            for(i=nrl; i<= nrh; i++)
         for(jk=1; jk <=nlstate ; jk++){          for(k=ncolol; k<=ncoloh; k++)
           if( i <= (int) agemax){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
             if(pos>=1.e-5){          out[i][k] +=in[i][j]*b[j][k];
               probs[i][jk][j1]= pp[jk]/pos;  
             }    return out;
           }  }
         }  
          
       }  /************* Higher Matrix Product ***************/
     }  
   }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
      /* Computes the transition matrix starting at age 'age' over 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);       'nhstepm*hstepm*stepm' months (i.e. until
   free_vector(pp,1,nlstate);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         nhstepm*hstepm matrices. 
 }  /* End of Freq */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
 /************* Waves Concatenation ***************/       for the memory).
        Model is determined by parameters x and covariates have to be 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)       included manually here. 
 {  
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.       */
      Death is a valid wave (if date is known).  
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    int i, j, d, h, k;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    double **out, cov[NCOVMAX+1];
      and mw[mi+1][i]. dh depends on stepm.    double **newm;
      */  
     /* Hstepm could be zero and should return the unit matrix */
   int i, mi, m;    for (i=1;i<=nlstate+ndeath;i++)
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      for (j=1;j<=nlstate+ndeath;j++){
      double sum=0., jmean=0.;*/        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
   int j, k=0,jk, ju, jl;      }
   double sum=0.;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   jmin=1e+5;    for(h=1; h <=nhstepm; h++){
   jmax=-1;      for(d=1; d <=hstepm; d++){
   jmean=0.;        newm=savm;
   for(i=1; i<=imx; i++){        /* Covariates have to be included here again */
     mi=0;        cov[1]=1.;
     m=firstpass;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     while(s[m][i] <= nlstate){        for (k=1; k<=cptcovn;k++) 
       if(s[m][i]>=1)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         mw[++mi][i]=m;        for (k=1; k<=cptcovage;k++)
       if(m >=lastpass)          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         break;        for (k=1; k<=cptcovprod;k++)
       else          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         m++;  
     }/* end while */  
     if (s[m][i] > nlstate){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       mi++;     /* Death is another wave */        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       /* if(mi==0)  never been interviewed correctly before death */        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
          /* Only death is a correct wave */                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       mw[mi][i]=m;        savm=oldm;
     }        oldm=newm;
       }
     wav[i]=mi;      for(i=1; i<=nlstate+ndeath; i++)
     if(mi==0)        for(j=1;j<=nlstate+ndeath;j++) {
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          po[i][j][h]=newm[i][j];
   }          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
   for(i=1; i<=imx; i++){      /*printf("h=%d ",h);*/
     for(mi=1; mi<wav[i];mi++){    } /* end h */
       if (stepm <=0)  /*     printf("\n H=%d \n",h); */
         dh[mi][i]=1;    return po;
       else{  }
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  /*************** log-likelihood *************/
           if(j==0) j=1;  /* Survives at least one month after exam */  double func( double *x)
           k=k+1;  {
           if (j >= jmax) jmax=j;    int i, ii, j, k, mi, d, kk;
           if (j <= jmin) jmin=j;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           sum=sum+j;    double **out;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    double sw; /* Sum of weights */
           }    double lli; /* Individual log likelihood */
         }    int s1, s2;
         else{    double bbh, survp;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    long ipmx;
           k=k+1;    /*extern weight */
           if (j >= jmax) jmax=j;    /* We are differentiating ll according to initial status */
           else if (j <= jmin)jmin=j;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    /*for(i=1;i<imx;i++) 
           sum=sum+j;      printf(" %d\n",s[4][i]);
         }    */
         jk= j/stepm;    cov[1]=1.;
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;    for(k=1; k<=nlstate; k++) ll[k]=0.;
         if(jl <= -ju)  
           dh[mi][i]=jk;    if(mle==1){
         else      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           dh[mi][i]=jk+1;        /* Computes the values of the ncovmodel covariates of the model
         if(dh[mi][i]==0)           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
           dh[mi][i]=1; /* At least one step */           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
       }           to be observed in j being in i according to the model.
     }         */
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   jmean=sum/k;        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
  }           has been calculated etc */
 /*********** Tricode ****************************/        for(mi=1; mi<= wav[i]-1; mi++){
 void tricode(int *Tvar, int **nbcode, int imx)          for (ii=1;ii<=nlstate+ndeath;ii++)
 {            for (j=1;j<=nlstate+ndeath;j++){
   int Ndum[20],ij=1, k, j, i;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int cptcode=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   cptcoveff=0;            }
            for(d=0; d<dh[mi][i]; d++){
   for (k=0; k<19; k++) Ndum[k]=0;            newm=savm;
   for (k=1; k<=7; k++) ncodemax[k]=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
     for (i=1; i<=imx; i++) {            }
       ij=(int)(covar[Tvar[j]][i]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       Ndum[ij]++;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            savm=oldm;
       if (ij > cptcode) cptcode=ij;            oldm=newm;
     }          } /* end mult */
         
     for (i=0; i<=cptcode; i++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       if(Ndum[i]!=0) ncodemax[j]++;          /* But now since version 0.9 we anticipate for bias at large stepm.
     }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     ij=1;           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for (i=1; i<=ncodemax[j]; i++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       for (k=0; k<=19; k++) {           * probability in order to take into account the bias as a fraction of the way
         if (Ndum[k] != 0) {           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           nbcode[Tvar[j]][ij]=k;           * -stepm/2 to stepm/2 .
                     * For stepm=1 the results are the same as for previous versions of Imach.
           ij++;           * For stepm > 1 the results are less biased than in previous versions. 
         }           */
         if (ij > ncodemax[j]) break;          s1=s[mw[mi][i]][i];
       }            s2=s[mw[mi+1][i]][i];
     }          bbh=(double)bh[mi][i]/(double)stepm; 
   }            /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
  for (k=0; k<19; k++) Ndum[k]=0;           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
  for (i=1; i<=ncovmodel-2; i++) {          if( s2 > nlstate){ 
       ij=Tvar[i];            /* i.e. if s2 is a death state and if the date of death is known 
       Ndum[ij]++;               then the contribution to the likelihood is the probability to 
     }               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
  ij=1;               minus probability to die before dh-stepm . 
  for (i=1; i<=10; i++) {               In version up to 0.92 likelihood was computed
    if((Ndum[i]!=0) && (i<=ncovcol)){          as if date of death was unknown. Death was treated as any other
      Tvaraff[ij]=i;          health state: the date of the interview describes the actual state
      ij++;          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
            introduced the exact date of death then we should have modified
     cptcoveff=ij-1;          the contribution of an exact death to the likelihood. This new
 }          contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
 /*********** Health Expectancies ****************/          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
 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 )          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
 {          mortality artificially. The bad side is that we add another loop
   /* Health expectancies */          which slows down the processing. The difference can be up to 10%
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          lower mortality.
   double age, agelim, hf;            */
   double ***p3mat,***varhe;            lli=log(out[s1][s2] - savm[s1][s2]);
   double **dnewm,**doldm;  
   double *xp;  
   double **gp, **gm;          } else if  (s2==-2) {
   double ***gradg, ***trgradg;            for (j=1,survp=0. ; j<=nlstate; j++) 
   int theta;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            lli= log(survp);
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate*2,1,npar);          
   doldm=matrix(1,nlstate*2,1,nlstate*2);          else if  (s2==-4) { 
              for (j=3,survp=0. ; j<=nlstate; j++)  
   fprintf(ficreseij,"# Health expectancies\n");              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   fprintf(ficreseij,"# Age");            lli= log(survp); 
   for(i=1; i<=nlstate;i++)          } 
     for(j=1; j<=nlstate;j++)  
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          else if  (s2==-5) { 
   fprintf(ficreseij,"\n");            for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   if(estepm < stepm){            lli= log(survp); 
     printf ("Problem %d lower than %d\n",estepm, stepm);          } 
   }          
   else  hstepm=estepm;            else{
   /* We compute the life expectancy from trapezoids spaced every estepm months            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
    * This is mainly to measure the difference between two models: for example            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
    * if stepm=24 months pijx are given only every 2 years and by summing them          } 
    * we are calculating an estimate of the Life Expectancy assuming a linear          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
    * progression inbetween and thus overestimating or underestimating according          /*if(lli ==000.0)*/
    * to the curvature of the survival function. If, for the same date, we          /*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); */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months          ipmx +=1;
    * to compare the new estimate of Life expectancy with the same linear          sw += weight[i];
    * hypothesis. A more precise result, taking into account a more precise          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    * curvature will be obtained if estepm is as small as stepm. */        } /* end of wave */
       } /* end of individual */
   /* For example we decided to compute the life expectancy with the smallest unit */    }  else if(mle==2){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      nhstepm is the number of hstepm from age to agelim        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      nstepm is the number of stepm from age to agelin.        for(mi=1; mi<= wav[i]-1; mi++){
      Look at hpijx to understand the reason of that which relies in memory size          for (ii=1;ii<=nlstate+ndeath;ii++)
      and note for a fixed period like estepm months */            for (j=1;j<=nlstate+ndeath;j++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      survival function given by stepm (the optimization length). Unfortunately it              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      means that if the survival funtion is printed only each two years of age and if            }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          for(d=0; d<=dh[mi][i]; d++){
      results. So we changed our mind and took the option of the best precision.            newm=savm;
   */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   agelim=AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     /* nhstepm age range expressed in number of stepm */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     nstepm=(int) rint((agelim-age)*YEARM/stepm);            savm=oldm;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            oldm=newm;
     /* if (stepm >= YEARM) hstepm=1;*/          } /* end mult */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          s1=s[mw[mi][i]][i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          s2=s[mw[mi+1][i]][i];
     gp=matrix(0,nhstepm,1,nlstate*2);          bbh=(double)bh[mi][i]/(double)stepm; 
     gm=matrix(0,nhstepm,1,nlstate*2);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          sw += weight[i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          } /* end of wave */
        } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     /* Computing Variances of health expectancies */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
      for(theta=1; theta <=npar; theta++){            for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
       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, gp[h][cptj]=0.; h<=nhstepm-1; h++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           }            savm=oldm;
         }            oldm=newm;
       }          } /* end mult */
              
                s1=s[mw[mi][i]][i];
       for(i=1; i<=npar; i++)          s2=s[mw[mi+1][i]][i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          bbh=(double)bh[mi][i]/(double)stepm; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            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 */
                ipmx +=1;
       cptj=0;          sw += weight[i];
       for(j=1; j<= nlstate; j++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(i=1;i<=nlstate;i++){        } /* end of wave */
           cptj=cptj+1;      } /* end of individual */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    }else if (mle==4){  /* ml=4 no inter-extrapolation */
             gm[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*2; j++)            for (j=1;j<=nlstate+ndeath;j++){
         for(h=0; h<=nhstepm-1; h++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
      }          for(d=0; d<dh[mi][i]; d++){
                newm=savm;
 /* End theta */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
      for(h=0; h<=nhstepm-1; h++)          
       for(j=1; j<=nlstate*2;j++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(theta=1; theta <=npar; theta++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           trgradg[h][j][theta]=gradg[h][theta][j];            savm=oldm;
                  oldm=newm;
           } /* end mult */
      for(i=1;i<=nlstate*2;i++)        
       for(j=1;j<=nlstate*2;j++)          s1=s[mw[mi][i]][i];
         varhe[i][j][(int)age] =0.;          s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
      printf("%d|",(int)age);fflush(stdout);            lli=log(out[s1][s2] - savm[s1][s2]);
      for(h=0;h<=nhstepm-1;h++){          }else{
       for(k=0;k<=nhstepm-1;k++){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);          }
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          ipmx +=1;
         for(i=1;i<=nlstate*2;i++)          sw += weight[i];
           for(j=1;j<=nlstate*2;j++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       }        } /* end of wave */
     }      } /* end of individual */
     /* Computing expectancies */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for(i=1; i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(j=1; j<=nlstate;j++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        for(mi=1; mi<= wav[i]-1; mi++){
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          for (ii=1;ii<=nlstate+ndeath;ii++)
                      for (j=1;j<=nlstate+ndeath;j++){
 /* 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]);*/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
           for(d=0; d<dh[mi][i]; d++){
     fprintf(ficreseij,"%3.0f",age );            newm=savm;
     cptj=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(i=1; i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<=nlstate;j++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         cptj++;            }
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficreseij,"\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
     free_matrix(gm,0,nhstepm,1,nlstate*2);            oldm=newm;
     free_matrix(gp,0,nhstepm,1,nlstate*2);          } /* end mult */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          s1=s[mw[mi][i]][i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          s2=s[mw[mi+1][i]][i];
   }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   printf("\n");          ipmx +=1;
           sw += weight[i];
   free_vector(xp,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_matrix(dnewm,1,nlstate*2,1,npar);          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        } /* end of wave */
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);      } /* end of individual */
 }    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 /************ Variance ******************/    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 void varevsij(char fileres[], 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)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 {    return -l;
   /* Variance of health expectancies */  }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;  /*************** log-likelihood *************/
   double **dnewm,**doldm;  double funcone( double *x)
   int i, j, nhstepm, hstepm, h, nstepm ;  {
   int k, cptcode;    /* Same as likeli but slower because of a lot of printf and if */
   double *xp;    int i, ii, j, k, mi, d, kk;
   double **gp, **gm;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double ***gradg, ***trgradg;    double **out;
   double ***p3mat;    double lli; /* Individual log likelihood */
   double age,agelim, hf;    double llt;
   int theta;    int s1, s2;
     double bbh, survp;
   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");    /*extern weight */
   fprintf(ficresvij,"# Age");    /* We are differentiating ll according to initial status */
   for(i=1; i<=nlstate;i++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(j=1; j<=nlstate;j++)    /*for(i=1;i<imx;i++) 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      printf(" %d\n",s[4][i]);
   fprintf(ficresvij,"\n");    */
     cov[1]=1.;
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   doldm=matrix(1,nlstate,1,nlstate);  
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if(estepm < stepm){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     printf ("Problem %d lower than %d\n",estepm, stepm);      for(mi=1; mi<= wav[i]-1; mi++){
   }        for (ii=1;ii<=nlstate+ndeath;ii++)
   else  hstepm=estepm;            for (j=1;j<=nlstate+ndeath;j++){
   /* For example we decided to compute the life expectancy with the smallest unit */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            savm[ii][j]=(ii==j ? 1.0 : 0.0);
      nhstepm is the number of hstepm from age to agelim          }
      nstepm is the number of stepm from age to agelin.        for(d=0; d<dh[mi][i]; d++){
      Look at hpijx to understand the reason of that which relies in memory size          newm=savm;
      and note for a fixed period like k years */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for (kk=1; kk<=cptcovage;kk++) {
      survival function given by stepm (the optimization length). Unfortunately it            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      means that if the survival funtion is printed only each two years of age and if          }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      results. So we changed our mind and took the option of the best precision.                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   */          savm=oldm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          oldm=newm;
   agelim = AGESUP;        } /* end mult */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        s1=s[mw[mi][i]][i];
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        s2=s[mw[mi+1][i]][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        bbh=(double)bh[mi][i]/(double)stepm; 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        /* bias is positive if real duration
     gp=matrix(0,nhstepm,1,nlstate);         * is higher than the multiple of stepm and negative otherwise.
     gm=matrix(0,nhstepm,1,nlstate);         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
     for(theta=1; theta <=npar; theta++){          lli=log(out[s1][s2] - savm[s1][s2]);
       for(i=1; i<=npar; i++){ /* Computes gradient */        } else if  (s2==-2) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for (j=1,survp=0. ; j<=nlstate; j++) 
       }            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            lli= log(survp);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       if (popbased==1) {        } else if(mle==2){
         for(i=1; i<=nlstate;i++)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           prlim[i][i]=probs[(int)age][i][ij];        } else if(mle==3){  /* exponential inter-extrapolation */
       }          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 */
          } else if (mle==4){  /* mle=4 no inter-extrapolation */
       for(j=1; j<= nlstate; j++){          lli=log(out[s1][s2]); /* Original formula */
         for(h=0; h<=nhstepm; h++){        } else{  /* mle=0 back to 1 */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          /*lli=log(out[s1][s2]); */ /* Original formula */
         }        } /* End of if */
       }        ipmx +=1;
            sw += weight[i];
       for(i=1; i<=npar; i++) /* Computes gradient */        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        /*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]); */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          if(globpr){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     %11.6f %11.6f %11.6f ", \
       if (popbased==1) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         for(i=1; i<=nlstate;i++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           prlim[i][i]=probs[(int)age][i][ij];          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       }            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       for(j=1; j<= nlstate; j++){          }
         for(h=0; h<=nhstepm; h++){          fprintf(ficresilk," %10.6f\n", -llt);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      } /* end of wave */
         }    } /* end of individual */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(j=1; j<= nlstate; j++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(h=0; h<=nhstepm; h++){    if(globpr==0){ /* First time we count the contributions and weights */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      gipmx=ipmx;
         }      gsw=sw;
     } /* End theta */    }
     return -l;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  }
   
     for(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)  /*************** function likelione ***********/
         for(theta=1; theta <=npar; theta++)  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
           trgradg[h][j][theta]=gradg[h][theta][j];  {
     /* This routine should help understanding what is done with 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */       the selection of individuals/waves and
     for(i=1;i<=nlstate;i++)       to check the exact contribution to the likelihood.
       for(j=1;j<=nlstate;j++)       Plotting could be done.
         vareij[i][j][(int)age] =0.;     */
     int k;
     for(h=0;h<=nhstepm;h++){  
       for(k=0;k<=nhstepm;k++){    if(*globpri !=0){ /* Just counts and sums, no printings */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      strcpy(fileresilk,"ilk"); 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      strcat(fileresilk,fileres);
         for(i=1;i<=nlstate;i++)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
           for(j=1;j<=nlstate;j++)        printf("Problem with resultfile: %s\n", fileresilk);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }      }
     }      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     fprintf(ficresvij,"%.0f ",age );      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(i=1; i<=nlstate;i++)      for(k=1; k<=nlstate; k++) 
       for(j=1; j<=nlstate;j++){        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       }    }
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);    *fretone=(*funcone)(p);
     free_matrix(gm,0,nhstepm,1,nlstate);    if(*globpri !=0){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      fclose(ficresilk);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fflush(fichtm); 
   } /* End age */    } 
      return;
   free_vector(xp,1,npar);  }
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   /*********** Maximum Likelihood Estimation ***************/
 }  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 /************ 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)    int i,j, iter;
 {    double **xi;
   /* Variance of prevalence limit */    double fret;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double fretone; /* Only one call to likelihood */
   double **newm;    /*  char filerespow[FILENAMELENGTH];*/
   double **dnewm,**doldm;    xi=matrix(1,npar,1,npar);
   int i, j, nhstepm, hstepm;    for (i=1;i<=npar;i++)
   int k, cptcode;      for (j=1;j<=npar;j++)
   double *xp;        xi[i][j]=(i==j ? 1.0 : 0.0);
   double *gp, *gm;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double **gradg, **trgradg;    strcpy(filerespow,"pow"); 
   double age,agelim;    strcat(filerespow,fileres);
   int theta;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", filerespow);
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   fprintf(ficresvpl,"# Age");    }
   for(i=1; i<=nlstate;i++)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       fprintf(ficresvpl," %1d-%1d",i,i);    for (i=1;i<=nlstate;i++)
   fprintf(ficresvpl,"\n");      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   xp=vector(1,npar);    fprintf(ficrespow,"\n");
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);    powell(p,xi,npar,ftol,&iter,&fret,func);
    
   hstepm=1*YEARM; /* Every year of age */    free_matrix(xi,1,npar,1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    fclose(ficrespow);
   agelim = AGESUP;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  }
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);  /**** Computes Hessian and covariance matrix ***/
     gm=vector(1,nlstate);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
     for(theta=1; theta <=npar; theta++){    double  **a,**y,*x,pd;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double **hess;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int i, j,jk;
       }    int *indx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         gp[i] = prlim[i][i];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
        void lubksb(double **a, int npar, int *indx, double b[]) ;
       for(i=1; i<=npar; i++) /* Computes gradient */    void ludcmp(double **a, int npar, int *indx, double *d) ;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double gompertz(double p[]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    hess=matrix(1,npar,1,npar);
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       for(i=1;i<=nlstate;i++)    for (i=1;i<=npar;i++){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      printf("%d",i);fflush(stdout);
     } /* End theta */      fprintf(ficlog,"%d",i);fflush(ficlog);
      
     trgradg =matrix(1,nlstate,1,npar);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
     for(j=1; j<=nlstate;j++)      /*  printf(" %f ",p[i]);
       for(theta=1; theta <=npar; theta++)          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         trgradg[j][theta]=gradg[theta][j];    }
     
     for(i=1;i<=nlstate;i++)    for (i=1;i<=npar;i++) {
       varpl[i][(int)age] =0.;      for (j=1;j<=npar;j++)  {
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        if (j>i) { 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          printf(".%d%d",i,j);fflush(stdout);
     for(i=1;i<=nlstate;i++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
     fprintf(ficresvpl,"%.0f ",age );          hess[j][i]=hess[i][j];    
     for(i=1; i<=nlstate;i++)          /*printf(" %lf ",hess[i][j]);*/
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        }
     fprintf(ficresvpl,"\n");      }
     free_vector(gp,1,nlstate);    }
     free_vector(gm,1,nlstate);    printf("\n");
     free_matrix(gradg,1,npar,1,nlstate);    fprintf(ficlog,"\n");
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   free_vector(xp,1,npar);    
   free_matrix(doldm,1,nlstate,1,npar);    a=matrix(1,npar,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
 }    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
 /************ Variance of one-step probabilities  ******************/      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    ludcmp(a,npar,indx,&pd);
 {  
   int i, j,  i1, k1, l1;    for (j=1;j<=npar;j++) {
   int k2, l2, j1,  z1;      for (i=1;i<=npar;i++) x[i]=0;
   int k=0,l, cptcode;      x[j]=1;
   int first=1;      lubksb(a,npar,indx,x);
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;      for (i=1;i<=npar;i++){ 
   double **dnewm,**doldm;        matcov[i][j]=x[i];
   double *xp;      }
   double *gp, *gm;    }
   double **gradg, **trgradg;  
   double **mu;    printf("\n#Hessian matrix#\n");
   double age,agelim, cov[NCOVMAX];    fprintf(ficlog,"\n#Hessian matrix#\n");
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    for (i=1;i<=npar;i++) { 
   int theta;      for (j=1;j<=npar;j++) { 
   char fileresprob[FILENAMELENGTH];        printf("%.3e ",hess[i][j]);
   char fileresprobcov[FILENAMELENGTH];        fprintf(ficlog,"%.3e ",hess[i][j]);
   char fileresprobcor[FILENAMELENGTH];      }
       printf("\n");
   double ***varpij;      fprintf(ficlog,"\n");
     }
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);    /* Recompute Inverse */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    for (i=1;i<=npar;i++)
     printf("Problem with resultfile: %s\n", fileresprob);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   }    ludcmp(a,npar,indx,&pd);
   strcpy(fileresprobcov,"probcov");  
   strcat(fileresprobcov,fileres);    /*  printf("\n#Hessian matrix recomputed#\n");
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcov);    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
   strcpy(fileresprobcor,"probcor");      x[j]=1;
   strcat(fileresprobcor,fileres);      lubksb(a,npar,indx,x);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {      for (i=1;i<=npar;i++){ 
     printf("Problem with resultfile: %s\n", fileresprobcor);        y[i][j]=x[i];
   }        printf("%.3e ",y[i][j]);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);        fprintf(ficlog,"%.3e ",y[i][j]);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);      }
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);      printf("\n");
        fprintf(ficlog,"\n");
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    }
   fprintf(ficresprob,"# Age");    */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");  
   fprintf(ficresprobcov,"# Age");    free_matrix(a,1,npar,1,npar);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    free_matrix(y,1,npar,1,npar);
   fprintf(ficresprobcov,"# Age");    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  }
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  /*************** hessian matrix ****************/
     }    double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   fprintf(ficresprob,"\n");  {
   fprintf(ficresprobcov,"\n");    int i;
   fprintf(ficresprobcor,"\n");    int l=1, lmax=20;
   xp=vector(1,npar);    double k1,k2;
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    double p2[MAXPARM+1]; /* identical to x */
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    double res;
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    double fx;
   first=1;    int k=0,kmax=10;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    double l1;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);  
     exit(0);    fx=func(x);
   }    for (i=1;i<=npar;i++) p2[i]=x[i];
   else{    for(l=0 ; l <=lmax; l++){
     fprintf(ficgp,"\n# Routine varprob");      l1=pow(10,l);
   }      delts=delt;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {      for(k=1 ; k <kmax; k=k+1){
     printf("Problem with html file: %s\n", optionfilehtm);        delt = delta*(l1*k);
     exit(0);        p2[theta]=x[theta] +delt;
   }        k1=func(p2)-fx;
   else{        p2[theta]=x[theta]-delt;
     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");        k2=func(p2)-fx;
     fprintf(fichtm,"\n<br> We 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");        /*res= (k1-2.0*fx+k2)/delt/delt; */
     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");        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   }  #ifdef DEBUGHESS
   cov[1]=1;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   j=cptcoveff;        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  #endif
   j1=0;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   for(k1=1; k1<=1;k1++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     for(i1=1; i1<=ncodemax[k1];i1++){          k=kmax;
     j1++;        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     if  (cptcovn>0) {          k=kmax; l=lmax*10.;
       fprintf(ficresprob, "\n#********** Variable ");        }
       fprintf(ficresprobcov, "\n#********** Variable ");        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       fprintf(ficgp, "\n#********** Variable ");          delts=delt;
       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");        }
       fprintf(ficresprobcor, "\n#********** Variable ");      }
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    }
       fprintf(ficresprob, "**********\n#");    delti[theta]=delts;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    return res; 
       fprintf(ficresprobcov, "**********\n#");    
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  }
       fprintf(ficgp, "**********\n#");  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       fprintf(ficgp, "**********\n#");  {
       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    int i;
       fprintf(fichtm, "**********\n#");    int l=1, l1, lmax=20;
     }    double k1,k2,k3,k4,res,fx;
        double p2[MAXPARM+1];
       for (age=bage; age<=fage; age ++){    int k;
         cov[2]=age;  
         for (k=1; k<=cptcovn;k++) {    fx=func(x);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    for (k=1; k<=2; k++) {
         }      for (i=1;i<=npar;i++) p2[i]=x[i];
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      p2[thetai]=x[thetai]+delti[thetai]/k;
         for (k=1; k<=cptcovprod;k++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      k1=func(p2)-fx;
            
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));      p2[thetai]=x[thetai]+delti[thetai]/k;
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         gp=vector(1,(nlstate)*(nlstate+ndeath));      k2=func(p2)-fx;
         gm=vector(1,(nlstate)*(nlstate+ndeath));    
          p2[thetai]=x[thetai]-delti[thetai]/k;
         for(theta=1; theta <=npar; theta++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           for(i=1; i<=npar; i++)      k3=func(p2)-fx;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    
                p2[thetai]=x[thetai]-delti[thetai]/k;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                k4=func(p2)-fx;
           k=0;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           for(i=1; i<= (nlstate); i++){  #ifdef DEBUG
             for(j=1; j<=(nlstate+ndeath);j++){      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);
               k=k+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);
               gp[k]=pmmij[i][j];  #endif
             }    }
           }    return res;
            }
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:0);  /************** Inverse of matrix **************/
      void ludcmp(double **a, int n, int *indx, double *d) 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  { 
           k=0;    int i,imax,j,k; 
           for(i=1; i<=(nlstate); i++){    double big,dum,sum,temp; 
             for(j=1; j<=(nlstate+ndeath);j++){    double *vv; 
               k=k+1;   
               gm[k]=pmmij[i][j];    vv=vector(1,n); 
             }    *d=1.0; 
           }    for (i=1;i<=n;i++) { 
            big=0.0; 
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)      for (j=1;j<=n;j++) 
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          if ((temp=fabs(a[i][j])) > big) big=temp; 
         }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)    } 
           for(theta=1; theta <=npar; theta++)    for (j=1;j<=n;j++) { 
             trgradg[j][theta]=gradg[theta][j];      for (i=1;i<j;i++) { 
                sum=a[i][j]; 
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);        a[i][j]=sum; 
              } 
         pmij(pmmij,cov,ncovmodel,x,nlstate);      big=0.0; 
              for (i=j;i<=n;i++) { 
         k=0;        sum=a[i][j]; 
         for(i=1; i<=(nlstate); i++){        for (k=1;k<j;k++) 
           for(j=1; j<=(nlstate+ndeath);j++){          sum -= a[i][k]*a[k][j]; 
             k=k+1;        a[i][j]=sum; 
             mu[k][(int) age]=pmmij[i][j];        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           }          big=dum; 
         }          imax=i; 
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)        } 
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)      } 
             varpij[i][j][(int)age] = doldm[i][j];      if (j != imax) { 
         for (k=1;k<=n;k++) { 
         /*printf("\n%d ",(int)age);          dum=a[imax][k]; 
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          a[imax][k]=a[j][k]; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          a[j][k]=dum; 
      }*/        } 
         *d = -(*d); 
         fprintf(ficresprob,"\n%d ",(int)age);        vv[imax]=vv[j]; 
         fprintf(ficresprobcov,"\n%d ",(int)age);      } 
         fprintf(ficresprobcor,"\n%d ",(int)age);      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)      if (j != n) { 
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));        dum=1.0/(a[j][j]); 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);      } 
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);    } 
         }    free_vector(vv,1,n);  /* Doesn't work */
         i=0;  ;
         for (k=1; k<=(nlstate);k++){  } 
           for (l=1; l<=(nlstate+ndeath);l++){  
             i=i++;  void lubksb(double **a, int n, int *indx, double b[]) 
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);  { 
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    int i,ii=0,ip,j; 
             for (j=1; j<=i;j++){    double sum; 
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);   
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));    for (i=1;i<=n;i++) { 
             }      ip=indx[i]; 
           }      sum=b[ip]; 
         }/* end of loop for state */      b[ip]=b[i]; 
       } /* end of loop for age */      if (ii) 
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       for (k1=1; k1<=(nlstate);k1++){      else if (sum) ii=i; 
         for (l1=1; l1<=(nlstate+ndeath);l1++){      b[i]=sum; 
           if(l1==k1) continue;    } 
           i=(k1-1)*(nlstate+ndeath)+l1;    for (i=n;i>=1;i--) { 
           for (k2=1; k2<=(nlstate);k2++){      sum=b[i]; 
             for (l2=1; l2<=(nlstate+ndeath);l2++){      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
               if(l2==k2) continue;      b[i]=sum/a[i][i]; 
               j=(k2-1)*(nlstate+ndeath)+l2;    } 
               if(j<=i) continue;  } 
               for (age=bage; age<=fage; age ++){  
                 if ((int)age %5==0){  void pstamp(FILE *fichier)
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;  {
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;  }
                   mu1=mu[i][(int) age]/stepm*YEARM ;  
                   mu2=mu[j][(int) age]/stepm*YEARM;  /************ Frequencies ********************/
                   /* Computing eigen value of matrix of covariance */  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[])
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));  {  /* Some frequencies */
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);    int i, m, jk, k1,i1, j1, bool, z1,j;
                   /* Eigen vectors */    int first;
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    double ***freq; /* Frequencies */
                   v21=sqrt(1.-v11*v11);    double *pp, **prop;
                   v12=-v21;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
                   v22=v11;    char fileresp[FILENAMELENGTH];
                   /*printf(fignu*/    
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    pp=vector(1,nlstate);
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */    prop=matrix(1,nlstate,iagemin,iagemax+3);
                   if(first==1){    strcpy(fileresp,"p");
                     first=0;    strcat(fileresp,fileres);
                     fprintf(ficgp,"\nset parametric;set nolabel");    if((ficresp=fopen(fileresp,"w"))==NULL) {
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);      printf("Problem with prevalence resultfile: %s\n", fileresp);
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);      exit(0);
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);    }
                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    j1=0;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    j=cptcoveff;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    if (cptcovn<1) {j=1;ncodemax[1]=1;}
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  
                   }else{    first=1;
                     first=0;  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    for(k1=1; k1<=j;k1++){
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);      for(i1=1; i1<=ncodemax[k1];i1++){
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\        j1++;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);          scanf("%d", i);*/
                   }/* if first */        for (i=-5; i<=nlstate+ndeath; i++)  
                 } /* age mod 5 */          for (jk=-5; jk<=nlstate+ndeath; jk++)  
               } /* end loop age */            for(m=iagemin; m <= iagemax+3; m++)
               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);              freq[i][jk][m]=0;
               first=1;  
             } /*l12 */      for (i=1; i<=nlstate; i++)  
           } /* k12 */        for(m=iagemin; m <= iagemax+3; m++)
         } /*l1 */          prop[i][m]=0;
       }/* k1 */        
     } /* loop covariates */        dateintsum=0;
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);        k2cpt=0;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        for (i=1; i<=imx; i++) {
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          bool=1;
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);          if  (cptcovn>0) {
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            for (z1=1; z1<=cptcoveff; z1++) 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   }                bool=0;
   free_vector(xp,1,npar);          }
   fclose(ficresprob);          if (bool==1){
   fclose(ficresprobcov);            for(m=firstpass; m<=lastpass; m++){
   fclose(ficresprobcor);              k2=anint[m][i]+(mint[m][i]/12.);
   fclose(ficgp);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   fclose(fichtm);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 if (m<lastpass) {
 /******************* Printing html file ***********/                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                   int lastpass, int stepm, int weightopt, char model[],\                }
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                
                   int popforecast, int estepm ,\                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   double jprev1, double mprev1,double anprev1, \                  dateintsum=dateintsum+k2;
                   double jprev2, double mprev2,double anprev2){                  k2cpt++;
   int jj1, k1, i1, cpt;                }
   /*char optionfilehtm[FILENAMELENGTH];*/                /*}*/
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {            }
     printf("Problem with %s \n",optionfilehtm), exit(0);          }
   }        }
          
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
  - 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        pstamp(ficresp);
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n        if  (cptcovn>0) {
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n          fprintf(ficresp, "\n#********** Variable "); 
  - Life expectancies by age and initial health status (estepm=%2d months):          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \          fprintf(ficresp, "**********\n#");
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);        }
         for(i=1; i<=nlstate;i++) 
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n        fprintf(ficresp, "\n");
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n        
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n        for(i=iagemin; i <= iagemax+3; i++){
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n          if(i==iagemax+3){
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n            fprintf(ficlog,"Total");
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n          }else{
  - 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);            if(first==1){
               first=0;
  if(popforecast==1) fprintf(fichtm,"\n              printf("See log file for details...\n");
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n            }
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n            fprintf(ficlog,"Age %d", i);
         <br>",fileres,fileres,fileres,fileres);          }
  else          for(jk=1; jk <=nlstate ; jk++){
    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);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 fprintf(fichtm," <li>Graphs</li><p>");              pp[jk] += freq[jk][m][i]; 
           }
  m=cptcoveff;          for(jk=1; jk <=nlstate ; jk++){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
  jj1=0;            if(pp[jk]>=1.e-10){
  for(k1=1; k1<=m;k1++){              if(first==1){
    for(i1=1; i1<=ncodemax[k1];i1++){                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      jj1++;              }
      if (cptcovn > 0) {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            }else{
        for (cpt=1; cpt<=cptcoveff;cpt++)              if(first==1)
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      }            }
      /* Pij */          }
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>  
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              for(jk=1; jk <=nlstate ; jk++){
      /* Quasi-incidences */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
      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>              pp[jk] += freq[jk][m][i];
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          }       
        /* Stable prevalence in each health state */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
        for(cpt=1; cpt<nlstate;cpt++){            pos += pp[jk];
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>            posprop += prop[jk][i];
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          }
        }          for(jk=1; jk <=nlstate ; jk++){
     for(cpt=1; cpt<=nlstate;cpt++) {            if(pos>=1.e-5){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              if(first==1)
 interval) in state (%d): v%s%d%d.png <br>                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      }            }else{
      for(cpt=1; cpt<=nlstate;cpt++) {              if(first==1)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      }            }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            if( i <= iagemax){
 health expectancies in states (1) and (2): e%s%d.png<br>              if(pos>=1.e-5){
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
    }                /*probs[i][jk][j1]= pp[jk]/pos;*/
  }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 fclose(fichtm);              }
 }              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 /******************* Gnuplot file **************/            }
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          }
           
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   int ng;            for(m=-1; m <=nlstate+ndeath; m++)
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {              if(freq[jk][m][i] !=0 ) {
     printf("Problem with file %s",optionfilegnuplot);              if(first==1)
   }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
 #ifdef windows              }
     fprintf(ficgp,"cd \"%s\" \n",pathc);          if(i <= iagemax)
 #endif            fprintf(ficresp,"\n");
 m=pow(2,cptcoveff);          if(first==1)
              printf("Others in log...\n");
  /* 1eme*/          fprintf(ficlog,"\n");
   for (cpt=1; cpt<= nlstate ; cpt ++) {        }
    for (k1=1; k1<= m ; k1 ++) {      }
     }
 #ifdef windows    dateintmean=dateintsum/k2cpt; 
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);   
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    fclose(ficresp);
 #endif    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
 #ifdef unix    free_vector(pp,1,nlstate);
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    /* End of Freq */
 #endif  }
   
 for (i=1; i<= nlstate ; i ++) {  /************ Prevalence ********************/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  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)
   else fprintf(ficgp," \%%*lf (\%%*lf)");  {  
 }    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);       in each health status at the date of interview (if between dateprev1 and dateprev2).
     for (i=1; i<= nlstate ; i ++) {       We still use firstpass and lastpass as another selection.
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    */
   else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }    int i, m, jk, k1, i1, j1, bool, z1,j;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    double ***freq; /* Frequencies */
      for (i=1; i<= nlstate ; i ++) {    double *pp, **prop;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double pos,posprop; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double  y2; /* in fractional years */
 }      int iagemin, iagemax;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix    iagemin= (int) agemin;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    iagemax= (int) agemax;
 #endif    /*pp=vector(1,nlstate);*/
    }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   /*2 eme*/    j1=0;
     
   for (k1=1; k1<= m ; k1 ++) {    j=cptcoveff;
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    
        for(k1=1; k1<=j;k1++){
     for (i=1; i<= nlstate+1 ; i ++) {      for(i1=1; i1<=ncodemax[k1];i1++){
       k=2*i;        j1++;
       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<=nlstate; i++)  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(m=iagemin; m <= iagemax+3; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");            prop[i][m]=0.0;
 }         
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        for (i=1; i<=imx; i++) { /* Each individual */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          bool=1;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          if  (cptcovn>0) {
       for (j=1; j<= nlstate+1 ; j ++) {            for (z1=1; z1<=cptcoveff; z1++) 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         else fprintf(ficgp," \%%*lf (\%%*lf)");                bool=0;
 }            } 
       fprintf(ficgp,"\" t\"\" w l 0,");          if (bool==1) { 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       for (j=1; j<= nlstate+1 ; j ++) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   else fprintf(ficgp," \%%*lf (\%%*lf)");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 }                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       else fprintf(ficgp,"\" t\"\" w l 0,");                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                    prop[s[m][i]][iagemax+3] += weight[i]; 
   /*3eme*/                } 
               }
   for (k1=1; k1<= m ; k1 ++) {            } /* end selection of waves */
     for (cpt=1; cpt<= nlstate ; cpt ++) {          }
       k=2+nlstate*(2*cpt-2);        }
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for(i=iagemin; i <= iagemax+3; i++){  
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            posprop += prop[jk][i]; 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          } 
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for(jk=1; jk <=nlstate ; jk++){     
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
 */                probs[i][jk][j1]= prop[jk][i]/posprop;
       for (i=1; i< nlstate ; i ++) {              } else
         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);                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
             } 
       }          }/* end jk */ 
     }        }/* end i */ 
   }      } /* end i1 */
      } /* end k1 */
   /* CV preval stat */    
     for (k1=1; k1<= m ; k1 ++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     for (cpt=1; cpt<nlstate ; cpt ++) {    /*free_vector(pp,1,nlstate);*/
       k=3;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  }  /* End of prevalence */
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);  
   /************* Waves Concatenation ***************/
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);  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(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  {
          /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       l=3+(nlstate+ndeath)*cpt;       Death is a valid wave (if date is known).
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       for (i=1; i< nlstate ; i ++) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         l=3+(nlstate+ndeath)*cpt;       and mw[mi+1][i]. dh depends on stepm.
         fprintf(ficgp,"+$%d",l+i+1);       */
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      int i, mi, m;
     }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   }         double sum=0., jmean=0.;*/
      int first;
   /* proba elementaires */    int j, k=0,jk, ju, jl;
    for(i=1,jk=1; i <=nlstate; i++){    double sum=0.;
     for(k=1; k <=(nlstate+ndeath); k++){    first=0;
       if (k != i) {    jmin=1e+5;
         for(j=1; j <=ncovmodel; j++){    jmax=-1;
            jmean=0.;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    for(i=1; i<=imx; i++){
           jk++;      mi=0;
           fprintf(ficgp,"\n");      m=firstpass;
         }      while(s[m][i] <= nlstate){
       }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     }          mw[++mi][i]=m;
    }        if(m >=lastpass)
           break;
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/        else
      for(jk=1; jk <=m; jk++) {          m++;
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);      }/* end while */
        if (ng==2)      if (s[m][i] > nlstate){
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");        mi++;     /* Death is another wave */
        else        /* if(mi==0)  never been interviewed correctly before death */
          fprintf(ficgp,"\nset title \"Probability\"\n");           /* Only death is a correct wave */
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        mw[mi][i]=m;
        i=1;      }
        for(k2=1; k2<=nlstate; k2++) {  
          k3=i;      wav[i]=mi;
          for(k=1; k<=(nlstate+ndeath); k++) {      if(mi==0){
            if (k != k2){        nbwarn++;
              if(ng==2)        if(first==0){
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
              else          first=1;
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        }
              ij=1;        if(first==1){
              for(j=3; j <=ncovmodel; j++) {          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        }
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      } /* end mi==0 */
                  ij++;    } /* End individuals */
                }  
                else    for(i=1; i<=imx; i++){
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for(mi=1; mi<wav[i];mi++){
              }        if (stepm <=0)
              fprintf(ficgp,")/(1");          dh[mi][i]=1;
                      else{
              for(k1=1; k1 <=nlstate; k1++){            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            if (agedc[i] < 2*AGESUP) {
                ij=1;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                for(j=3; j <=ncovmodel; j++){              if(j==0) j=1;  /* Survives at least one month after exam */
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              else if(j<0){
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                nberr++;
                    ij++;                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                  }                j=1; /* Temporary Dangerous patch */
                  else                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                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(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);
                fprintf(ficgp,")");              }
              }              k=k+1;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);              if (j >= jmax){
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                jmax=j;
              i=i+ncovmodel;                ijmax=i;
            }              }
          }              if (j <= jmin){
        }                jmin=j;
      }                ijmin=i;
    }              }
    fclose(ficgp);              sum=sum+j;
 }  /* end gnuplot */              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
 /*************** Moving average **************/          }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   int i, cpt, cptcod;  /*        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]); */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)            k=k+1;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            if (j >= jmax) {
           mobaverage[(int)agedeb][i][cptcod]=0.;              jmax=j;
                  ijmax=i;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){            }
       for (i=1; i<=nlstate;i++){            else if (j <= jmin){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              jmin=j;
           for (cpt=0;cpt<=4;cpt++){              ijmin=i;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            }
           }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         }            if(j<0){
       }              nberr++;
     }              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]);
                  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]);
 }            }
             sum=sum+j;
           }
 /************** Forecasting ******************/          jk= j/stepm;
 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){          jl= j -jk*stepm;
            ju= j -(jk+1)*stepm;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   int *popage;            if(jl==0){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              dh[mi][i]=jk;
   double *popeffectif,*popcount;              bh[mi][i]=0;
   double ***p3mat;            }else{ /* We want a negative bias in order to only have interpolation ie
   char fileresf[FILENAMELENGTH];                    * to avoid the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
  agelim=AGESUP;              bh[mi][i]=ju;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            }
           }else{
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            if(jl <= -ju){
                dh[mi][i]=jk;
                bh[mi][i]=jl;       /* bias is positive if real duration
   strcpy(fileresf,"f");                                   * is higher than the multiple of stepm and negative otherwise.
   strcat(fileresf,fileres);                                   */
   if((ficresf=fopen(fileresf,"w"))==NULL) {            }
     printf("Problem with forecast resultfile: %s\n", fileresf);            else{
   }              dh[mi][i]=jk+1;
   printf("Computing forecasting: result on file '%s' \n", fileresf);              bh[mi][i]=ju;
             }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
   if (mobilav==1) {              bh[mi][i]=ju; /* At least one step */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              /*  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);*/
     movingaverage(agedeb, fage, ageminpar, mobaverage);            }
   }          } /* end if mle */
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;      } /* end wave */
   if (stepm<=12) stepsize=1;    }
      jmean=sum/k;
   agelim=AGESUP;    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
      fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   hstepm=1;   }
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);  /*********** Tricode ****************************/
   anprojmean=yp;  void tricode(int *Tvar, int **nbcode, int imx)
   yp2=modf((yp1*12),&yp);  {
   mprojmean=yp;    /* Uses cptcovn+2*cptcovprod as the number of covariates */
   yp1=modf((yp2*30.5),&yp);    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   if(mprojmean==0) jprojmean=1;    int modmaxcovj=0; /* Modality max of covariates j */
      cptcoveff=0; 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);   
      for (k=0; k<maxncov; k++) Ndum[k]=0;
   for(cptcov=1;cptcov<=i2;cptcov++){    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
       fprintf(ficresf,"\n#******");      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
       for(j=1;j<=cptcoveff;j++) {                                 modality of this covariate Vj*/ 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
       }                                        modality of the nth covariate of individual i. */
       fprintf(ficresf,"******\n");        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
       fprintf(ficresf,"# StartingAge FinalAge");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        if (ij > modmaxcovj) modmaxcovj=ij; 
              /* getting the maximum value of the modality of the covariate
                 (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {           female is 1, then modmaxcovj=1.*/
         fprintf(ficresf,"\n");      }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        if( Ndum[i] != 0 )
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          ncodemax[j]++; 
           nhstepm = nhstepm/hstepm;        /* Number of modalities of the j th covariate. In fact
                     ncodemax[j]=2 (dichotom. variables only) but it could be more for
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           historical reasons */
           oldm=oldms;savm=savms;      } /* Ndum[-1] number of undefined modalities */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
              /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
           for (h=0; h<=nhstepm; h++){      ij=1; 
             if (h==(int) (calagedate+YEARM*cpt)) {      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
             }          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             for(j=1; j<=nlstate+ndeath;j++) {            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
               kk1=0.;kk2=0;                                       k is a modality. If we have model=V1+V1*sex 
               for(i=1; i<=nlstate;i++) {                                                     then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                 if (mobilav==1)            ij++;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          }
                 else {          if (ij > ncodemax[j]) break; 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        }  /* end of loop on */
                 }      } /* 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*/  
               }    
               if (h==(int)(calagedate+12*cpt)){    for (k=0; k< maxncov; k++) Ndum[k]=0;
                 fprintf(ficresf," %.3f", kk1);    
                            for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
               }     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
             }     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
           }     Ndum[ij]++;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   }
         }  
       }   ij=1;
     }   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   }     if((Ndum[i]!=0) && (i<=ncovcol)){
               Tvaraff[ij]=i; /*For printing */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       ij++;
      }
   fclose(ficresf);   }
 }   ij--;
 /************** Forecasting ******************/   cptcoveff=ij; /*Number of simple covariates*/
 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;  /*********** Health Expectancies ****************/
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;  {
   char filerespop[FILENAMELENGTH];    /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int nhstepma, nstepma; /* Decreasing with age */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double age, agelim, hf;
   agelim=AGESUP;    double ***p3mat;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    double eip;
    
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    pstamp(ficreseij);
      fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
      fprintf(ficreseij,"# Age");
   strcpy(filerespop,"pop");    for(i=1; i<=nlstate;i++){
   strcat(filerespop,fileres);      for(j=1; j<=nlstate;j++){
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        fprintf(ficreseij," e%1d%1d ",i,j);
     printf("Problem with forecast resultfile: %s\n", filerespop);      }
   }      fprintf(ficreseij," e%1d. ",i);
   printf("Computing forecasting: result on file '%s' \n", filerespop);    }
     fprintf(ficreseij,"\n");
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
     
   if (mobilav==1) {    if(estepm < stepm){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf ("Problem %d lower than %d\n",estepm, stepm);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    }
   }    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   stepsize=(int) (stepm+YEARM-1)/YEARM;     * This is mainly to measure the difference between two models: for example
   if (stepm<=12) stepsize=1;     * if stepm=24 months pijx are given only every 2 years and by summing them
       * we are calculating an estimate of the Life Expectancy assuming a linear 
   agelim=AGESUP;     * progression in between and thus overestimating or underestimating according
       * to the curvature of the survival function. If, for the same date, we 
   hstepm=1;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   hstepm=hstepm/stepm;     * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
   if (popforecast==1) {     * curvature will be obtained if estepm is as small as stepm. */
     if((ficpop=fopen(popfile,"r"))==NULL) {  
       printf("Problem with population file : %s\n",popfile);exit(0);    /* 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. 
     popage=ivector(0,AGESUP);       nhstepm is the number of hstepm from age to agelim 
     popeffectif=vector(0,AGESUP);       nstepm is the number of stepm from age to agelin. 
     popcount=vector(0,AGESUP);       Look at hpijx to understand the reason of that which relies in memory size
           and note for a fixed period like estepm months */
     i=1;      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;       survival function given by stepm (the optimization length). Unfortunately it
           means that if the survival funtion is printed only each two years of age and if
     imx=i;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];       results. So we changed our mind and took the option of the best precision.
   }    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    agelim=AGESUP;
       k=k+1;    /* If stepm=6 months */
       fprintf(ficrespop,"\n#******");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       for(j=1;j<=cptcoveff;j++) {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      
       }  /* nhstepm age range expressed in number of stepm */
       fprintf(ficrespop,"******\n");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       fprintf(ficrespop,"# Age");    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    /* if (stepm >= YEARM) hstepm=1;*/
       if (popforecast==1)  fprintf(ficrespop," [Population]");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for (cpt=0; cpt<=0;cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      for (age=bage; age<=fage; age ++){ 
              nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      /* if (stepm >= YEARM) hstepm=1;*/
           nhstepm = nhstepm/hstepm;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* If stepm=6 months */
           oldm=oldms;savm=savms;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
              
           for (h=0; h<=nhstepm; h++){      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
             if (h==(int) (calagedate+YEARM*cpt)) {      
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             }      
             for(j=1; j<=nlstate+ndeath;j++) {      printf("%d|",(int)age);fflush(stdout);
               kk1=0.;kk2=0;      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
               for(i=1; i<=nlstate;i++) {                    
                 if (mobilav==1)      /* Computing expectancies */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      for(i=1; i<=nlstate;i++)
                 else {        for(j=1; j<=nlstate;j++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                 }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
               }            
               if (h==(int)(calagedate+12*cpt)){            /* 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]);*/
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  
                   /*fprintf(ficrespop," %.3f", kk1);          }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }      fprintf(ficreseij,"%3.0f",age );
             }      for(i=1; i<=nlstate;i++){
             for(i=1; i<=nlstate;i++){        eip=0;
               kk1=0.;        for(j=1; j<=nlstate;j++){
                 for(j=1; j<=nlstate;j++){          eip +=eij[i][j][(int)age];
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
                 }        }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        fprintf(ficreseij,"%9.4f", eip );
             }      }
       fprintf(ficreseij,"\n");
             if (h==(int)(calagedate+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);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("\n");
         }    fprintf(ficlog,"\n");
       }    
    }
   /******/  
   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
       for (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--){    /* Covariances of health expectancies eij and of total life expectancies according
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     to initial status i, ei. .
           nhstepm = nhstepm/hstepm;    */
              int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int nhstepma, nstepma; /* Decreasing with age */
           oldm=oldms;savm=savms;    double age, agelim, hf;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double ***p3matp, ***p3matm, ***varhe;
           for (h=0; h<=nhstepm; h++){    double **dnewm,**doldm;
             if (h==(int) (calagedate+YEARM*cpt)) {    double *xp, *xm;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    double **gp, **gm;
             }    double ***gradg, ***trgradg;
             for(j=1; j<=nlstate+ndeath;j++) {    int theta;
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                  double eip, vip;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    xp=vector(1,npar);
             }    xm=vector(1,npar);
           }    dnewm=matrix(1,nlstate*nlstate,1,npar);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         }    
       }    pstamp(ficresstdeij);
    }    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   }    fprintf(ficresstdeij,"# Age");
      for(i=1; i<=nlstate;i++){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   if (popforecast==1) {      fprintf(ficresstdeij," e%1d. ",i);
     free_ivector(popage,0,AGESUP);    }
     free_vector(popeffectif,0,AGESUP);    fprintf(ficresstdeij,"\n");
     free_vector(popcount,0,AGESUP);  
   }    pstamp(ficrescveij);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficrescveij,"# Age");
   fclose(ficrespop);    for(i=1; i<=nlstate;i++)
 }      for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
 /***********************************************/        for(i2=1; i2<=nlstate;i2++)
 /**************** Main Program *****************/          for(j2=1; j2<=nlstate;j2++){
 /***********************************************/            cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
 int main(int argc, char *argv[])              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
 {          }
       }
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    fprintf(ficrescveij,"\n");
   double agedeb, agefin,hf;    
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   double fret;    }
   double **xi,tmp,delta;    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   double dum; /* Dummy variable */     * This is mainly to measure the difference between two models: for example
   double ***p3mat;     * if stepm=24 months pijx are given only every 2 years and by summing them
   int *indx;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   char line[MAXLINE], linepar[MAXLINE];     * progression in between and thus overestimating or underestimating according
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];     * to the curvature of the survival function. If, for the same date, we 
   int firstobs=1, lastobs=10;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   int sdeb, sfin; /* Status at beginning and end */     * to compare the new estimate of Life expectancy with the same linear 
   int c,  h , cpt,l;     * hypothesis. A more precise result, taking into account a more precise
   int ju,jl, mi;     * curvature will be obtained if estepm is as small as stepm. */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    /* For example we decided to compute the life expectancy with the smallest unit */
   int mobilav=0,popforecast=0;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   int hstepm, nhstepm;       nhstepm is the number of hstepm from age to agelim 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   double bage, fage, age, agelim, agebase;       and note for a fixed period like estepm months */
   double ftolpl=FTOL;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double **prlim;       survival function given by stepm (the optimization length). Unfortunately it
   double *severity;       means that if the survival funtion is printed only each two years of age and if
   double ***param; /* Matrix of parameters */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double  *p;       results. So we changed our mind and took the option of the best precision.
   double **matcov; /* Matrix of covariance */    */
   double ***delti3; /* Scale */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double *delti; /* Scale */  
   double ***eij, ***vareij;    /* If stepm=6 months */
   double **varpl; /* Variances of prevalence limits by age */    /* nhstepm age range expressed in number of stepm */
   double *epj, vepp;    agelim=AGESUP;
   double kk1, kk2;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   char *alph[]={"a","a","b","c","d","e"}, str[4];    
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   char z[1]="c", occ;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 #include <sys/time.h>    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
 #include <time.h>    gp=matrix(0,nhstepm,1,nlstate*nlstate);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    gm=matrix(0,nhstepm,1,nlstate*nlstate);
    
   /* long total_usecs;    for (age=bage; age<=fage; age ++){ 
   struct timeval start_time, end_time;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      /* if (stepm >= YEARM) hstepm=1;*/
   getcwd(pathcd, size);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
   printf("\n%s",version);      /* If stepm=6 months */
   if(argc <=1){      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     printf("\nEnter the parameter file name: ");         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     scanf("%s",pathtot);      
   }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   else{  
     strcpy(pathtot,argv[1]);      /* Computing  Variances of health expectancies */
   }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/         decrease memory allocation */
   /*cygwin_split_path(pathtot,path,optionfile);      for(theta=1; theta <=npar; theta++){
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        for(i=1; i<=npar; i++){ 
   /* cutv(path,optionfile,pathtot,'\\');*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        }
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   chdir(path);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
   replace(pathc,path);    
         for(j=1; j<= nlstate; j++){
 /*-------- arguments in the command line --------*/          for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
   strcpy(fileres,"r");              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
   strcat(fileres, optionfilefiname);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   strcat(fileres,".txt");    /* Other files have txt extension */            }
           }
   /*---------arguments file --------*/        }
        
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        for(ij=1; ij<= nlstate*nlstate; ij++)
     printf("Problem with optionfile %s\n",optionfile);          for(h=0; h<=nhstepm-1; h++){
     goto end;            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   }          }
       }/* End theta */
   strcpy(filereso,"o");      
   strcat(filereso,fileres);      
   if((ficparo=fopen(filereso,"w"))==NULL) {      for(h=0; h<=nhstepm-1; h++)
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        for(j=1; j<=nlstate*nlstate;j++)
   }          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   /* Reads comments: lines beginning with '#' */      
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);       for(ij=1;ij<=nlstate*nlstate;ij++)
     fgets(line, MAXLINE, ficpar);        for(ji=1;ji<=nlstate*nlstate;ji++)
     puts(line);          varhe[ij][ji][(int)age] =0.;
     fputs(line,ficparo);  
   }       printf("%d|",(int)age);fflush(stdout);
   ungetc(c,ficpar);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        for(k=0;k<=nhstepm-1;k++){
   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);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   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);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
 while((c=getc(ficpar))=='#' && c!= EOF){          for(ij=1;ij<=nlstate*nlstate;ij++)
     ungetc(c,ficpar);            for(ji=1;ji<=nlstate*nlstate;ji++)
     fgets(line, MAXLINE, ficpar);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     puts(line);        }
     fputs(line,ficparo);      }
   }  
   ungetc(c,ficpar);      /* Computing expectancies */
        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
          for(i=1; i<=nlstate;i++)
   covar=matrix(0,NCOVMAX,1,n);        for(j=1; j<=nlstate;j++)
   cptcovn=0;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
   ncovmodel=2+cptcovn;            /* 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]);*/
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
            }
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */      fprintf(ficresstdeij,"%3.0f",age );
   while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1; i<=nlstate;i++){
     ungetc(c,ficpar);        eip=0.;
     fgets(line, MAXLINE, ficpar);        vip=0.;
     puts(line);        for(j=1; j<=nlstate;j++){
     fputs(line,ficparo);          eip += eij[i][j][(int)age];
   }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   ungetc(c,ficpar);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
            fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        }
     for(i=1; i <=nlstate; i++)        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     for(j=1; j <=nlstate+ndeath-1; j++){      }
       fscanf(ficpar,"%1d%1d",&i1,&j1);      fprintf(ficresstdeij,"\n");
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);      fprintf(ficrescveij,"%3.0f",age );
       for(k=1; k<=ncovmodel;k++){      for(i=1; i<=nlstate;i++)
         fscanf(ficpar," %lf",&param[i][j][k]);        for(j=1; j<=nlstate;j++){
         printf(" %lf",param[i][j][k]);          cptj= (j-1)*nlstate+i;
         fprintf(ficparo," %lf",param[i][j][k]);          for(i2=1; i2<=nlstate;i2++)
       }            for(j2=1; j2<=nlstate;j2++){
       fscanf(ficpar,"\n");              cptj2= (j2-1)*nlstate+i2;
       printf("\n");              if(cptj2 <= cptj)
       fprintf(ficparo,"\n");                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
     }            }
          }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      fprintf(ficrescveij,"\n");
      
   p=param[1][1];    }
      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   /* Reads comments: lines beginning with '#' */    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     ungetc(c,ficpar);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     fgets(line, MAXLINE, ficpar);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     puts(line);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fputs(line,ficparo);    printf("\n");
   }    fprintf(ficlog,"\n");
   ungetc(c,ficpar);  
     free_vector(xm,1,npar);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    free_vector(xp,1,npar);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   for(i=1; i <=nlstate; i++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     for(j=1; j <=nlstate+ndeath-1; j++){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  }
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);  /************ Variance ******************/
       for(k=1; k<=ncovmodel;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[])
         fscanf(ficpar,"%le",&delti3[i][j][k]);  {
         printf(" %le",delti3[i][j][k]);    /* Variance of health expectancies */
         fprintf(ficparo," %le",delti3[i][j][k]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       }    /* double **newm;*/
       fscanf(ficpar,"\n");    double **dnewm,**doldm;
       printf("\n");    double **dnewmp,**doldmp;
       fprintf(ficparo,"\n");    int i, j, nhstepm, hstepm, h, nstepm ;
     }    int k, cptcode;
   }    double *xp;
   delti=delti3[1][1];    double **gp, **gm;  /* for var eij */
      double ***gradg, ***trgradg; /*for var eij */
   /* Reads comments: lines beginning with '#' */    double **gradgp, **trgradgp; /* for var p point j */
   while((c=getc(ficpar))=='#' && c!= EOF){    double *gpp, *gmp; /* for var p point j */
     ungetc(c,ficpar);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     fgets(line, MAXLINE, ficpar);    double ***p3mat;
     puts(line);    double age,agelim, hf;
     fputs(line,ficparo);    double ***mobaverage;
   }    int theta;
   ungetc(c,ficpar);    char digit[4];
      char digitp[25];
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){    char fileresprobmorprev[FILENAMELENGTH];
     fscanf(ficpar,"%s",&str);  
     printf("%s",str);    if(popbased==1){
     fprintf(ficparo,"%s",str);      if(mobilav!=0)
     for(j=1; j <=i; j++){        strcpy(digitp,"-populbased-mobilav-");
       fscanf(ficpar," %le",&matcov[i][j]);      else strcpy(digitp,"-populbased-nomobil-");
       printf(" %.5le",matcov[i][j]);    }
       fprintf(ficparo," %.5le",matcov[i][j]);    else 
     }      strcpy(digitp,"-stablbased-");
     fscanf(ficpar,"\n");  
     printf("\n");    if (mobilav!=0) {
     fprintf(ficparo,"\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   for(i=1; i <=npar; i++)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     for(j=i+1;j<=npar;j++)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       matcov[i][j]=matcov[j][i];      }
        }
   printf("\n");  
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*-------- Rewriting paramater file ----------*/    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      strcpy(rfileres,"r");    /* "Rparameterfile */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      strcat(rfileres,".");    /* */    strcat(fileresprobmorprev,fileres);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     if((ficres =fopen(rfileres,"w"))==NULL) {      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }    }
     fprintf(ficres,"#%s\n",version);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       
     /*-------- data file ----------*/    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     if((fic=fopen(datafile,"r"))==NULL)    {    pstamp(ficresprobmorprev);
       printf("Problem with datafile: %s\n", datafile);goto end;    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);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     n= lastobs;      fprintf(ficresprobmorprev," p.%-d SE",j);
     severity = vector(1,maxwav);      for(i=1; i<=nlstate;i++)
     outcome=imatrix(1,maxwav+1,1,n);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     num=ivector(1,n);    }  
     moisnais=vector(1,n);    fprintf(ficresprobmorprev,"\n");
     annais=vector(1,n);    fprintf(ficgp,"\n# Routine varevsij");
     moisdc=vector(1,n);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     andc=vector(1,n);    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");
     agedc=vector(1,n);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     cod=ivector(1,n);  /*   } */
     weight=vector(1,n);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    pstamp(ficresvij);
     mint=matrix(1,maxwav,1,n);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     anint=matrix(1,maxwav,1,n);    if(popbased==1)
     s=imatrix(1,maxwav+1,1,n);      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);
     adl=imatrix(1,maxwav+1,1,n);        else
     tab=ivector(1,NCOVMAX);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     ncodemax=ivector(1,8);    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
     i=1;      for(j=1; j<=nlstate;j++)
     while (fgets(line, MAXLINE, fic) != NULL)    {        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
       if ((i >= firstobs) && (i <=lastobs)) {    fprintf(ficresvij,"\n");
          
         for (j=maxwav;j>=1;j--){    xp=vector(1,npar);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    dnewm=matrix(1,nlstate,1,npar);
           strcpy(line,stra);    doldm=matrix(1,nlstate,1,nlstate);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }  
            gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    gpp=vector(nlstate+1,nlstate+ndeath);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    }
         for (j=ncovcol;j>=1;j--){    else  hstepm=estepm;   
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /* 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. 
         num[i]=atol(stra);       nhstepm is the number of hstepm from age to agelim 
               nstepm is the number of stepm from age to agelin. 
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){       Look at function hpijx to understand why (it is linked to memory size questions) */
           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;}*/    /* 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
         i=i+1;       means that if the survival funtion is printed every two years of age and if
       }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     }       results. So we changed our mind and took the option of the best precision.
     /* printf("ii=%d", ij);    */
        scanf("%d",i);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   imx=i-1; /* Number of individuals */    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /* for (i=1; i<=imx; i++){      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     }*/      gp=matrix(0,nhstepm,1,nlstate);
    /*  for (i=1; i<=imx; i++){      gm=matrix(0,nhstepm,1,nlstate);
      if (s[4][i]==9)  s[4][i]=-1;  
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/  
        for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   /* Calculation of the number of parameter from char model*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   Tvar=ivector(1,15);        }
   Tprod=ivector(1,15);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   Tvaraff=ivector(1,15);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);              if (popbased==1) {
              if(mobilav ==0){
   if (strlen(model) >1){            for(i=1; i<=nlstate;i++)
     j=0, j1=0, k1=1, k2=1;              prlim[i][i]=probs[(int)age][i][ij];
     j=nbocc(model,'+');          }else{ /* mobilav */ 
     j1=nbocc(model,'*');            for(i=1; i<=nlstate;i++)
     cptcovn=j+1;              prlim[i][i]=mobaverage[(int)age][i][ij];
     cptcovprod=j1;          }
            }
     strcpy(modelsav,model);    
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        for(j=1; j<= nlstate; j++){
       printf("Error. Non available option model=%s ",model);          for(h=0; h<=nhstepm; h++){
       goto end;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
              }
     for(i=(j+1); i>=1;i--){        }
       cutv(stra,strb,modelsav,'+');        /* This for computing probability of death (h=1 means
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);           computed over hstepm matrices product = hstepm*stepm months) 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/           as a weighted average of prlim.
       /*scanf("%d",i);*/        */
       if (strchr(strb,'*')) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         cutv(strd,strc,strb,'*');          for(i=1,gpp[j]=0.; i<= nlstate; i++)
         if (strcmp(strc,"age")==0) {            gpp[j] += prlim[i][i]*p3mat[i][j][1];
           cptcovprod--;        }    
           cutv(strb,stre,strd,'V');        /* end probability of death */
           Tvar[i]=atoi(stre);  
           cptcovage++;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
             Tage[cptcovage]=i;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             /*printf("stre=%s ", stre);*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         else if (strcmp(strd,"age")==0) {   
           cptcovprod--;        if (popbased==1) {
           cutv(strb,stre,strc,'V');          if(mobilav ==0){
           Tvar[i]=atoi(stre);            for(i=1; i<=nlstate;i++)
           cptcovage++;              prlim[i][i]=probs[(int)age][i][ij];
           Tage[cptcovage]=i;          }else{ /* mobilav */ 
         }            for(i=1; i<=nlstate;i++)
         else {              prlim[i][i]=mobaverage[(int)age][i][ij];
           cutv(strb,stre,strc,'V');          }
           Tvar[i]=ncovcol+k1;        }
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           Tvard[k1][1]=atoi(strc);          for(h=0; h<=nhstepm; h++){
           Tvard[k1][2]=atoi(stre);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
           Tvar[cptcovn+k2]=Tvard[k1][1];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          }
           for (k=1; k<=lastobs;k++)        }
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        /* This for computing probability of death (h=1 means
           k1++;           computed over hstepm matrices product = hstepm*stepm months) 
           k2=k2+2;           as a weighted average of prlim.
         }        */
       }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       else {          for(i=1,gmp[j]=0.; i<= nlstate; i++)
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/           gmp[j] += prlim[i][i]*p3mat[i][j][1];
        /*  scanf("%d",i);*/        }    
       cutv(strd,strc,strb,'V');        /* end probability of death */
       Tvar[i]=atoi(strc);  
       }        for(j=1; j<= nlstate; j++) /* vareij */
       strcpy(modelsav,stra);            for(h=0; h<=nhstepm; h++){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         scanf("%d",i);*/          }
     }  
 }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        }
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/      } /* End theta */
     fclose(fic);  
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/      for(h=0; h<=nhstepm; h++) /* veij */
       for(i=1;i<=n;i++) weight[i]=1.0;        for(j=1; j<=nlstate;j++)
     }          for(theta=1; theta <=npar; theta++)
     /*-calculation of age at interview from date of interview and age at death -*/            trgradg[h][j][theta]=gradg[h][theta][j];
     agev=matrix(1,maxwav,1,imx);  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     for (i=1; i<=imx; i++) {        for(theta=1; theta <=npar; theta++)
       for(m=2; (m<= maxwav); m++) {          trgradgp[j][theta]=gradgp[theta][j];
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    
          anint[m][i]=9999;  
          s[m][i]=-1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        }      for(i=1;i<=nlstate;i++)
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        for(j=1;j<=nlstate;j++)
       }          vareij[i][j][(int)age] =0.;
     }  
       for(h=0;h<=nhstepm;h++){
     for (i=1; i<=imx; i++)  {        for(k=0;k<=nhstepm;k++){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       for(m=1; (m<= maxwav); m++){          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         if(s[m][i] >0){          for(i=1;i<=nlstate;i++)
           if (s[m][i] >= nlstate+1) {            for(j=1;j<=nlstate;j++)
             if(agedc[i]>0)              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
               if(moisdc[i]!=99 && andc[i]!=9999)        }
                 agev[m][i]=agedc[i];      }
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    
            else {      /* pptj */
               if (andc[i]!=9999){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
               agev[m][i]=-1;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
               }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
             }          varppt[j][i]=doldmp[j][i];
           }      /* end ppptj */
           else if(s[m][i] !=9){ /* Should no more exist */      /*  x centered again */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
             if(mint[m][i]==99 || anint[m][i]==9999)      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
               agev[m][i]=1;   
             else if(agev[m][i] <agemin){      if (popbased==1) {
               agemin=agev[m][i];        if(mobilav ==0){
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          for(i=1; i<=nlstate;i++)
             }            prlim[i][i]=probs[(int)age][i][ij];
             else if(agev[m][i] >agemax){        }else{ /* mobilav */ 
               agemax=agev[m][i];          for(i=1; i<=nlstate;i++)
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            prlim[i][i]=mobaverage[(int)age][i][ij];
             }        }
             /*agev[m][i]=anint[m][i]-annais[i];*/      }
             /*   agev[m][i] = age[i]+2*m;*/               
           }      /* This for computing probability of death (h=1 means
           else { /* =9 */         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
             agev[m][i]=1;         as a weighted average of prlim.
             s[m][i]=-1;      */
           }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         else /*= 0 Unknown */          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           agev[m][i]=1;      }    
       }      /* end probability of death */
      
     }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     for (i=1; i<=imx; i++)  {      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       for(m=1; (m<= maxwav); m++){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         if (s[m][i] > (nlstate+ndeath)) {        for(i=1; i<=nlstate;i++){
           printf("Error: Wrong value in nlstate or ndeath\n");            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           goto end;        }
         }      } 
       }      fprintf(ficresprobmorprev,"\n");
     }  
       fprintf(ficresvij,"%.0f ",age );
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
     free_vector(severity,1,maxwav);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     free_imatrix(outcome,1,maxwav+1,1,n);        }
     free_vector(moisnais,1,n);      fprintf(ficresvij,"\n");
     free_vector(annais,1,n);      free_matrix(gp,0,nhstepm,1,nlstate);
     /* free_matrix(mint,1,maxwav,1,n);      free_matrix(gm,0,nhstepm,1,nlstate);
        free_matrix(anint,1,maxwav,1,n);*/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     free_vector(moisdc,1,n);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     free_vector(andc,1,n);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
        free_vector(gpp,nlstate+1,nlstate+ndeath);
     wav=ivector(1,imx);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
     /* Concatenates waves */    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       Tcode=ivector(1,100);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
       ncodemax[1]=1;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",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));
    codtab=imatrix(1,100,1,10);    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);
    h=0;    /*  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);
    m=pow(2,cptcoveff);  */
    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
    for(k=1;k<=cptcoveff; k++){    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){    free_vector(xp,1,npar);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    free_matrix(doldm,1,nlstate,1,nlstate);
            h++;    free_matrix(dnewm,1,nlstate,1,npar);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
          }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      }    fclose(ficresprobmorprev);
    }    fflush(ficgp);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    fflush(fichtm); 
       codtab[1][2]=1;codtab[2][2]=2; */  }  /* end varevsij */
    /* for(i=1; i <=m ;i++){  
       for(k=1; k <=cptcovn; k++){  /************ Variance of prevlim ******************/
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);  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[])
       }  {
       printf("\n");    /* Variance of prevalence limit */
       }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       scanf("%d",i);*/    double **newm;
        double **dnewm,**doldm;
    /* Calculates basic frequencies. Computes observed prevalence at single age    int i, j, nhstepm, hstepm;
        and prints on file fileres'p'. */    int k, cptcode;
     double *xp;
        double *gp, *gm;
        double **gradg, **trgradg;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double age,agelim;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int theta;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pstamp(ficresvpl);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
          fprintf(ficresvpl,"# Age");
     /* For Powell, parameters are in a vector p[] starting at p[1]    for(i=1; i<=nlstate;i++)
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        fprintf(ficresvpl," %1d-%1d",i,i);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    fprintf(ficresvpl,"\n");
   
     if(mle==1){    xp=vector(1,npar);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
        
     /*--------- results files --------------*/    hstepm=1*YEARM; /* Every year of age */
     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);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
      agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
    jk=1;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      if (stepm >= YEARM) hstepm=1;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
    for(i=1,jk=1; i <=nlstate; i++){      gradg=matrix(1,npar,1,nlstate);
      for(k=1; k <=(nlstate+ndeath); k++){      gp=vector(1,nlstate);
        if (k != i)      gm=vector(1,nlstate);
          {  
            printf("%d%d ",i,k);      for(theta=1; theta <=npar; theta++){
            fprintf(ficres,"%1d%1d ",i,k);        for(i=1; i<=npar; i++){ /* Computes gradient */
            for(j=1; j <=ncovmodel; j++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
              printf("%f ",p[jk]);        }
              fprintf(ficres,"%f ",p[jk]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
              jk++;        for(i=1;i<=nlstate;i++)
            }          gp[i] = prlim[i][i];
            printf("\n");      
            fprintf(ficres,"\n");        for(i=1; i<=npar; i++) /* Computes gradient */
          }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    }        for(i=1;i<=nlstate;i++)
  if(mle==1){          gm[i] = prlim[i][i];
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */        for(i=1;i<=nlstate;i++)
     hesscov(matcov, p, npar, delti, ftolhess, func);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
  }      } /* End theta */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  
     printf("# Scales (for hessian or gradient estimation)\n");      trgradg =matrix(1,nlstate,1,npar);
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){      for(j=1; j<=nlstate;j++)
         if (j!=i) {        for(theta=1; theta <=npar; theta++)
           fprintf(ficres,"%1d%1d",i,j);          trgradg[j][theta]=gradg[theta][j];
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){      for(i=1;i<=nlstate;i++)
             printf(" %.5e",delti[jk]);        varpl[i][(int)age] =0.;
             fprintf(ficres," %.5e",delti[jk]);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
             jk++;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           }      for(i=1;i<=nlstate;i++)
           printf("\n");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           fprintf(ficres,"\n");  
         }      fprintf(ficresvpl,"%.0f ",age );
       }      for(i=1; i<=nlstate;i++)
      }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
          fprintf(ficresvpl,"\n");
     k=1;      free_vector(gp,1,nlstate);
     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");      free_vector(gm,1,nlstate);
     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");      free_matrix(gradg,1,npar,1,nlstate);
     for(i=1;i<=npar;i++){      free_matrix(trgradg,1,nlstate,1,npar);
       /*  if (k>nlstate) k=1;    } /* End age */
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    free_vector(xp,1,npar);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    free_matrix(doldm,1,nlstate,1,npar);
       fprintf(ficres,"%3d",i);    free_matrix(dnewm,1,nlstate,1,nlstate);
       printf("%3d",i);  
       for(j=1; j<=i;j++){  }
         fprintf(ficres," %.5e",matcov[i][j]);  
         printf(" %.5e",matcov[i][j]);  /************ Variance of one-step probabilities  ******************/
       }  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
       fprintf(ficres,"\n");  {
       printf("\n");    int i, j=0,  i1, k1, l1, t, tj;
       k++;    int k2, l2, j1,  z1;
     }    int k=0,l, cptcode;
        int first=1, first1;
     while((c=getc(ficpar))=='#' && c!= EOF){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
       ungetc(c,ficpar);    double **dnewm,**doldm;
       fgets(line, MAXLINE, ficpar);    double *xp;
       puts(line);    double *gp, *gm;
       fputs(line,ficparo);    double **gradg, **trgradg;
     }    double **mu;
     ungetc(c,ficpar);    double age,agelim, cov[NCOVMAX];
     estepm=0;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    int theta;
     if (estepm==0 || estepm < stepm) estepm=stepm;    char fileresprob[FILENAMELENGTH];
     if (fage <= 2) {    char fileresprobcov[FILENAMELENGTH];
       bage = ageminpar;    char fileresprobcor[FILENAMELENGTH];
       fage = agemaxpar;  
     }    double ***varpij;
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    strcpy(fileresprob,"prob"); 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    strcat(fileresprob,fileres);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
     while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    strcpy(fileresprobcov,"probcov"); 
     puts(line);    strcat(fileresprobcov,fileres);
     fputs(line,ficparo);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcov);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    strcpy(fileresprobcor,"probcor"); 
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    strcat(fileresprobcor,fileres);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
            printf("Problem with resultfile: %s\n", fileresprobcor);
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     puts(line);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fputs(line,ficparo);    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);
   ungetc(c,ficpar);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
   fscanf(ficpar,"pop_based=%d\n",&popbased);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   fprintf(ficparo,"pop_based=%d\n",popbased);      fprintf(ficresprobcov,"# Age");
   fprintf(ficres,"pop_based=%d\n",popbased);      pstamp(ficresprobcor);
      fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresprobcor,"# Age");
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);    for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);      for(j=1; j<=(nlstate+ndeath);j++){
   }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   ungetc(c,ficpar);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);      }  
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);   /* fprintf(ficresprob,"\n");
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
 while((c=getc(ficpar))=='#' && c!= EOF){    xp=vector(1,npar);
     ungetc(c,ficpar);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     fgets(line, MAXLINE, ficpar);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     puts(line);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     fputs(line,ficparo);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   }    first=1;
   ungetc(c,ficpar);    fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    fprintf(fichtm,"\n");
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
 /*------------ gnuplot -------------*/  and drawn. It helps understanding how is the covariance between two incidences.\
   strcpy(optionfilegnuplot,optionfilefiname);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   strcat(optionfilegnuplot,".gp");    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     printf("Problem with file %s",optionfilegnuplot);  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>\
   fclose(ficgp);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
 /*--------- index.htm --------*/  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
   strcpy(optionfilehtm,optionfile);    cov[1]=1;
   strcat(optionfilehtm,".htm");    tj=cptcoveff;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     printf("Problem with %s \n",optionfilehtm), exit(0);    j1=0;
   }    for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n        j1++;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        if  (cptcovn>0) {
 \n          fprintf(ficresprob, "\n#********** Variable "); 
 Total number of observations=%d <br>\n          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n          fprintf(ficresprob, "**********\n#\n");
 <hr  size=\"2\" color=\"#EC5E5E\">          fprintf(ficresprobcov, "\n#********** Variable "); 
  <ul><li>Parameter files<br>\n          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          fprintf(ficresprobcov, "**********\n#\n");
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);          
   fclose(fichtm);          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);          fprintf(ficgp, "**********\n#\n");
            
 /*------------ free_vector  -------------*/          
  chdir(path);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  free_ivector(wav,1,imx);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            fprintf(ficresprobcor, "\n#********** Variable ");    
  free_ivector(num,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  free_vector(agedc,1,n);          fprintf(ficresprobcor, "**********\n#");    
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        }
  fclose(ficparo);        
  fclose(ficres);        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
   /*--------------- Prevalence limit --------------*/            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
            }
   strcpy(filerespl,"pl");          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   strcat(filerespl,fileres);          for (k=1; k<=cptcovprod;k++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          
   }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   fprintf(ficrespl,"#Prevalence limit\n");          gp=vector(1,(nlstate)*(nlstate+ndeath));
   fprintf(ficrespl,"#Age ");          gm=vector(1,(nlstate)*(nlstate+ndeath));
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      
   fprintf(ficrespl,"\n");          for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++)
   prlim=matrix(1,nlstate,1,nlstate);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            k=0;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            for(i=1; i<= (nlstate); i++){
   k=0;              for(j=1; j<=(nlstate+ndeath);j++){
   agebase=ageminpar;                k=k+1;
   agelim=agemaxpar;                gp[k]=pmmij[i][j];
   ftolpl=1.e-10;              }
   i1=cptcoveff;            }
   if (cptcovn < 1){i1=1;}            
             for(i=1; i<=npar; i++)
   for(cptcov=1;cptcov<=i1;cptcov++){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      
         k=k+1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/            k=0;
         fprintf(ficrespl,"\n#******");            for(i=1; i<=(nlstate); i++){
         for(j=1;j<=cptcoveff;j++)              for(j=1; j<=(nlstate+ndeath);j++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                k=k+1;
         fprintf(ficrespl,"******\n");                gm[k]=pmmij[i][j];
                      }
         for (age=agebase; age<=agelim; age++){            }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       
           fprintf(ficrespl,"%.0f",age );            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
           for(i=1; i<=nlstate;i++)              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           fprintf(ficrespl," %.5f", prlim[i][i]);          }
           fprintf(ficrespl,"\n");  
         }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       }            for(theta=1; theta <=npar; theta++)
     }              trgradg[j][theta]=gradg[theta][j];
   fclose(ficrespl);          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   /*------------- h Pij x at various ages ------------*/          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
            free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);          pmij(pmmij,cov,ncovmodel,x,nlstate);
            
   stepsize=(int) (stepm+YEARM-1)/YEARM;          k=0;
   /*if (stepm<=24) stepsize=2;*/          for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
   agelim=AGESUP;              k=k+1;
   hstepm=stepsize*YEARM; /* Every year of age */              mu[k][(int) age]=pmmij[i][j];
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            }
            }
   k=0;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   for(cptcov=1;cptcov<=i1;cptcov++){            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              varpij[i][j][(int)age] = doldm[i][j];
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");          /*printf("\n%d ",(int)age);
         for(j=1;j<=cptcoveff;j++)            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         fprintf(ficrespij,"******\n");            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                    }*/
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          fprintf(ficresprob,"\n%d ",(int)age);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          fprintf(ficresprobcov,"\n%d ",(int)age);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprobcor,"\n%d ",(int)age);
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           fprintf(ficrespij,"# Age");            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for(i=1; i<=nlstate;i++)          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             for(j=1; j<=nlstate+ndeath;j++)            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
               fprintf(ficrespij," %1d-%1d",i,j);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           fprintf(ficrespij,"\n");          }
            for (h=0; h<=nhstepm; h++){          i=0;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          for (k=1; k<=(nlstate);k++){
             for(i=1; i<=nlstate;i++)            for (l=1; l<=(nlstate+ndeath);l++){ 
               for(j=1; j<=nlstate+ndeath;j++)              i=i++;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
             fprintf(ficrespij,"\n");              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
              }              for (j=1; j<=i;j++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
           fprintf(ficrespij,"\n");                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
         }              }
     }            }
   }          }/* end of loop for state */
         } /* end of loop for age */
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);  
         /* Confidence intervalle of pij  */
   fclose(ficrespij);        /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   /*---------- Forecasting ------------------*/          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   if((stepm == 1) && (strcmp(model,".")==0)){          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);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   }          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   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);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   }        first1=1;
          for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   /*---------- Health expectancies and variances ------------*/            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
   strcpy(filerest,"t");            for (k1=1; k1<=(nlstate);k1++){
   strcat(filerest,fileres);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   if((ficrest=fopen(filerest,"w"))==NULL) {                if(l1==k1) continue;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                i=(k1-1)*(nlstate+ndeath)+l1;
   }                if(i<=j) continue;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   strcpy(filerese,"e");                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   strcat(filerese,fileres);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   if((ficreseij=fopen(filerese,"w"))==NULL) {                    mu1=mu[i][(int) age]/stepm*YEARM ;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                    mu2=mu[j][(int) age]/stepm*YEARM;
   }                    c12=cv12/sqrt(v1*v2);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                    /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
  strcpy(fileresv,"v");                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   strcat(fileresv,fileres);                    if ((lc2 <0) || (lc1 <0) ){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                      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);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                      fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
   }                      lc1=fabs(lc1);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                      lc2=fabs(lc2);
   calagedate=-1;                    }
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
                     /* Eigen vectors */
   k=0;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   for(cptcov=1;cptcov<=i1;cptcov++){                    /*v21=sqrt(1.-v11*v11); *//* error */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    v21=(lc1-v1)/cv12*v11;
       k=k+1;                    v12=-v21;
       fprintf(ficrest,"\n#****** ");                    v22=v11;
       for(j=1;j<=cptcoveff;j++)                    tnalp=v21/v11;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    if(first1==1){
       fprintf(ficrest,"******\n");                      first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
       fprintf(ficreseij,"\n#****** ");                    }
       for(j=1;j<=cptcoveff;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);
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    /*printf(fignu*/
       fprintf(ficreseij,"******\n");                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       fprintf(ficresvij,"\n#****** ");                    if(first==1){
       for(j=1;j<=cptcoveff;j++)                      first=0;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                      fprintf(ficgp,"\nset parametric;unset label");
       fprintf(ficresvij,"******\n");                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
       oldm=oldms;savm=savms;   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       oldm=oldms;savm=savms;                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);                      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);
                        fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       fprintf(ficrest,"\n");                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
       epj=vector(1,nlstate+1);                      first=0;
       for(age=bage; age <=fage ;age++){                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         if (popbased==1) {                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           for(i=1; i<=nlstate;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",\
             prlim[i][i]=probs[(int)age][i][k];                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                            }/* if first */
         fprintf(ficrest," %4.0f",age);                  } /* age mod 5 */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                } /* end loop age */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                first=1;
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/              } /*l12 */
           }            } /* k12 */
           epj[nlstate+1] +=epj[j];          } /*l1 */
         }        }/* k1 */
       } /* loop covariates */
         for(i=1, vepp=0.;i <=nlstate;i++)    }
           for(j=1;j <=nlstate;j++)    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
             vepp += vareij[i][j][(int)age];    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         for(j=1;j <=nlstate;j++){    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    free_vector(xp,1,npar);
         }    fclose(ficresprob);
         fprintf(ficrest,"\n");    fclose(ficresprobcov);
       }    fclose(ficresprobcor);
     }    fflush(ficgp);
   }    fflush(fichtmcov);
 free_matrix(mint,1,maxwav,1,n);  }
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);  
   fclose(ficreseij);  /******************* Printing html file ***********/
   fclose(ficresvij);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   fclose(ficrest);                    int lastpass, int stepm, int weightopt, char model[],\
   fclose(ficpar);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   free_vector(epj,1,nlstate+1);                    int popforecast, int estepm ,\
                      double jprev1, double mprev1,double anprev1, \
   /*------- Variance limit prevalence------*/                      double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  </ul>");
     exit(0);     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
   }   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
   k=0;   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
   for(cptcov=1;cptcov<=i1;cptcov++){             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     fprintf(fichtm,"\
       k=k+1;   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
       fprintf(ficresvpl,"\n#****** ");             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
       for(j=1;j<=cptcoveff;j++)     fprintf(fichtm,"\
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   - (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): \
       fprintf(ficresvpl,"******\n");     <a href=\"%s\">%s</a> <br>\n",
                   estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
       varpl=matrix(1,nlstate,(int) bage, (int) fage);     fprintf(fichtm,"\
       oldm=oldms;savm=savms;   - Population projections by age and states: \
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
     }  
  }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
   fclose(ficresvpl);   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);   jj1=0;
     for(k1=1; k1<=m;k1++){
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);     for(i1=1; i1<=ncodemax[k1];i1++){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       jj1++;
         if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       }
         /* Pij */
   free_matrix(matcov,1,npar,1,npar);       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> \
   free_vector(delti,1,npar);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   free_matrix(agev,1,maxwav,1,imx);       /* Quasi-incidences */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       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> \
   fprintf(fichtm,"\n</body>");  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   fclose(fichtm);         /* Period (stable) prevalence in each health state */
   fclose(ficgp);         for(cpt=1; cpt<nlstate;cpt++){
             fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   if(erreur >0)         }
     printf("End of Imach with error or warning %d\n",erreur);       for(cpt=1; cpt<=nlstate;cpt++) {
   else   printf("End of Imach\n");          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> \
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
         }
   /* 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);*/     } /* end i1 */
   /*printf("Total time was %d uSec.\n", total_usecs);*/   }/* End k1 */
   /*------ End -----------*/   fprintf(fichtm,"</ul>");
   
   
  end:   fprintf(fichtm,"\
 #ifdef windows  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
   /* chdir(pathcd);*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
 #endif  
  /*system("wgnuplot graph.plt");*/   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
  /*system("../gp37mgw/wgnuplot graph.plt");*/           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
  /*system("cd ../gp37mgw");*/   fprintf(fichtm,"\
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
  strcpy(plotcmd,GNUPLOTPROGRAM);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);   fprintf(fichtm,"\
  system(plotcmd);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
 #ifdef windows   fprintf(fichtm,"\
   while (z[0] != 'q') {   - 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): \
     /* chdir(path); */     <a href=\"%s\">%s</a> <br>\n</li>",
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
     scanf("%s",z);   fprintf(fichtm,"\
     if (z[0] == 'c') system("./imach");   - (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): \
     else if (z[0] == 'e') system(optionfilehtm);     <a href=\"%s\">%s</a> <br>\n</li>",
     else if (z[0] == 'g') system(plotcmd);             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
     else if (z[0] == 'q') exit(0);   fprintf(fichtm,"\
   }   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
 #endif           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
 }   fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        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\
   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);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   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);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           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);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                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++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** 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){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     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;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     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 %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   
   int decodemodel ( char model[], int lastobs)
   {
     int i, j, k;
     int i1, j1, k1, k2;
     char modelsav[80];
      char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3 
                     but the covariates which are product must be computed and stored. */
       cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
       
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for(k=cptcovn; k>=1;k--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 
                                       */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V'); /* stre="V3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
             Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
             Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
             k1++;
             k2=k2+2;
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutv(strd,strc,strb,'V');
           Tvar[k]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       cptcovn=nbocc(model,'+')+1;
     /* ncovprod */
     ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8); /* hard coded ? */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,15); 
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2); /* For V3*V2 Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) {
               h=1;
               codtab[h][k]=j;
               codtab[h][Tvar[k]]=j;
             }
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
    endfree:
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.48  
changed lines
  Added in v.1.138


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>