Diff for /imach/src/imach.c between versions 1.51 and 1.135

version 1.51, 2002/07/19 12:22:25 version 1.135, 2009/10/29 15:33:14
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.135  2009/10/29 15:33:14  brouard
      (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.134  2009/10/29 13:18:53  brouard
   first survey ("cross") where individuals from different ages are    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.133  2009/07/06 10:21:25  brouard
   second wave of interviews ("longitudinal") which measure each change    just nforces
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.132  2009/07/06 08:22:05  brouard
   model. More health states you consider, more time is necessary to reach the    Many tings
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.131  2009/06/20 16:22:47  brouard
   probability to be observed in state j at the second wave    Some dimensions resccaled
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.130  2009/05/26 06:44:34  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    (Module): Max Covariate is now set to 20 instead of 8. A
   complex model than "constant and age", you should modify the program    lot of cleaning with variables initialized to 0. Trying to make
   where the markup *Covariates have to be included here again* invites    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.128  2006/06/30 13:02:05  brouard
   identical for each individual. Also, if a individual missed an    (Module): Clarifications on computing e.j
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
   hPijx is the probability to be observed in state i at age x+h    imach-114 because nhstepm was no more computed in the age
   conditional to the observed state i at age x. The delay 'h' can be    loop. Now we define nhstepma in the age loop.
   split into an exact number (nh*stepm) of unobserved intermediate    (Module): In order to speed up (in case of numerous covariates) we
   states. This elementary transition (by month or quarter trimester,    compute health expectancies (without variances) in a first step
   semester or year) is model as a multinomial logistic.  The hPx    and then all the health expectancies with variances or standard
   matrix is simply the matrix product of nh*stepm elementary matrices    deviation (needs data from the Hessian matrices) which slows the
   and the contribution of each individual to the likelihood is simply    computation.
   hPijx.    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.126  2006/04/28 17:23:28  brouard
      (Module): Yes the sum of survivors was wrong since
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    imach-114 because nhstepm was no more computed in the age
            Institut national d'études démographiques, Paris.    loop. Now we define nhstepma in the age loop.
   This software have been partly granted by Euro-REVES, a concerted action    Version 0.98h
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.125  2006/04/04 15:20:31  lievre
   software can be distributed freely for non commercial use. Latest version    Errors in calculation of health expectancies. Age was not initialized.
   can be accessed at http://euroreves.ined.fr/imach .    Forecasting file added.
   **********************************************************************/  
      Revision 1.124  2006/03/22 17:13:53  lievre
 #include <math.h>    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #include <stdio.h>    The log-likelihood is printed in the log file
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
 #define MAXLINE 256    name. <head> headers where missing.
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    * imach.c (Module): Weights can have a decimal point as for
 #define FILENAMELENGTH 80    English (a comma might work with a correct LC_NUMERIC environment,
 /*#define DEBUG*/    otherwise the weight is truncated).
 #define windows    Modification of warning when the covariates values are not 0 or
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    1.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Version 0.98g
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.122  2006/03/20 09:45:41  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 #define NINTERVMAX 8    otherwise the weight is truncated).
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Modification of warning when the covariates values are not 0 or
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    1.
 #define NCOVMAX 8 /* Maximum number of covariates */    Version 0.98g
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.121  2006/03/16 17:45:01  lievre
 #define AGESUP 130    * imach.c (Module): Comments concerning covariates added
 #define AGEBASE 40  
 #ifdef windows    * imach.c (Module): refinements in the computation of lli if
 #define DIRSEPARATOR '\\'    status=-2 in order to have more reliable computation if stepm is
 #define ODIRSEPARATOR '/'    not 1 month. Version 0.98f
 #else  
 #define DIRSEPARATOR '/'    Revision 1.120  2006/03/16 15:10:38  lievre
 #define ODIRSEPARATOR '\\'    (Module): refinements in the computation of lli if
 #endif    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";  
 int erreur; /* Error number */    Revision 1.119  2006/03/15 17:42:26  brouard
 int nvar;    (Module): Bug if status = -2, the loglikelihood was
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    computed as likelihood omitting the logarithm. Version O.98e
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.118  2006/03/14 18:20:07  brouard
 int ndeath=1; /* Number of dead states */    (Module): varevsij Comments added explaining the second
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    table of variances if popbased=1 .
 int popbased=0;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Version 0.98d
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.117  2006/03/14 17:16:22  brouard
 int mle, weightopt;    (Module): varevsij Comments added explaining the second
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    table of variances if popbased=1 .
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 double jmean; /* Mean space between 2 waves */    (Module): Function pstamp added
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Version 0.98d
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.116  2006/03/06 10:29:27  brouard
 FILE *ficlog;    (Module): Variance-covariance wrong links and
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    varian-covariance of ej. is needed (Saito).
 FILE *ficresprobmorprev;  
 FILE *fichtm; /* Html File */    Revision 1.115  2006/02/27 12:17:45  brouard
 FILE *ficreseij;    (Module): One freematrix added in mlikeli! 0.98c
 char filerese[FILENAMELENGTH];  
 FILE  *ficresvij;    Revision 1.114  2006/02/26 12:57:58  brouard
 char fileresv[FILENAMELENGTH];    (Module): Some improvements in processing parameter
 FILE  *ficresvpl;    filename with strsep.
 char fileresvpl[FILENAMELENGTH];  
 char title[MAXLINE];    Revision 1.113  2006/02/24 14:20:24  brouard
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    (Module): Memory leaks checks with valgrind and:
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
 char filelog[FILENAMELENGTH]; /* Log file */    Revision 1.112  2006/01/30 09:55:26  brouard
 char filerest[FILENAMELENGTH];    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 char fileregp[FILENAMELENGTH];  
 char popfile[FILENAMELENGTH];    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.110  2006/01/25 00:51:50  brouard
 #define FTOL 1.0e-10    (Module): Lots of cleaning and bugs added (Gompertz)
   
 #define NRANSI    Revision 1.109  2006/01/24 19:37:15  brouard
 #define ITMAX 200    (Module): Comments (lines starting with a #) are allowed in data.
   
 #define TOL 2.0e-4    Revision 1.108  2006/01/19 18:05:42  lievre
     Gnuplot problem appeared...
 #define CGOLD 0.3819660    To be fixed
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.106  2006/01/19 13:24:36  brouard
 #define TINY 1.0e-20    Some cleaning and links added in html output
   
 static double maxarg1,maxarg2;    Revision 1.105  2006/01/05 20:23:19  lievre
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    *** empty log message ***
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.104  2005/09/30 16:11:43  lievre
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): sump fixed, loop imx fixed, and simplifications.
 #define rint(a) floor(a+0.5)    (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
 static double sqrarg;    (instead of missing=-1 in earlier versions) and his/her
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    contributions to the likelihood is 1 - Prob of dying from last
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     the healthy state at last known wave). Version is 0.98
 int imx;  
 int stepm;    Revision 1.103  2005/09/30 15:54:49  lievre
 /* Stepm, step in month: minimum step interpolation*/    (Module): sump fixed, loop imx fixed, and simplifications.
   
 int estepm;    Revision 1.102  2004/09/15 17:31:30  brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Add the possibility to read data file including tab characters.
   
 int m,nb;    Revision 1.101  2004/09/15 10:38:38  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Fix on curr_time
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.100  2004/07/12 18:29:06  brouard
 double dateintmean=0;    Add version for Mac OS X. Just define UNIX in Makefile
   
 double *weight;    Revision 1.99  2004/06/05 08:57:40  brouard
 int **s; /* Status */    *** empty log message ***
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    directly from the data i.e. without the need of knowing the health
 double ftolhess; /* Tolerance for computing hessian */    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
 /**************** split *************************/    other analysis, in order to test if the mortality estimated from the
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    cross-longitudinal survey is different from the mortality estimated
 {    from other sources like vital statistic data.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    The same imach parameter file can be used but the option for mle should be -3.
   
    l1 = strlen( path );                 /* length of path */    Agnès, who wrote this part of the code, tried to keep most of the
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    former routines in order to include the new code within the former code.
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    The output is very simple: only an estimate of the intercept and of
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    the slope with 95% confident intervals.
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  
 #if     defined(__bsd__)                /* get current working directory */    Current limitations:
       extern char       *getwd( );    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
       if ( getwd( dirc ) == NULL ) {    B) There is no computation of Life Expectancy nor Life Table.
 #else  
       extern char       *getcwd( );    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    suppressed.
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.96  2003/07/15 15:38:55  brouard
       }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
       strcpy( name, path );             /* we've got it */    rewritten within the same printf. Workaround: many printfs.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.95  2003/07/08 07:54:34  brouard
       l2 = strlen( s );                 /* length of filename */    * imach.c (Repository):
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    (Repository): Using imachwizard code to output a more meaningful covariance
       strcpy( name, s );                /* save file name */    matrix (cov(a12,c31) instead of numbers.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.94  2003/06/27 13:00:02  brouard
    }    Just cleaning
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.93  2003/06/25 16:33:55  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): On windows (cygwin) function asctime_r doesn't
 #else    exist so I changed back to asctime which exists.
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (Module): Version 0.96b
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.92  2003/06/25 16:30:45  brouard
    s++;    (Module): On windows (cygwin) function asctime_r doesn't
    strcpy(ext,s);                       /* save extension */    exist so I changed back to asctime which exists.
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.91  2003/06/25 15:30:29  brouard
    strncpy( finame, name, l1-l2);    * imach.c (Repository): Duplicated warning errors corrected.
    finame[l1-l2]= 0;    (Repository): Elapsed time after each iteration is now output. It
    return( 0 );                         /* we're done */    helps to forecast when convergence will be reached. Elapsed time
 }    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
   
 /******************************************/    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 void replace(char *s, char*t)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   int i;  
   int lg=20;    Revision 1.89  2003/06/24 12:30:52  brouard
   i=0;    (Module): Some bugs corrected for windows. Also, when
   lg=strlen(t);    mle=-1 a template is output in file "or"mypar.txt with the design
   for(i=0; i<= lg; i++) {    of the covariance matrix to be input.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.88  2003/06/23 17:54:56  brouard
   }    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 }  
     Revision 1.87  2003/06/18 12:26:01  brouard
 int nbocc(char *s, char occ)    Version 0.96
 {  
   int i,j=0;    Revision 1.86  2003/06/17 20:04:08  brouard
   int lg=20;    (Module): Change position of html and gnuplot routines and added
   i=0;    routine fileappend.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.85  2003/06/17 13:12:43  brouard
   if  (s[i] == occ ) j++;    * imach.c (Repository): Check when date of death was earlier that
   }    current date of interview. It may happen when the death was just
   return j;    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
 void cutv(char *u,char *v, char*t, char occ)    interview.
 {    (Repository): Because some people have very long ID (first column)
   /* cuts string t into u and v where u is ended by char occ excluding it    we changed int to long in num[] and we added a new lvector for
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    memory allocation. But we also truncated to 8 characters (left
      gives u="abcedf" and v="ghi2j" */    truncation)
   int i,lg,j,p=0;    (Repository): No more line truncation errors.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.84  2003/06/13 21:44:43  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    * imach.c (Repository): Replace "freqsummary" at a correct
   }    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
   lg=strlen(t);    parcimony.
   for(j=0; j<p; j++) {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
     (u[j] = t[j]);  
   }    Revision 1.83  2003/06/10 13:39:11  lievre
      u[p]='\0';    *** empty log message ***
   
    for(j=0; j<= lg; j++) {    Revision 1.82  2003/06/05 15:57:20  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    Add log in  imach.c and  fullversion number is now printed.
   }  
 }  */
   /*
 /********************** nrerror ********************/     Interpolated Markov Chain
   
 void nrerror(char error_text[])    Short summary of the programme:
 {    
   fprintf(stderr,"ERREUR ...\n");    This program computes Healthy Life Expectancies from
   fprintf(stderr,"%s\n",error_text);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   exit(1);    first survey ("cross") where individuals from different ages are
 }    interviewed on their health status or degree of disability (in the
 /*********************** vector *******************/    case of a health survey which is our main interest) -2- at least a
 double *vector(int nl, int nh)    second wave of interviews ("longitudinal") which measure each change
 {    (if any) in individual health status.  Health expectancies are
   double *v;    computed from the time spent in each health state according to a
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    model. More health states you consider, more time is necessary to reach the
   if (!v) nrerror("allocation failure in vector");    Maximum Likelihood of the parameters involved in the model.  The
   return v-nl+NR_END;    simplest model is the multinomial logistic model where pij is the
 }    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
 /************************ free vector ******************/    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 void free_vector(double*v, int nl, int nh)    'age' is age and 'sex' is a covariate. If you want to have a more
 {    complex model than "constant and age", you should modify the program
   free((FREE_ARG)(v+nl-NR_END));    where the markup *Covariates have to be included here again* invites
 }    you to do it.  More covariates you add, slower the
     convergence.
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    The advantage of this computer programme, compared to a simple
 {    multinomial logistic model, is clear when the delay between waves is not
   int *v;    identical for each individual. Also, if a individual missed an
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    intermediate interview, the information is lost, but taken into
   if (!v) nrerror("allocation failure in ivector");    account using an interpolation or extrapolation.  
   return v-nl+NR_END;  
 }    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
 /******************free ivector **************************/    split into an exact number (nh*stepm) of unobserved intermediate
 void free_ivector(int *v, long nl, long nh)    states. This elementary transition (by month, quarter,
 {    semester or year) is modelled as a multinomial logistic.  The hPx
   free((FREE_ARG)(v+nl-NR_END));    matrix is simply the matrix product of nh*stepm elementary matrices
 }    and the contribution of each individual to the likelihood is simply
     hPijx.
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Also this programme outputs the covariance matrix of the parameters but also
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    of the life expectancies. It also computes the period (stable) prevalence. 
 {    
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   int **m;             Institut national d'études démographiques, Paris.
      This software have been partly granted by Euro-REVES, a concerted action
   /* allocate pointers to rows */    from the European Union.
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    It is copyrighted identically to a GNU software product, ie programme and
   if (!m) nrerror("allocation failure 1 in matrix()");    software can be distributed freely for non commercial use. Latest version
   m += NR_END;    can be accessed at http://euroreves.ined.fr/imach .
   m -= nrl;  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
      or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   /* allocate rows and set pointers to them */    
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    **********************************************************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /*
   m[nrl] += NR_END;    main
   m[nrl] -= ncl;    read parameterfile
      read datafile
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    concatwav
      freqsummary
   /* return pointer to array of pointers to rows */    if (mle >= 1)
   return m;      mlikeli
 }    print results files
     if mle==1 
 /****************** free_imatrix *************************/       computes hessian
 void free_imatrix(m,nrl,nrh,ncl,nch)    read end of parameter file: agemin, agemax, bage, fage, estepm
       int **m;        begin-prev-date,...
       long nch,ncl,nrh,nrl;    open gnuplot file
      /* free an int matrix allocated by imatrix() */    open html file
 {    period (stable) prevalence
   free((FREE_ARG) (m[nrl]+ncl-NR_END));     for age prevalim()
   free((FREE_ARG) (m+nrl-NR_END));    h Pij x
 }    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 /******************* matrix *******************************/    health expectancies
 double **matrix(long nrl, long nrh, long ncl, long nch)    Variance-covariance of DFLE
 {    prevalence()
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;     movingaverage()
   double **m;    varevsij() 
     if popbased==1 varevsij(,popbased)
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    total life expectancies
   if (!m) nrerror("allocation failure 1 in matrix()");    Variance of period (stable) prevalence
   m += NR_END;   end
   m -= nrl;  */
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;   
   m[nrl] -= ncl;  #include <math.h>
   #include <stdio.h>
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <stdlib.h>
   return m;  #include <string.h>
 }  #include <unistd.h>
   
 /*************************free matrix ************************/  #include <limits.h>
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #include <sys/types.h>
 {  #include <sys/stat.h>
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #include <errno.h>
   free((FREE_ARG)(m+nrl-NR_END));  extern int errno;
 }  
   /* #include <sys/time.h> */
 /******************* ma3x *******************************/  #include <time.h>
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #include "timeval.h"
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  /* #include <libintl.h> */
   double ***m;  /* #define _(String) gettext (String) */
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define MAXLINE 256
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #define GNUPLOTPROGRAM "gnuplot"
   m -= nrl;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   m[nrl] += NR_END;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   m[nrl] -= ncl;  
   #define MAXPARM 128 /* Maximum number of parameters for the optimization */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define NINTERVMAX 8
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   m[nrl][ncl] += NR_END;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   m[nrl][ncl] -= nll;  #define NCOVMAX 20 /* Maximum number of covariates */
   for (j=ncl+1; j<=nch; j++)  #define MAXN 20000
     m[nrl][j]=m[nrl][j-1]+nlay;  #define YEARM 12. /* Number of months per year */
    #define AGESUP 130
   for (i=nrl+1; i<=nrh; i++) {  #define AGEBASE 40
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
     for (j=ncl+1; j<=nch; j++)  #ifdef UNIX
       m[i][j]=m[i][j-1]+nlay;  #define DIRSEPARATOR '/'
   }  #define CHARSEPARATOR "/"
   return m;  #define ODIRSEPARATOR '\\'
 }  #else
   #define DIRSEPARATOR '\\'
 /*************************free ma3x ************************/  #define CHARSEPARATOR "\\"
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define ODIRSEPARATOR '/'
 {  #endif
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /* $Id$ */
   free((FREE_ARG)(m+nrl-NR_END));  /* $State$ */
 }  
   char version[]="Imach version 0.98l, October 2009, INED-EUROREVES-Institut de longevite ";
 /***************** f1dim *************************/  char fullversion[]="$Revision$ $Date$"; 
 extern int ncom;  char strstart[80];
 extern double *pcom,*xicom;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 extern double (*nrfunc)(double []);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    int nvar=0, nforce=0; /* Number of variables, number of forces */
 double f1dim(double x)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
 {  int npar=NPARMAX;
   int j;  int nlstate=2; /* Number of live states */
   double f;  int ndeath=1; /* Number of dead states */
   double *xt;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    int popbased=0;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int *wav; /* Number of waves for this individuual 0 is possible */
   f=(*nrfunc)(xt);  int maxwav=0; /* Maxim number of waves */
   free_vector(xt,1,ncom);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   return f;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
 }  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 /*****************brent *************************/  int mle=1, weightopt=0;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int iter;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   double a,b,d,etemp;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double fu,fv,fw,fx;  double jmean=1; /* Mean space between 2 waves */
   double ftemp;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   double e=0.0;  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    FILE *ficlog, *ficrespow;
   a=(ax < cx ? ax : cx);  int globpr=0; /* Global variable for printing or not */
   b=(ax > cx ? ax : cx);  double fretone; /* Only one call to likelihood */
   x=w=v=bx;  long ipmx=0; /* Number of contributions */
   fw=fv=fx=(*f)(x);  double sw; /* Sum of weights */
   for (iter=1;iter<=ITMAX;iter++) {  char filerespow[FILENAMELENGTH];
     xm=0.5*(a+b);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  FILE *ficresilk;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     printf(".");fflush(stdout);  FILE *ficresprobmorprev;
     fprintf(ficlog,".");fflush(ficlog);  FILE *fichtm, *fichtmcov; /* Html File */
 #ifdef DEBUG  FILE *ficreseij;
     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);  char filerese[FILENAMELENGTH];
     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);  FILE *ficresstdeij;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  char fileresstde[FILENAMELENGTH];
 #endif  FILE *ficrescveij;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  char filerescve[FILENAMELENGTH];
       *xmin=x;  FILE  *ficresvij;
       return fx;  char fileresv[FILENAMELENGTH];
     }  FILE  *ficresvpl;
     ftemp=fu;  char fileresvpl[FILENAMELENGTH];
     if (fabs(e) > tol1) {  char title[MAXLINE];
       r=(x-w)*(fx-fv);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       q=(x-v)*(fx-fw);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       p=(x-v)*q-(x-w)*r;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       q=2.0*(q-r);  char command[FILENAMELENGTH];
       if (q > 0.0) p = -p;  int  outcmd=0;
       q=fabs(q);  
       etemp=e;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  char filelog[FILENAMELENGTH]; /* Log file */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  char filerest[FILENAMELENGTH];
       else {  char fileregp[FILENAMELENGTH];
         d=p/q;  char popfile[FILENAMELENGTH];
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
           d=SIGN(tol1,xm-x);  
       }  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
     } else {  struct timezone tzp;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  extern int gettimeofday();
     }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  long time_value;
     fu=(*f)(u);  extern long time();
     if (fu <= fx) {  char strcurr[80], strfor[80];
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  char *endptr;
         SHFT(fv,fw,fx,fu)  long lval;
         } else {  double dval;
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  #define NR_END 1
             v=w;  #define FREE_ARG char*
             w=u;  #define FTOL 1.0e-10
             fv=fw;  
             fw=fu;  #define NRANSI 
           } else if (fu <= fv || v == x || v == w) {  #define ITMAX 200 
             v=u;  
             fv=fu;  #define TOL 2.0e-4 
           }  
         }  #define CGOLD 0.3819660 
   }  #define ZEPS 1.0e-10 
   nrerror("Too many iterations in brent");  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   *xmin=x;  
   return fx;  #define GOLD 1.618034 
 }  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
 /****************** mnbrak ***********************/  
   static double maxarg1,maxarg2;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
             double (*func)(double))  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 {    
   double ulim,u,r,q, dum;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   double fu;  #define rint(a) floor(a+0.5)
    
   *fa=(*func)(*ax);  static double sqrarg;
   *fb=(*func)(*bx);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   if (*fb > *fa) {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     SHFT(dum,*ax,*bx,dum)  int agegomp= AGEGOMP;
       SHFT(dum,*fb,*fa,dum)  
       }  int imx; 
   *cx=(*bx)+GOLD*(*bx-*ax);  int stepm=1;
   *fc=(*func)(*cx);  /* Stepm, step in month: minimum step interpolation*/
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  int estepm;
     q=(*bx-*cx)*(*fb-*fa);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int m,nb;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  long *num;
     if ((*bx-u)*(u-*cx) > 0.0) {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       fu=(*func)(u);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  double **pmmij, ***probs;
       fu=(*func)(u);  double *ageexmed,*agecens;
       if (fu < *fc) {  double dateintmean=0;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  double *weight;
           }  int **s; /* Status */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  double *agedc, **covar, idx;
       u=ulim;  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       fu=(*func)(u);  double *lsurv, *lpop, *tpop;
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       fu=(*func)(u);  double ftolhess; /* Tolerance for computing hessian */
     }  
     SHFT(*ax,*bx,*cx,u)  /**************** split *************************/
       SHFT(*fa,*fb,*fc,fu)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       }  {
 }    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
        the name of the file (name), its extension only (ext) and its first part of the name (finame)
 /*************** linmin ************************/    */ 
     char  *ss;                            /* pointer */
 int ncom;    int   l1, l2;                         /* length counters */
 double *pcom,*xicom;  
 double (*nrfunc)(double []);    l1 = strlen(path );                   /* length of path */
      if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 {    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   double brent(double ax, double bx, double cx,      strcpy( name, path );               /* we got the fullname name because no directory */
                double (*f)(double), double tol, double *xmin);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   double f1dim(double x);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      /* get current working directory */
               double *fc, double (*func)(double));      /*    extern  char* getcwd ( char *buf , int len);*/
   int j;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   double xx,xmin,bx,ax;        return( GLOCK_ERROR_GETCWD );
   double fx,fb,fa;      }
        /* got dirc from getcwd*/
   ncom=n;      printf(" DIRC = %s \n",dirc);
   pcom=vector(1,n);    } else {                              /* strip direcotry from path */
   xicom=vector(1,n);      ss++;                               /* after this, the filename */
   nrfunc=func;      l2 = strlen( ss );                  /* length of filename */
   for (j=1;j<=n;j++) {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     pcom[j]=p[j];      strcpy( name, ss );         /* save file name */
     xicom[j]=xi[j];      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   }      dirc[l1-l2] = 0;                    /* add zero */
   ax=0.0;      printf(" DIRC2 = %s \n",dirc);
   xx=1.0;    }
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    /* We add a separator at the end of dirc if not exists */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    l1 = strlen( dirc );                  /* length of directory */
 #ifdef DEBUG    if( dirc[l1-1] != DIRSEPARATOR ){
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      dirc[l1] =  DIRSEPARATOR;
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      dirc[l1+1] = 0; 
 #endif      printf(" DIRC3 = %s \n",dirc);
   for (j=1;j<=n;j++) {    }
     xi[j] *= xmin;    ss = strrchr( name, '.' );            /* find last / */
     p[j] += xi[j];    if (ss >0){
   }      ss++;
   free_vector(xicom,1,n);      strcpy(ext,ss);                     /* save extension */
   free_vector(pcom,1,n);      l1= strlen( name);
 }      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
 /*************** powell ************************/      finame[l1-l2]= 0;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    }
             double (*func)(double []))  
 {    return( 0 );                          /* we're done */
   void linmin(double p[], double xi[], int n, double *fret,  }
               double (*func)(double []));  
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  /******************************************/
   double fp,fptt;  
   double *xits;  void replace_back_to_slash(char *s, char*t)
   pt=vector(1,n);  {
   ptt=vector(1,n);    int i;
   xit=vector(1,n);    int lg=0;
   xits=vector(1,n);    i=0;
   *fret=(*func)(p);    lg=strlen(t);
   for (j=1;j<=n;j++) pt[j]=p[j];    for(i=0; i<= lg; i++) {
   for (*iter=1;;++(*iter)) {      (s[i] = t[i]);
     fp=(*fret);      if (t[i]== '\\') s[i]='/';
     ibig=0;    }
     del=0.0;  }
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  char *trimbb(char *out, char *in)
     for (i=1;i<=n;i++)  { /* Trim multiple blanks in line */
       printf(" %d %.12f",i, p[i]);    char *s;
     fprintf(ficlog," %d %.12f",i, p[i]);    s=out;
     printf("\n");    while (*in != '\0'){
     fprintf(ficlog,"\n");      while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
     for (i=1;i<=n;i++) {        in++;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      }
       fptt=(*fret);      *out++ = *in++;
 #ifdef DEBUG    }
       printf("fret=%lf \n",*fret);    *out='\0';
       fprintf(ficlog,"fret=%lf \n",*fret);    return s;
 #endif  }
       printf("%d",i);fflush(stdout);  
       fprintf(ficlog,"%d",i);fflush(ficlog);  int nbocc(char *s, char occ)
       linmin(p,xit,n,fret,func);  {
       if (fabs(fptt-(*fret)) > del) {    int i,j=0;
         del=fabs(fptt-(*fret));    int lg=20;
         ibig=i;    i=0;
       }    lg=strlen(s);
 #ifdef DEBUG    for(i=0; i<= lg; i++) {
       printf("%d %.12e",i,(*fret));    if  (s[i] == occ ) j++;
       fprintf(ficlog,"%d %.12e",i,(*fret));    }
       for (j=1;j<=n;j++) {    return j;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  }
         printf(" x(%d)=%.12e",j,xit[j]);  
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  void cutv(char *u,char *v, char*t, char occ)
       }  {
       for(j=1;j<=n;j++) {    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
         printf(" p=%.12e",p[j]);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
         fprintf(ficlog," p=%.12e",p[j]);       gives u="abcedf" and v="ghi2j" */
       }    int i,lg,j,p=0;
       printf("\n");    i=0;
       fprintf(ficlog,"\n");    for(j=0; j<=strlen(t)-1; j++) {
 #endif      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }    }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG    lg=strlen(t);
       int k[2],l;    for(j=0; j<p; j++) {
       k[0]=1;      (u[j] = t[j]);
       k[1]=-1;    }
       printf("Max: %.12e",(*func)(p));       u[p]='\0';
       fprintf(ficlog,"Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++) {     for(j=0; j<= lg; j++) {
         printf(" %.12e",p[j]);      if (j>=(p+1))(v[j-p-1] = t[j]);
         fprintf(ficlog," %.12e",p[j]);    }
       }  }
       printf("\n");  
       fprintf(ficlog,"\n");  /********************** nrerror ********************/
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  void nrerror(char error_text[])
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  {
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    fprintf(stderr,"ERREUR ...\n");
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    fprintf(stderr,"%s\n",error_text);
         }    exit(EXIT_FAILURE);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  }
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /*********************** vector *******************/
       }  double *vector(int nl, int nh)
 #endif  {
     double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       free_vector(xit,1,n);    if (!v) nrerror("allocation failure in vector");
       free_vector(xits,1,n);    return v-nl+NR_END;
       free_vector(ptt,1,n);  }
       free_vector(pt,1,n);  
       return;  /************************ free vector ******************/
     }  void free_vector(double*v, int nl, int nh)
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  {
     for (j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
       ptt[j]=2.0*p[j]-pt[j];  }
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  /************************ivector *******************************/
     }  int *ivector(long nl,long nh)
     fptt=(*func)(ptt);  {
     if (fptt < fp) {    int *v;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       if (t < 0.0) {    if (!v) nrerror("allocation failure in ivector");
         linmin(p,xit,n,fret,func);    return v-nl+NR_END;
         for (j=1;j<=n;j++) {  }
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  /******************free ivector **************************/
         }  void free_ivector(int *v, long nl, long nh)
 #ifdef DEBUG  {
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    free((FREE_ARG)(v+nl-NR_END));
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  }
         for(j=1;j<=n;j++){  
           printf(" %.12e",xit[j]);  /************************lvector *******************************/
           fprintf(ficlog," %.12e",xit[j]);  long *lvector(long nl,long nh)
         }  {
         printf("\n");    long *v;
         fprintf(ficlog,"\n");    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 #endif    if (!v) nrerror("allocation failure in ivector");
       }    return v-nl+NR_END;
     }  }
   }  
 }  /******************free lvector **************************/
   void free_lvector(long *v, long nl, long nh)
 /**** Prevalence limit ****************/  {
     free((FREE_ARG)(v+nl-NR_END));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  }
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  /******************* imatrix *******************************/
      matrix by transitions matrix until convergence is reached */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   int i, ii,j,k;  { 
   double min, max, maxmin, maxmax,sumnew=0.;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   double **matprod2();    int **m; 
   double **out, cov[NCOVMAX], **pmij();    
   double **newm;    /* allocate pointers to rows */ 
   double agefin, delaymax=50 ; /* Max number of years to converge */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
   for (ii=1;ii<=nlstate+ndeath;ii++)    m += NR_END; 
     for (j=1;j<=nlstate+ndeath;j++){    m -= nrl; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    
     }    
     /* allocate rows and set pointers to them */ 
    cov[1]=1.;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m[nrl] += NR_END; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    m[nrl] -= ncl; 
     newm=savm;    
     /* Covariates have to be included here again */    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
      cov[2]=agefin;    
      /* return pointer to array of pointers to rows */ 
       for (k=1; k<=cptcovn;k++) {    return m; 
         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]]);*/  
       }  /****************** free_imatrix *************************/
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  void free_imatrix(m,nrl,nrh,ncl,nch)
       for (k=1; k<=cptcovprod;k++)        int **m;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
       /*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]);*/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    free((FREE_ARG) (m+nrl-NR_END)); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  } 
   
     savm=oldm;  /******************* matrix *******************************/
     oldm=newm;  double **matrix(long nrl, long nrh, long ncl, long nch)
     maxmax=0.;  {
     for(j=1;j<=nlstate;j++){    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       min=1.;    double **m;
       max=0.;  
       for(i=1; i<=nlstate; i++) {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         sumnew=0;    if (!m) nrerror("allocation failure 1 in matrix()");
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    m += NR_END;
         prlim[i][j]= newm[i][j]/(1-sumnew);    m -= nrl;
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       maxmin=max-min;    m[nrl] += NR_END;
       maxmax=FMAX(maxmax,maxmin);    m[nrl] -= ncl;
     }  
     if(maxmax < ftolpl){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       return prlim;    return m;
     }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   }     */
 }  }
   
 /*************** transition probabilities ***************/  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  {
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double s1, s2;    free((FREE_ARG)(m+nrl-NR_END));
   /*double t34;*/  }
   int i,j,j1, nc, ii, jj;  
   /******************* ma3x *******************************/
     for(i=1; i<= nlstate; i++){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     for(j=1; j<i;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         /*s2 += param[i][j][nc]*cov[nc];*/    double ***m;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
       ps[i][j]=s2;    m += NR_END;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    m -= nrl;
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    m[nrl] += NR_END;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    m[nrl] -= ncl;
       }  
       ps[i][j]=s2;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }  
   }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     /*ps[3][2]=1;*/    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
   for(i=1; i<= nlstate; i++){    m[nrl][ncl] -= nll;
      s1=0;    for (j=ncl+1; j<=nch; j++) 
     for(j=1; j<i; j++)      m[nrl][j]=m[nrl][j-1]+nlay;
       s1+=exp(ps[i][j]);    
     for(j=i+1; j<=nlstate+ndeath; j++)    for (i=nrl+1; i<=nrh; i++) {
       s1+=exp(ps[i][j]);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     ps[i][i]=1./(s1+1.);      for (j=ncl+1; j<=nch; j++) 
     for(j=1; j<i; j++)        m[i][j]=m[i][j-1]+nlay;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    }
     for(j=i+1; j<=nlstate+ndeath; j++)    return m; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   } /* end i */    */
   }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /*************************free ma3x ************************/
       ps[ii][jj]=0;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       ps[ii][ii]=1;  {
     }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /*************** function subdirf ***********/
      printf("%lf ",ps[ii][jj]);  char *subdirf(char fileres[])
    }  {
     printf("\n ");    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
     printf("\n ");printf("%lf ",cov[2]);*/    strcat(tmpout,"/"); /* Add to the right */
 /*    strcat(tmpout,fileres);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    return tmpout;
   goto end;*/  }
     return ps;  
 }  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
 /**************** Product of 2 matrices ******************/  {
     
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    /* Caution optionfilefiname is hidden */
 {    strcpy(tmpout,optionfilefiname);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    strcat(tmpout,"/");
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    strcat(tmpout,preop);
   /* in, b, out are matrice of pointers which should have been initialized    strcat(tmpout,fileres);
      before: only the contents of out is modified. The function returns    return tmpout;
      a pointer to pointers identical to out */  }
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /*************** function subdirf3 ***********/
     for(k=ncolol; k<=ncoloh; k++)  char *subdirf3(char fileres[], char *preop, char *preop2)
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  {
         out[i][k] +=in[i][j]*b[j][k];    
     /* Caution optionfilefiname is hidden */
   return out;    strcpy(tmpout,optionfilefiname);
 }    strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,preop2);
 /************* Higher Matrix Product ***************/    strcat(tmpout,fileres);
     return tmpout;
 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 'nhstepm*hstepm*stepm' month  /***************** f1dim *************************/
      duration (i.e. until  extern int ncom; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  extern double *pcom,*xicom;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  extern double (*nrfunc)(double []); 
      (typically every 2 years instead of every month which is too big).   
      Model is determined by parameters x and covariates have to be  double f1dim(double x) 
      included manually here.  { 
     int j; 
      */    double f;
     double *xt; 
   int i, j, d, h, k;   
   double **out, cov[NCOVMAX];    xt=vector(1,ncom); 
   double **newm;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
   /* Hstepm could be zero and should return the unit matrix */    free_vector(xt,1,ncom); 
   for (i=1;i<=nlstate+ndeath;i++)    return f; 
     for (j=1;j<=nlstate+ndeath;j++){  } 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /*****************brent *************************/
     }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  { 
   for(h=1; h <=nhstepm; h++){    int iter; 
     for(d=1; d <=hstepm; d++){    double a,b,d,etemp;
       newm=savm;    double fu,fv,fw,fx;
       /* Covariates have to be included here again */    double ftemp;
       cov[1]=1.;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    double e=0.0; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];   
       for (k=1; k<=cptcovage;k++)    a=(ax < cx ? ax : cx); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    b=(ax > cx ? ax : cx); 
       for (k=1; k<=cptcovprod;k++)    x=w=v=bx; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      printf(".");fflush(stdout);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      fprintf(ficlog,".");fflush(ficlog);
       savm=oldm;  #ifdef DEBUG
       oldm=newm;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     }      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for(i=1; i<=nlstate+ndeath; i++)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       for(j=1;j<=nlstate+ndeath;j++) {  #endif
         po[i][j][h]=newm[i][j];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        *xmin=x; 
          */        return fx; 
       }      } 
   } /* end h */      ftemp=fu;
   return po;      if (fabs(e) > tol1) { 
 }        r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
 /*************** log-likelihood *************/        q=2.0*(q-r); 
 double func( double *x)        if (q > 0.0) p = -p; 
 {        q=fabs(q); 
   int i, ii, j, k, mi, d, kk;        etemp=e; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        e=d; 
   double **out;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double sw; /* Sum of weights */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double lli; /* Individual log likelihood */        else { 
   long ipmx;          d=p/q; 
   /*extern weight */          u=x+d; 
   /* We are differentiating ll according to initial status */          if (u-a < tol2 || b-u < tol2) 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/            d=SIGN(tol1,xm-x); 
   /*for(i=1;i<imx;i++)        } 
     printf(" %d\n",s[4][i]);      } else { 
   */        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   cov[1]=1.;      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      fu=(*f)(u); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      if (fu <= fx) { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        if (u >= x) a=x; else b=x; 
     for(mi=1; mi<= wav[i]-1; mi++){        SHFT(v,w,x,u) 
       for (ii=1;ii<=nlstate+ndeath;ii++)          SHFT(fv,fw,fx,fu) 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          } else { 
       for(d=0; d<dh[mi][i]; d++){            if (u < x) a=u; else b=u; 
         newm=savm;            if (fu <= fw || w == x) { 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;              v=w; 
         for (kk=1; kk<=cptcovage;kk++) {              w=u; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];              fv=fw; 
         }              fw=fu; 
                    } else if (fu <= fv || v == x || v == w) { 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,              v=u; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));              fv=fu; 
         savm=oldm;            } 
         oldm=newm;          } 
            } 
            nrerror("Too many iterations in brent"); 
       } /* end mult */    *xmin=x; 
          return fx; 
       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]]);*/  
       ipmx +=1;  /****************** mnbrak ***********************/
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     } /* end of wave */              double (*func)(double)) 
   } /* end of individual */  { 
     double ulim,u,r,q, dum;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    double fu; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */   
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    *fa=(*func)(*ax); 
   return -l;    *fb=(*func)(*bx); 
 }    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
 /*********** Maximum Likelihood Estimation ***************/        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    *fc=(*func)(*cx); 
 {    while (*fb > *fc) { 
   int i,j, iter;      r=(*bx-*ax)*(*fb-*fc); 
   double **xi,*delti;      q=(*bx-*cx)*(*fb-*fa); 
   double fret;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   xi=matrix(1,npar,1,npar);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   for (i=1;i<=npar;i++)      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     for (j=1;j<=npar;j++)      if ((*bx-u)*(u-*cx) > 0.0) { 
       xi[i][j]=(i==j ? 1.0 : 0.0);        fu=(*func)(u); 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   powell(p,xi,npar,ftol,&iter,&fret,func);        fu=(*func)(u); 
         if (fu < *fc) { 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));            SHFT(*fb,*fc,fu,(*func)(u)) 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 }        u=ulim; 
         fu=(*func)(u); 
 /**** Computes Hessian and covariance matrix ***/      } else { 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        u=(*cx)+GOLD*(*cx-*bx); 
 {        fu=(*func)(u); 
   double  **a,**y,*x,pd;      } 
   double **hess;      SHFT(*ax,*bx,*cx,u) 
   int i, j,jk;        SHFT(*fa,*fb,*fc,fu) 
   int *indx;        } 
   } 
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);  /*************** linmin ************************/
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  int ncom; 
   double *pcom,*xicom;
   hess=matrix(1,npar,1,npar);  double (*nrfunc)(double []); 
    
   printf("\nCalculation of the hessian matrix. Wait...\n");  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");  { 
   for (i=1;i<=npar;i++){    double brent(double ax, double bx, double cx, 
     printf("%d",i);fflush(stdout);                 double (*f)(double), double tol, double *xmin); 
     fprintf(ficlog,"%d",i);fflush(ficlog);    double f1dim(double x); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     /*printf(" %f ",p[i]);*/                double *fc, double (*func)(double)); 
     /*printf(" %lf ",hess[i][i]);*/    int j; 
   }    double xx,xmin,bx,ax; 
      double fx,fb,fa;
   for (i=1;i<=npar;i++) {   
     for (j=1;j<=npar;j++)  {    ncom=n; 
       if (j>i) {    pcom=vector(1,n); 
         printf(".%d%d",i,j);fflush(stdout);    xicom=vector(1,n); 
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    nrfunc=func; 
         hess[i][j]=hessij(p,delti,i,j);    for (j=1;j<=n;j++) { 
         hess[j][i]=hess[i][j];          pcom[j]=p[j]; 
         /*printf(" %lf ",hess[i][j]);*/      xicom[j]=xi[j]; 
       }    } 
     }    ax=0.0; 
   }    xx=1.0; 
   printf("\n");    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   fprintf(ficlog,"\n");    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
    #endif
   a=matrix(1,npar,1,npar);    for (j=1;j<=n;j++) { 
   y=matrix(1,npar,1,npar);      xi[j] *= xmin; 
   x=vector(1,npar);      p[j] += xi[j]; 
   indx=ivector(1,npar);    } 
   for (i=1;i<=npar;i++)    free_vector(xicom,1,n); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    free_vector(pcom,1,n); 
   ludcmp(a,npar,indx,&pd);  } 
   
   for (j=1;j<=npar;j++) {  char *asc_diff_time(long time_sec, char ascdiff[])
     for (i=1;i<=npar;i++) x[i]=0;  {
     x[j]=1;    long sec_left, days, hours, minutes;
     lubksb(a,npar,indx,x);    days = (time_sec) / (60*60*24);
     for (i=1;i<=npar;i++){    sec_left = (time_sec) % (60*60*24);
       matcov[i][j]=x[i];    hours = (sec_left) / (60*60) ;
     }    sec_left = (sec_left) %(60*60);
   }    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
   printf("\n#Hessian matrix#\n");    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   fprintf(ficlog,"\n#Hessian matrix#\n");    return ascdiff;
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  /*************** powell ************************/
       fprintf(ficlog,"%.3e ",hess[i][j]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     }              double (*func)(double [])) 
     printf("\n");  { 
     fprintf(ficlog,"\n");    void linmin(double p[], double xi[], int n, double *fret, 
   }                double (*func)(double [])); 
     int i,ibig,j; 
   /* Recompute Inverse */    double del,t,*pt,*ptt,*xit;
   for (i=1;i<=npar;i++)    double fp,fptt;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    double *xits;
   ludcmp(a,npar,indx,&pd);    int niterf, itmp;
   
   /*  printf("\n#Hessian matrix recomputed#\n");    pt=vector(1,n); 
     ptt=vector(1,n); 
   for (j=1;j<=npar;j++) {    xit=vector(1,n); 
     for (i=1;i<=npar;i++) x[i]=0;    xits=vector(1,n); 
     x[j]=1;    *fret=(*func)(p); 
     lubksb(a,npar,indx,x);    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (i=1;i<=npar;i++){    for (*iter=1;;++(*iter)) { 
       y[i][j]=x[i];      fp=(*fret); 
       printf("%.3e ",y[i][j]);      ibig=0; 
       fprintf(ficlog,"%.3e ",y[i][j]);      del=0.0; 
     }      last_time=curr_time;
     printf("\n");      (void) gettimeofday(&curr_time,&tzp);
     fprintf(ficlog,"\n");      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
   */  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
      for (i=1;i<=n;i++) {
   free_matrix(a,1,npar,1,npar);        printf(" %d %.12f",i, p[i]);
   free_matrix(y,1,npar,1,npar);        fprintf(ficlog," %d %.12lf",i, p[i]);
   free_vector(x,1,npar);        fprintf(ficrespow," %.12lf", p[i]);
   free_ivector(indx,1,npar);      }
   free_matrix(hess,1,npar,1,npar);      printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
 }      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
 /*************** hessian matrix ****************/        strcpy(strcurr,asctime(&tm));
 double hessii( double x[], double delta, int theta, double delti[])  /*       asctime_r(&tm,strcurr); */
 {        forecast_time=curr_time; 
   int i;        itmp = strlen(strcurr);
   int l=1, lmax=20;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   double k1,k2;          strcurr[itmp-1]='\0';
   double p2[NPARMAX+1];        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double res;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        for(niterf=10;niterf<=30;niterf+=10){
   double fx;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   int k=0,kmax=10;          tmf = *localtime(&forecast_time.tv_sec);
   double l1;  /*      asctime_r(&tmf,strfor); */
           strcpy(strfor,asctime(&tmf));
   fx=func(x);          itmp = strlen(strfor);
   for (i=1;i<=npar;i++) p2[i]=x[i];          if(strfor[itmp-1]=='\n')
   for(l=0 ; l <=lmax; l++){          strfor[itmp-1]='\0';
     l1=pow(10,l);          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);
     delts=delt;          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     for(k=1 ; k <kmax; k=k+1){        }
       delt = delta*(l1*k);      }
       p2[theta]=x[theta] +delt;      for (i=1;i<=n;i++) { 
       k1=func(p2)-fx;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       p2[theta]=x[theta]-delt;        fptt=(*fret); 
       k2=func(p2)-fx;  #ifdef DEBUG
       /*res= (k1-2.0*fx+k2)/delt/delt; */        printf("fret=%lf \n",*fret);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        fprintf(ficlog,"fret=%lf \n",*fret);
        #endif
 #ifdef DEBUG        printf("%d",i);fflush(stdout);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        fprintf(ficlog,"%d",i);fflush(ficlog);
       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);        linmin(p,xit,n,fret,func); 
 #endif        if (fabs(fptt-(*fret)) > del) { 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          del=fabs(fptt-(*fret)); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          ibig=i; 
         k=kmax;        } 
       }  #ifdef DEBUG
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        printf("%d %.12e",i,(*fret));
         k=kmax; l=lmax*10.;        fprintf(ficlog,"%d %.12e",i,(*fret));
       }        for (j=1;j<=n;j++) {
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         delts=delt;          printf(" x(%d)=%.12e",j,xit[j]);
       }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     }        }
   }        for(j=1;j<=n;j++) {
   delti[theta]=delts;          printf(" p=%.12e",p[j]);
   return res;          fprintf(ficlog," p=%.12e",p[j]);
          }
 }        printf("\n");
         fprintf(ficlog,"\n");
 double hessij( double x[], double delti[], int thetai,int thetaj)  #endif
 {      } 
   int i;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   int l=1, l1, lmax=20;  #ifdef DEBUG
   double k1,k2,k3,k4,res,fx;        int k[2],l;
   double p2[NPARMAX+1];        k[0]=1;
   int k;        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
   fx=func(x);        fprintf(ficlog,"Max: %.12e",(*func)(p));
   for (k=1; k<=2; k++) {        for (j=1;j<=n;j++) {
     for (i=1;i<=npar;i++) p2[i]=x[i];          printf(" %.12e",p[j]);
     p2[thetai]=x[thetai]+delti[thetai]/k;          fprintf(ficlog," %.12e",p[j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        }
     k1=func(p2)-fx;        printf("\n");
          fprintf(ficlog,"\n");
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(l=0;l<=1;l++) {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          for (j=1;j<=n;j++) {
     k2=func(p2)-fx;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
              printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          }
     k3=func(p2)-fx;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
            fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     p2[thetai]=x[thetai]-delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  #endif
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG        free_vector(xit,1,n); 
     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);        free_vector(xits,1,n); 
     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);        free_vector(ptt,1,n); 
 #endif        free_vector(pt,1,n); 
   }        return; 
   return res;      } 
 }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
 /************** Inverse of matrix **************/        ptt[j]=2.0*p[j]-pt[j]; 
 void ludcmp(double **a, int n, int *indx, double *d)        xit[j]=p[j]-pt[j]; 
 {        pt[j]=p[j]; 
   int i,imax,j,k;      } 
   double big,dum,sum,temp;      fptt=(*func)(ptt); 
   double *vv;      if (fptt < fp) { 
          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   vv=vector(1,n);        if (t < 0.0) { 
   *d=1.0;          linmin(p,xit,n,fret,func); 
   for (i=1;i<=n;i++) {          for (j=1;j<=n;j++) { 
     big=0.0;            xi[j][ibig]=xi[j][n]; 
     for (j=1;j<=n;j++)            xi[j][n]=xit[j]; 
       if ((temp=fabs(a[i][j])) > big) big=temp;          }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  #ifdef DEBUG
     vv[i]=1.0/big;          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);
   for (j=1;j<=n;j++) {          for(j=1;j<=n;j++){
     for (i=1;i<j;i++) {            printf(" %.12e",xit[j]);
       sum=a[i][j];            fprintf(ficlog," %.12e",xit[j]);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          }
       a[i][j]=sum;          printf("\n");
     }          fprintf(ficlog,"\n");
     big=0.0;  #endif
     for (i=j;i<=n;i++) {        }
       sum=a[i][j];      } 
       for (k=1;k<j;k++)    } 
         sum -= a[i][k]*a[k][j];  } 
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {  /**** Prevalence limit (stable or period prevalence)  ****************/
         big=dum;  
         imax=i;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       }  {
     }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     if (j != imax) {       matrix by transitions matrix until convergence is reached */
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];    int i, ii,j,k;
         a[imax][k]=a[j][k];    double min, max, maxmin, maxmax,sumnew=0.;
         a[j][k]=dum;    double **matprod2();
       }    double **out, cov[NCOVMAX+1], **pmij();
       *d = -(*d);    double **newm;
       vv[imax]=vv[j];    double agefin, delaymax=50 ; /* Max number of years to converge */
     }  
     indx[j]=imax;    for (ii=1;ii<=nlstate+ndeath;ii++)
     if (a[j][j] == 0.0) a[j][j]=TINY;      for (j=1;j<=nlstate+ndeath;j++){
     if (j != n) {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       dum=1.0/(a[j][j]);      }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }     cov[1]=1.;
   }   
   free_vector(vv,1,n);  /* Doesn't work */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 ;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 }      newm=savm;
       /* Covariates have to be included here again */
 void lubksb(double **a, int n, int *indx, double b[])       cov[2]=agefin;
 {    
   int i,ii=0,ip,j;        for (k=1; k<=cptcovn;k++) {
   double sum;          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 (i=1;i<=n;i++) {        }
     ip=indx[i];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     sum=b[ip];        for (k=1; k<=cptcovprod;k++)
     b[ip]=b[i];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     else if (sum) ii=i;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     b[i]=sum;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   for (i=n;i>=1;i--) {  
     sum=b[i];      savm=oldm;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      oldm=newm;
     b[i]=sum/a[i][i];      maxmax=0.;
   }      for(j=1;j<=nlstate;j++){
 }        min=1.;
         max=0.;
 /************ Frequencies ********************/        for(i=1; i<=nlstate; i++) {
 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)          sumnew=0;
 {  /* Some frequencies */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
            prlim[i][j]= newm[i][j]/(1-sumnew);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          max=FMAX(max,prlim[i][j]);
   int first;          min=FMIN(min,prlim[i][j]);
   double ***freq; /* Frequencies */        }
   double *pp;        maxmin=max-min;
   double pos, k2, dateintsum=0,k2cpt=0;        maxmax=FMAX(maxmax,maxmin);
   FILE *ficresp;      }
   char fileresp[FILENAMELENGTH];      if(maxmax < ftolpl){
          return prlim;
   pp=vector(1,nlstate);      }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
   strcpy(fileresp,"p");  }
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {  /*************** transition probabilities ***************/ 
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     exit(0);  {
   }    double s1, s2;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    /*double t34;*/
   j1=0;    int i,j,j1, nc, ii, jj;
    
   j=cptcoveff;      for(i=1; i<= nlstate; i++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for(j=1; j<i;j++){
           for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   first=1;            /*s2 += param[i][j][nc]*cov[nc];*/
             s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   for(k1=1; k1<=j;k1++){  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     for(i1=1; i1<=ncodemax[k1];i1++){          }
       j1++;          ps[i][j]=s2;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         scanf("%d", i);*/        }
       for (i=-1; i<=nlstate+ndeath; i++)          for(j=i+1; j<=nlstate+ndeath;j++){
         for (jk=-1; jk<=nlstate+ndeath; jk++)            for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           for(m=agemin; m <= agemax+3; m++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
             freq[i][jk][m]=0;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
                }
       dateintsum=0;          ps[i][j]=s2;
       k2cpt=0;        }
       for (i=1; i<=imx; i++) {      }
         bool=1;      /*ps[3][2]=1;*/
         if  (cptcovn>0) {      
           for (z1=1; z1<=cptcoveff; z1++)      for(i=1; i<= nlstate; i++){
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        s1=0;
               bool=0;        for(j=1; j<i; j++){
         }          s1+=exp(ps[i][j]);
         if (bool==1) {          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           for(m=firstpass; m<=lastpass; m++){        }
             k2=anint[m][i]+(mint[m][i]/12.);        for(j=i+1; j<=nlstate+ndeath; j++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          s1+=exp(ps[i][j]);
               if(agev[m][i]==0) agev[m][i]=agemax+1;          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
               if(agev[m][i]==1) agev[m][i]=agemax+2;        }
               if (m<lastpass) {        ps[i][i]=1./(s1+1.);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for(j=1; j<i; j++)
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
               }        for(j=i+1; j<=nlstate+ndeath; j++)
                        ps[i][j]= exp(ps[i][j])*ps[i][i];
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                 dateintsum=dateintsum+k2;      } /* end i */
                 k2cpt++;      
               }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
             }        for(jj=1; jj<= nlstate+ndeath; jj++){
           }          ps[ii][jj]=0;
         }          ps[ii][ii]=1;
       }        }
              }
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      
   
       if  (cptcovn>0) {  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
         fprintf(ficresp, "\n#********** Variable ");  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /*         printf("ddd %lf ",ps[ii][jj]); */
         fprintf(ficresp, "**********\n#");  /*       } */
       }  /*       printf("\n "); */
       for(i=1; i<=nlstate;i++)  /*        } */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  /*        printf("\n ");printf("%lf ",cov[2]); */
       fprintf(ficresp, "\n");         /*
              for(i=1; i<= npar; i++) printf("%f ",x[i]);
       for(i=(int)agemin; i <= (int)agemax+3; i++){        goto end;*/
         if(i==(int)agemax+3){      return ps;
           fprintf(ficlog,"Total");  }
         }else{  
           if(first==1){  /**************** Product of 2 matrices ******************/
             first=0;  
             printf("See log file for details...\n");  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
           }  {
           fprintf(ficlog,"Age %d", i);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         for(jk=1; jk <=nlstate ; jk++){    /* in, b, out are matrice of pointers which should have been initialized 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)       before: only the contents of out is modified. The function returns
             pp[jk] += freq[jk][m][i];       a pointer to pointers identical to out */
         }    long i, j, k;
         for(jk=1; jk <=nlstate ; jk++){    for(i=nrl; i<= nrh; i++)
           for(m=-1, pos=0; m <=0 ; m++)      for(k=ncolol; k<=ncoloh; k++)
             pos += freq[jk][m][i];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           if(pp[jk]>=1.e-10){          out[i][k] +=in[i][j]*b[j][k];
             if(first==1){  
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    return out;
             }  }
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
           }else{  
             if(first==1)  /************* Higher Matrix Product ***************/
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  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 
        'nhstepm*hstepm*stepm' months (i.e. until
         for(jk=1; jk <=nlstate ; jk++){       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)       nhstepm*hstepm matrices. 
             pp[jk] += freq[jk][m][i];       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 
        for the memory).
         for(jk=1,pos=0; jk <=nlstate ; jk++)       Model is determined by parameters x and covariates have to be 
           pos += pp[jk];       included manually here. 
         for(jk=1; jk <=nlstate ; jk++){  
           if(pos>=1.e-5){       */
             if(first==1)  
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    int i, j, d, h, k;
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    double **out, cov[NCOVMAX+1];
           }else{    double **newm;
             if(first==1)  
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    /* Hstepm could be zero and should return the unit matrix */
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for (i=1;i<=nlstate+ndeath;i++)
           }      for (j=1;j<=nlstate+ndeath;j++){
           if( i <= (int) agemax){        oldm[i][j]=(i==j ? 1.0 : 0.0);
             if(pos>=1.e-5){        po[i][j][0]=(i==j ? 1.0 : 0.0);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      }
               probs[i][jk][j1]= pp[jk]/pos;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    for(h=1; h <=nhstepm; h++){
             }      for(d=1; d <=hstepm; d++){
             else        newm=savm;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        /* Covariates have to be included here again */
           }        cov[1]=1.;
         }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
                for (k=1; k<=cptcovn;k++) 
         for(jk=-1; jk <=nlstate+ndeath; jk++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           for(m=-1; m <=nlstate+ndeath; m++)        for (k=1; k<=cptcovage;k++)
             if(freq[jk][m][i] !=0 ) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
             if(first==1)        for (k=1; k<=cptcovprod;k++)
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);  
             }  
         if(i <= (int) agemax)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
           fprintf(ficresp,"\n");        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         if(first==1)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
           printf("Others in log...\n");                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         fprintf(ficlog,"\n");        savm=oldm;
       }        oldm=newm;
     }      }
   }      for(i=1; i<=nlstate+ndeath; i++)
   dateintmean=dateintsum/k2cpt;        for(j=1;j<=nlstate+ndeath;j++) {
            po[i][j][h]=newm[i][j];
   fclose(ficresp);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        }
   free_vector(pp,1,nlstate);      /*printf("h=%d ",h);*/
      } /* end h */
   /* End of Freq */  /*     printf("\n H=%d \n",h); */
 }    return po;
   }
 /************ Prevalence ********************/  
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  
 {  /* Some frequencies */  /*************** log-likelihood *************/
    double func( double *x)
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  {
   double ***freq; /* Frequencies */    int i, ii, j, k, mi, d, kk;
   double *pp;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double pos, k2;    double **out;
     double sw; /* Sum of weights */
   pp=vector(1,nlstate);    double lli; /* Individual log likelihood */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int s1, s2;
      double bbh, survp;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    long ipmx;
   j1=0;    /*extern weight */
      /* We are differentiating ll according to initial status */
   j=cptcoveff;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
   for(k1=1; k1<=j;k1++){    */
     for(i1=1; i1<=ncodemax[k1];i1++){    cov[1]=1.;
       j1++;  
          for(k=1; k<=nlstate; k++) ll[k]=0.;
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)      if(mle==1){
           for(m=agemin; m <= agemax+3; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             freq[i][jk][m]=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              for(mi=1; mi<= wav[i]-1; mi++){
       for (i=1; i<=imx; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
         bool=1;            for (j=1;j<=nlstate+ndeath;j++){
         if  (cptcovn>0) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for (z1=1; z1<=cptcoveff; z1++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            }
               bool=0;          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
         if (bool==1) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(m=firstpass; m<=lastpass; m++){            for (kk=1; kk<=cptcovage;kk++) {
             k2=anint[m][i]+(mint[m][i]/12.);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            }
               if(agev[m][i]==0) agev[m][i]=agemax+1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               if(agev[m][i]==1) agev[m][i]=agemax+2;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               if (m<lastpass) {            savm=oldm;
                 if (calagedate>0)            oldm=newm;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          } /* end mult */
                 else        
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          /* 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 
             }           * (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
       }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       for(i=(int)agemin; i <= (int)agemax+3; i++){           * probability in order to take into account the bias as a fraction of the way
         for(jk=1; jk <=nlstate ; jk++){           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)           * -stepm/2 to stepm/2 .
             pp[jk] += freq[jk][m][i];           * For stepm=1 the results are the same as for previous versions of Imach.
         }           * For stepm > 1 the results are less biased than in previous versions. 
         for(jk=1; jk <=nlstate ; jk++){           */
           for(m=-1, pos=0; m <=0 ; m++)          s1=s[mw[mi][i]][i];
             pos += freq[jk][m][i];          s2=s[mw[mi+1][i]][i];
         }          bbh=(double)bh[mi][i]/(double)stepm; 
                  /* bias bh is positive if real duration
         for(jk=1; jk <=nlstate ; jk++){           * is higher than the multiple of stepm and negative otherwise.
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)           */
             pp[jk] += freq[jk][m][i];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         }          if( s2 > nlstate){ 
                    /* i.e. if s2 is a death state and if the date of death is known 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];               then the contribution to the likelihood is the probability to 
                       die between last step unit time and current  step unit time, 
         for(jk=1; jk <=nlstate ; jk++){                   which is also equal to probability to die before dh 
           if( i <= (int) agemax){               minus probability to die before dh-stepm . 
             if(pos>=1.e-5){               In version up to 0.92 likelihood was computed
               probs[i][jk][j1]= pp[jk]/pos;          as if date of death was unknown. Death was treated as any other
             }          health state: the date of the interview describes the actual state
           }          and not the date of a change in health state. The former idea was
         }/* end jk */          to consider that at each interview the state was recorded
       }/* end i */          (healthy, disable or death) and IMaCh was corrected; but when we
     } /* end i1 */          introduced the exact date of death then we should have modified
   } /* end k1 */          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
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          and month of death but the probability to survive from last
   free_vector(pp,1,nlstate);          interview up to one month before death multiplied by the
            probability to die within a month. Thanks to Chris
 }  /* End of Freq */          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
 /************* Waves Concatenation ***************/          which slows down the processing. The difference can be up to 10%
           lower mortality.
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            */
 {            lli=log(out[s1][s2] - savm[s1][s2]);
   /* 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          } else if  (s2==-2) {
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            for (j=1,survp=0. ; j<=nlstate; j++) 
      and mw[mi+1][i]. dh depends on stepm.              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
      */            /*survp += out[s1][j]; */
             lli= log(survp);
   int i, mi, m;          }
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          
      double sum=0., jmean=0.;*/          else if  (s2==-4) { 
   int first;            for (j=3,survp=0. ; j<=nlstate; j++)  
   int j, k=0,jk, ju, jl;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double sum=0.;            lli= log(survp); 
   first=0;          } 
   jmin=1e+5;  
   jmax=-1;          else if  (s2==-5) { 
   jmean=0.;            for (j=1,survp=0. ; j<=2; j++)  
   for(i=1; i<=imx; i++){              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     mi=0;            lli= log(survp); 
     m=firstpass;          } 
     while(s[m][i] <= nlstate){          
       if(s[m][i]>=1)          else{
         mw[++mi][i]=m;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       if(m >=lastpass)            /*  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 */
         break;          } 
       else          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         m++;          /*if(lli ==000.0)*/
     }/* end while */          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     if (s[m][i] > nlstate){          ipmx +=1;
       mi++;     /* Death is another wave */          sw += weight[i];
       /* if(mi==0)  never been interviewed correctly before death */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          /* Only death is a correct wave */        } /* end of wave */
       mw[mi][i]=m;      } /* end of individual */
     }    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     wav[i]=mi;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     if(mi==0){        for(mi=1; mi<= wav[i]-1; mi++){
       if(first==0){          for (ii=1;ii<=nlstate+ndeath;ii++)
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);            for (j=1;j<=nlstate+ndeath;j++){
         first=1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(first==1){            }
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);          for(d=0; d<=dh[mi][i]; d++){
       }            newm=savm;
     } /* end mi==0 */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(i=1; i<=imx; i++){            }
     for(mi=1; mi<wav[i];mi++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if (stepm <=0)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         dh[mi][i]=1;            savm=oldm;
       else{            oldm=newm;
         if (s[mw[mi+1][i]][i] > nlstate) {          } /* end mult */
           if (agedc[i] < 2*AGESUP) {        
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          s1=s[mw[mi][i]][i];
           if(j==0) j=1;  /* Survives at least one month after exam */          s2=s[mw[mi+1][i]][i];
           k=k+1;          bbh=(double)bh[mi][i]/(double)stepm; 
           if (j >= jmax) jmax=j;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           if (j <= jmin) jmin=j;          ipmx +=1;
           sum=sum+j;          sw += weight[i];
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           }        } /* end of wave */
         }      } /* end of individual */
         else{    }  else if(mle==3){  /* exponential inter-extrapolation */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           k=k+1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if (j >= jmax) jmax=j;        for(mi=1; mi<= wav[i]-1; mi++){
           else if (j <= jmin)jmin=j;          for (ii=1;ii<=nlstate+ndeath;ii++)
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            for (j=1;j<=nlstate+ndeath;j++){
           sum=sum+j;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         jk= j/stepm;            }
         jl= j -jk*stepm;          for(d=0; d<dh[mi][i]; d++){
         ju= j -(jk+1)*stepm;            newm=savm;
         if(jl <= -ju)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           dh[mi][i]=jk;            for (kk=1; kk<=cptcovage;kk++) {
         else              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           dh[mi][i]=jk+1;            }
         if(dh[mi][i]==0)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           dh[mi][i]=1; /* At least one step */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
     }            oldm=newm;
   }          } /* end mult */
   jmean=sum/k;        
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          s1=s[mw[mi][i]][i];
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          s2=s[mw[mi+1][i]][i];
  }          bbh=(double)bh[mi][i]/(double)stepm; 
           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 */
 /*********** Tricode ****************************/          ipmx +=1;
 void tricode(int *Tvar, int **nbcode, int imx)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int Ndum[20],ij=1, k, j, i;        } /* end of wave */
   int cptcode=0;      } /* end of individual */
   cptcoveff=0;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (k=0; k<19; k++) Ndum[k]=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (k=1; k<=7; k++) ncodemax[k]=0;        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            for (j=1;j<=nlstate+ndeath;j++){
     for (i=1; i<=imx; i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       ij=(int)(covar[Tvar[j]][i]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       Ndum[ij]++;            }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          for(d=0; d<dh[mi][i]; d++){
       if (ij > cptcode) cptcode=ij;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for (i=0; i<=cptcode; i++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if(Ndum[i]!=0) ncodemax[j]++;            }
     }          
     ij=1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for (i=1; i<=ncodemax[j]; i++) {            oldm=newm;
       for (k=0; k<=19; k++) {          } /* end mult */
         if (Ndum[k] != 0) {        
           nbcode[Tvar[j]][ij]=k;          s1=s[mw[mi][i]][i];
                    s2=s[mw[mi+1][i]][i];
           ij++;          if( s2 > nlstate){ 
         }            lli=log(out[s1][s2] - savm[s1][s2]);
         if (ij > ncodemax[j]) break;          }else{
       }              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     }          }
   }            ipmx +=1;
           sw += weight[i];
  for (k=0; k<19; k++) Ndum[k]=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
  for (i=1; i<=ncovmodel-2; i++) {        } /* end of wave */
    ij=Tvar[i];      } /* end of individual */
    Ndum[ij]++;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
  }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  ij=1;        for(mi=1; mi<= wav[i]-1; mi++){
  for (i=1; i<=10; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
    if((Ndum[i]!=0) && (i<=ncovcol)){            for (j=1;j<=nlstate+ndeath;j++){
      Tvaraff[ij]=i;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      ij++;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    }            }
  }          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
  cptcoveff=ij-1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /*********** Health Expectancies ****************/            }
           
 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 )            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {            savm=oldm;
   /* Health expectancies */            oldm=newm;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          } /* end mult */
   double age, agelim, hf;        
   double ***p3mat,***varhe;          s1=s[mw[mi][i]][i];
   double **dnewm,**doldm;          s2=s[mw[mi+1][i]][i];
   double *xp;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double **gp, **gm;          ipmx +=1;
   double ***gradg, ***trgradg;          sw += weight[i];
   int theta;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        } /* end of wave */
   xp=vector(1,npar);      } /* end of individual */
   dnewm=matrix(1,nlstate*2,1,npar);    } /* End of if */
   doldm=matrix(1,nlstate*2,1,nlstate*2);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   fprintf(ficreseij,"# Health expectancies\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   fprintf(ficreseij,"# Age");    return -l;
   for(i=1; i<=nlstate;i++)  }
     for(j=1; j<=nlstate;j++)  
       fprintf(ficreseij," %1d-%1d (SE)",i,j);  /*************** log-likelihood *************/
   fprintf(ficreseij,"\n");  double funcone( double *x)
   {
   if(estepm < stepm){    /* Same as likeli but slower because of a lot of printf and if */
     printf ("Problem %d lower than %d\n",estepm, stepm);    int i, ii, j, k, mi, d, kk;
   }    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   else  hstepm=estepm;      double **out;
   /* We compute the life expectancy from trapezoids spaced every estepm months    double lli; /* Individual log likelihood */
    * This is mainly to measure the difference between two models: for example    double llt;
    * if stepm=24 months pijx are given only every 2 years and by summing them    int s1, s2;
    * we are calculating an estimate of the Life Expectancy assuming a linear    double bbh, survp;
    * progression inbetween and thus overestimating or underestimating according    /*extern weight */
    * to the curvature of the survival function. If, for the same date, we    /* We are differentiating ll according to initial status */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
    * to compare the new estimate of Life expectancy with the same linear    /*for(i=1;i<imx;i++) 
    * hypothesis. A more precise result, taking into account a more precise      printf(" %d\n",s[4][i]);
    * curvature will be obtained if estepm is as small as stepm. */    */
     cov[1]=1.;
   /* 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.    for(k=1; k<=nlstate; k++) ll[k]=0.;
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      Look at hpijx to understand the reason of that which relies in memory size      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      and note for a fixed period like estepm months */      for(mi=1; mi<= wav[i]-1; mi++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        for (ii=1;ii<=nlstate+ndeath;ii++)
      survival function given by stepm (the optimization length). Unfortunately it          for (j=1;j<=nlstate+ndeath;j++){
      means that if the survival funtion is printed only each two years of age and if            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            savm[ii][j]=(ii==j ? 1.0 : 0.0);
      results. So we changed our mind and took the option of the best precision.          }
   */        for(d=0; d<dh[mi][i]; d++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   agelim=AGESUP;          for (kk=1; kk<=cptcovage;kk++) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     /* nhstepm age range expressed in number of stepm */          }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     /* if (stepm >= YEARM) hstepm=1;*/          savm=oldm;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          oldm=newm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } /* end mult */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        
     gp=matrix(0,nhstepm,1,nlstate*2);        s1=s[mw[mi][i]][i];
     gm=matrix(0,nhstepm,1,nlstate*2);        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        /* bias is positive if real duration
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */         * is higher than the multiple of stepm and negative otherwise.
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);           */
          if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++) 
     /* Computing Variances of health expectancies */            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
      for(theta=1; theta <=npar; theta++){        }else if (mle==1){
       for(i=1; i<=npar; i++){          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } else if(mle==2){
       }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, 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 */
       cptj=0;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       for(j=1; j<= nlstate; j++){          lli=log(out[s1][s2]); /* Original formula */
         for(i=1; i<=nlstate; i++){        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           cptj=cptj+1;          lli=log(out[s1][s2]); /* Original formula */
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){        } /* End of if */
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        ipmx +=1;
           }        sw += weight[i];
         }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
              if(globpr){
                fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       for(i=1; i<=npar; i++)   %11.6f %11.6f %11.6f ", \
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                    2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
                for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       cptj=0;            llt +=ll[k]*gipmx/gsw;
       for(j=1; j<= nlstate; j++){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         for(i=1;i<=nlstate;i++){          }
           cptj=cptj+1;          fprintf(ficresilk," %10.6f\n", -llt);
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){        }
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      } /* 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*2; j++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(h=0; h<=nhstepm-1; 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;
      }    }
        return -l;
 /* End theta */  }
   
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  
   /*************** function likelione ***********/
      for(h=0; h<=nhstepm-1; h++)  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       for(j=1; j<=nlstate*2;j++)  {
         for(theta=1; theta <=npar; theta++)    /* This routine should help understanding what is done with 
           trgradg[h][j][theta]=gradg[h][theta][j];       the selection of individuals/waves and
             to check the exact contribution to the likelihood.
        Plotting could be done.
      for(i=1;i<=nlstate*2;i++)     */
       for(j=1;j<=nlstate*2;j++)    int k;
         varhe[i][j][(int)age] =0.;  
     if(*globpri !=0){ /* Just counts and sums, no printings */
      printf("%d|",(int)age);fflush(stdout);      strcpy(fileresilk,"ilk"); 
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);      strcat(fileresilk,fileres);
      for(h=0;h<=nhstepm-1;h++){      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for(k=0;k<=nhstepm-1;k++){        printf("Problem with resultfile: %s\n", fileresilk);
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);      }
         for(i=1;i<=nlstate*2;i++)      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");
           for(j=1;j<=nlstate*2;j++)      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       }      for(k=1; k<=nlstate; k++) 
     }        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     /* Computing expectancies */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     for(i=1; i<=nlstate;i++)    }
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    *fretone=(*funcone)(p);
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    if(*globpri !=0){
                fclose(ficresilk);
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
         }    } 
     return;
     fprintf(ficreseij,"%3.0f",age );  }
     cptj=0;  
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  /*********** Maximum Likelihood Estimation ***************/
         cptj++;  
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       }  {
     fprintf(ficreseij,"\n");    int i,j, iter;
        double **xi;
     free_matrix(gm,0,nhstepm,1,nlstate*2);    double fret;
     free_matrix(gp,0,nhstepm,1,nlstate*2);    double fretone; /* Only one call to likelihood */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    /*  char filerespow[FILENAMELENGTH];*/
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    xi=matrix(1,npar,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=1;i<=npar;i++)
   }      for (j=1;j<=npar;j++)
   printf("\n");        xi[i][j]=(i==j ? 1.0 : 0.0);
   fprintf(ficlog,"\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
   free_vector(xp,1,npar);    strcat(filerespow,fileres);
   free_matrix(dnewm,1,nlstate*2,1,npar);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);      printf("Problem with resultfile: %s\n", filerespow);
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
 }    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
 /************ Variance ******************/    for (i=1;i<=nlstate;i++)
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased)      for(j=1;j<=nlstate+ndeath;j++)
 {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   /* Variance of health expectancies */    fprintf(ficrespow,"\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   /* double **newm;*/    powell(p,xi,npar,ftol,&iter,&fret,func);
   double **dnewm,**doldm;  
   double **dnewmp,**doldmp;    free_matrix(xi,1,npar,1,npar);
   int i, j, nhstepm, hstepm, h, nstepm ;    fclose(ficrespow);
   int k, cptcode;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   double *xp;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **gp, **gm;  /* for var eij */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double ***gradg, ***trgradg; /*for var eij */  
   double **gradgp, **trgradgp; /* for var p point j */  }
   double *gpp, *gmp; /* for var p point j */  
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */  /**** Computes Hessian and covariance matrix ***/
   double ***p3mat;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double age,agelim, hf;  {
   int theta;    double  **a,**y,*x,pd;
   char digit[4];    double **hess;
   char digitp[16];    int i, j,jk;
     int *indx;
   char fileresprobmorprev[FILENAMELENGTH];  
     double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   if(popbased==1)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     strcpy(digitp,"-populbased-");    void lubksb(double **a, int npar, int *indx, double b[]) ;
   else    void ludcmp(double **a, int npar, int *indx, double *d) ;
     strcpy(digitp,"-stablbased-");    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
   strcpy(fileresprobmorprev,"prmorprev");  
   sprintf(digit,"%-d",ij);    printf("\nCalculation of the hessian matrix. Wait...\n");
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   strcat(fileresprobmorprev,digit); /* Tvar to be done */    for (i=1;i<=npar;i++){
   strcat(fileresprobmorprev,digitp); /* Popbased or not */      printf("%d",i);fflush(stdout);
   strcat(fileresprobmorprev,fileres);      fprintf(ficlog,"%d",i);fflush(ficlog);
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {     
     printf("Problem with resultfile: %s\n", fileresprobmorprev);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);      
   }      /*  printf(" %f ",p[i]);
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    }
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");    
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    for (i=1;i<=npar;i++) {
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){      for (j=1;j<=npar;j++)  {
     fprintf(ficresprobmorprev," p.%-d SE",j);        if (j>i) { 
     for(i=1; i<=nlstate;i++)          printf(".%d%d",i,j);fflush(stdout);
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   }            hess[i][j]=hessij(p,delti,i,j,func,npar);
   fprintf(ficresprobmorprev,"\n");          
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          hess[j][i]=hess[i][j];    
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          /*printf(" %lf ",hess[i][j]);*/
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);        }
     exit(0);      }
   }    }
   else{    printf("\n");
     fprintf(ficgp,"\n# Routine varevsij");    fprintf(ficlog,"\n");
   }  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     printf("Problem with html file: %s\n", optionfilehtm);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    
     exit(0);    a=matrix(1,npar,1,npar);
   }    y=matrix(1,npar,1,npar);
   else{    x=vector(1,npar);
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");    indx=ivector(1,npar);
   }    for (i=1;i<=npar;i++)
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");  
   fprintf(ficresvij,"# Age");    for (j=1;j<=npar;j++) {
   for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++) x[i]=0;
     for(j=1; j<=nlstate;j++)      x[j]=1;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      lubksb(a,npar,indx,x);
   fprintf(ficresvij,"\n");      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
   xp=vector(1,npar);      }
   dnewm=matrix(1,nlstate,1,npar);    }
   doldm=matrix(1,nlstate,1,nlstate);  
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);    printf("\n#Hessian matrix#\n");
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);      for (j=1;j<=npar;j++) { 
   gpp=vector(nlstate+1,nlstate+ndeath);        printf("%.3e ",hess[i][j]);
   gmp=vector(nlstate+1,nlstate+ndeath);        fprintf(ficlog,"%.3e ",hess[i][j]);
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/      }
        printf("\n");
   if(estepm < stepm){      fprintf(ficlog,"\n");
     printf ("Problem %d lower than %d\n",estepm, stepm);    }
   }  
   else  hstepm=estepm;      /* Recompute Inverse */
   /* For example we decided to compute the life expectancy with the smallest unit */    for (i=1;i<=npar;i++)
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      nhstepm is the number of hstepm from age to agelim    ludcmp(a,npar,indx,&pd);
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size    /*  printf("\n#Hessian matrix recomputed#\n");
      and note for a fixed period like k years */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    for (j=1;j<=npar;j++) {
      survival function given by stepm (the optimization length). Unfortunately it      for (i=1;i<=npar;i++) x[i]=0;
      means that if the survival funtion is printed only each two years of age and if      x[j]=1;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      lubksb(a,npar,indx,x);
      results. So we changed our mind and took the option of the best precision.      for (i=1;i<=npar;i++){ 
   */        y[i][j]=x[i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        printf("%.3e ",y[i][j]);
   agelim = AGESUP;        fprintf(ficlog,"%.3e ",y[i][j]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      printf("\n");
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      fprintf(ficlog,"\n");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    */
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
     for(theta=1; theta <=npar; theta++){    free_ivector(indx,1,npar);
       for(i=1; i<=npar; i++){ /* Computes gradient */    free_matrix(hess,1,npar,1,npar);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
   /*************** hessian matrix ****************/
       if (popbased==1) {  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         for(i=1; i<=nlstate;i++)  {
           prlim[i][i]=probs[(int)age][i][ij];    int i;
       }    int l=1, lmax=20;
      double k1,k2;
       for(j=1; j<= nlstate; j++){    double p2[MAXPARM+1]; /* identical to x */
         for(h=0; h<=nhstepm; h++){    double res;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    double fx;
         }    int k=0,kmax=10;
       }    double l1;
       /* This for computing forces of mortality (h=1)as a weighted average */  
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    fx=func(x);
         for(i=1; i<= nlstate; i++)    for (i=1;i<=npar;i++) p2[i]=x[i];
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    for(l=0 ; l <=lmax; l++){
       }          l1=pow(10,l);
       /* end force of mortality */      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
       for(i=1; i<=npar; i++) /* Computes gradient */        delt = delta*(l1*k);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        p2[theta]=x[theta] +delt;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          k1=func(p2)-fx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
       if (popbased==1) {        /*res= (k1-2.0*fx+k2)/delt/delt; */
         for(i=1; i<=nlstate;i++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           prlim[i][i]=probs[(int)age][i][ij];        
       }  #ifdef DEBUGHESS
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       for(j=1; j<= nlstate; j++){        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         for(h=0; h<=nhstepm; h++){  #endif
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         }          k=kmax;
       }        }
       /* This for computing force of mortality (h=1)as a weighted average */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){          k=kmax; l=lmax*10.;
         for(i=1; i<= nlstate; i++)        }
           gmp[j] += prlim[i][i]*p3mat[i][j][1];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       }              delts=delt;
       /* end force of mortality */        }
       }
       for(j=1; j<= nlstate; j++) /* vareij */    }
         for(h=0; h<=nhstepm; h++){    delti[theta]=delts;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    return res; 
         }    
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */  }
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];  
       }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   {
     } /* End theta */    int i;
     int l=1, l1, lmax=20;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */    double k1,k2,k3,k4,res,fx;
     double p2[MAXPARM+1];
     for(h=0; h<=nhstepm; h++) /* veij */    int k;
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)    fx=func(x);
           trgradg[h][j][theta]=gradg[h][theta][j];    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */      p2[thetai]=x[thetai]+delti[thetai]/k;
       for(theta=1; theta <=npar; theta++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         trgradgp[j][theta]=gradgp[theta][j];      k1=func(p2)-fx;
     
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      p2[thetai]=x[thetai]+delti[thetai]/k;
     for(i=1;i<=nlstate;i++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(j=1;j<=nlstate;j++)      k2=func(p2)-fx;
         vareij[i][j][(int)age] =0.;    
       p2[thetai]=x[thetai]-delti[thetai]/k;
     for(h=0;h<=nhstepm;h++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       for(k=0;k<=nhstepm;k++){      k3=func(p2)-fx;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      p2[thetai]=x[thetai]-delti[thetai]/k;
         for(i=1;i<=nlstate;i++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           for(j=1;j<=nlstate;j++)      k4=func(p2)-fx;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       }  #ifdef DEBUG
     }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       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);
     /* pptj */  #endif
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);    }
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);    return res;
     for(j=nlstate+1;j<=nlstate+ndeath;j++)  }
       for(i=nlstate+1;i<=nlstate+ndeath;i++)  
         varppt[j][i]=doldmp[j][i];  /************** Inverse of matrix **************/
     /* end ppptj */  void ludcmp(double **a, int n, int *indx, double *d) 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);    { 
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    int i,imax,j,k; 
      double big,dum,sum,temp; 
     if (popbased==1) {    double *vv; 
       for(i=1; i<=nlstate;i++)   
         prlim[i][i]=probs[(int)age][i][ij];    vv=vector(1,n); 
     }    *d=1.0; 
        for (i=1;i<=n;i++) { 
     /* This for computing force of mortality (h=1)as a weighted average */      big=0.0; 
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){      for (j=1;j<=n;j++) 
       for(i=1; i<= nlstate; i++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
         gmp[j] += prlim[i][i]*p3mat[i][j][1];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     }          vv[i]=1.0/big; 
     /* end force of mortality */    } 
     for (j=1;j<=n;j++) { 
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);      for (i=1;i<j;i++) { 
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){        sum=a[i][j]; 
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       for(i=1; i<=nlstate;i++){        a[i][j]=sum; 
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);      } 
       }      big=0.0; 
     }      for (i=j;i<=n;i++) { 
     fprintf(ficresprobmorprev,"\n");        sum=a[i][j]; 
         for (k=1;k<j;k++) 
     fprintf(ficresvij,"%.0f ",age );          sum -= a[i][k]*a[k][j]; 
     for(i=1; i<=nlstate;i++)        a[i][j]=sum; 
       for(j=1; j<=nlstate;j++){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          big=dum; 
       }          imax=i; 
     fprintf(ficresvij,"\n");        } 
     free_matrix(gp,0,nhstepm,1,nlstate);      } 
     free_matrix(gm,0,nhstepm,1,nlstate);      if (j != imax) { 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for (k=1;k<=n;k++) { 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          dum=a[imax][k]; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          a[imax][k]=a[j][k]; 
   } /* End age */          a[j][k]=dum; 
   free_vector(gpp,nlstate+1,nlstate+ndeath);        } 
   free_vector(gmp,nlstate+1,nlstate+ndeath);        *d = -(*d); 
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);        vv[imax]=vv[j]; 
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/      } 
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");      indx[j]=imax; 
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */      if (a[j][j] == 0.0) a[j][j]=TINY; 
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");      if (j != n) { 
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);        dum=1.0/(a[j][j]); 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);      } 
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);    } 
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months 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);    free_vector(vv,1,n);  /* Doesn't work */
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);  ;
   } 
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,nlstate);  void lubksb(double **a, int n, int *indx, double b[]) 
   free_matrix(dnewm,1,nlstate,1,npar);  { 
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    int i,ii=0,ip,j; 
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);    double sum; 
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);   
   fclose(ficresprobmorprev);    for (i=1;i<=n;i++) { 
   fclose(ficgp);      ip=indx[i]; 
   fclose(fichtm);      sum=b[ip]; 
       b[ip]=b[i]; 
 }      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 /************ Variance of prevlim ******************/      else if (sum) ii=i; 
 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)      b[i]=sum; 
 {    } 
   /* Variance of prevalence limit */    for (i=n;i>=1;i--) { 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      sum=b[i]; 
   double **newm;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   double **dnewm,**doldm;      b[i]=sum/a[i][i]; 
   int i, j, nhstepm, hstepm;    } 
   int k, cptcode;  } 
   double *xp;  
   double *gp, *gm;  void pstamp(FILE *fichier)
   double **gradg, **trgradg;  {
   double age,agelim;    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   int theta;  }
      
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");  /************ Frequencies ********************/
   fprintf(ficresvpl,"# Age");  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[])
   for(i=1; i<=nlstate;i++)  {  /* Some frequencies */
       fprintf(ficresvpl," %1d-%1d",i,i);    
   fprintf(ficresvpl,"\n");    int i, m, jk, k1,i1, j1, bool, z1,j;
     int first;
   xp=vector(1,npar);    double ***freq; /* Frequencies */
   dnewm=matrix(1,nlstate,1,npar);    double *pp, **prop;
   doldm=matrix(1,nlstate,1,nlstate);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
      char fileresp[FILENAMELENGTH];
   hstepm=1*YEARM; /* Every year of age */    
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    pp=vector(1,nlstate);
   agelim = AGESUP;    prop=matrix(1,nlstate,iagemin,iagemax+3);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    strcpy(fileresp,"p");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    strcat(fileresp,fileres);
     if (stepm >= YEARM) hstepm=1;    if((ficresp=fopen(fileresp,"w"))==NULL) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      printf("Problem with prevalence resultfile: %s\n", fileresp);
     gradg=matrix(1,npar,1,nlstate);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     gp=vector(1,nlstate);      exit(0);
     gm=vector(1,nlstate);    }
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     for(theta=1; theta <=npar; theta++){    j1=0;
       for(i=1; i<=npar; i++){ /* Computes gradient */    
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    j=cptcoveff;
       }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    first=1;
         gp[i] = prlim[i][i];  
        for(k1=1; k1<=j;k1++){
       for(i=1; i<=npar; i++) /* Computes gradient */      for(i1=1; i1<=ncodemax[k1];i1++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        j1++;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       for(i=1;i<=nlstate;i++)          scanf("%d", i);*/
         gm[i] = prlim[i][i];        for (i=-5; i<=nlstate+ndeath; i++)  
           for (jk=-5; jk<=nlstate+ndeath; jk++)  
       for(i=1;i<=nlstate;i++)            for(m=iagemin; m <= iagemax+3; m++)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];              freq[i][jk][m]=0;
     } /* End theta */  
       for (i=1; i<=nlstate; i++)  
     trgradg =matrix(1,nlstate,1,npar);        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
     for(j=1; j<=nlstate;j++)        
       for(theta=1; theta <=npar; theta++)        dateintsum=0;
         trgradg[j][theta]=gradg[theta][j];        k2cpt=0;
         for (i=1; i<=imx; i++) {
     for(i=1;i<=nlstate;i++)          bool=1;
       varpl[i][(int)age] =0.;          if  (cptcovn>0) {
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            for (z1=1; z1<=cptcoveff; z1++) 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for(i=1;i<=nlstate;i++)                bool=0;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          }
           if (bool==1){
     fprintf(ficresvpl,"%.0f ",age );            for(m=firstpass; m<=lastpass; m++){
     for(i=1; i<=nlstate;i++)              k2=anint[m][i]+(mint[m][i]/12.);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     fprintf(ficresvpl,"\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     free_vector(gp,1,nlstate);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     free_vector(gm,1,nlstate);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     free_matrix(gradg,1,npar,1,nlstate);                if (m<lastpass) {
     free_matrix(trgradg,1,nlstate,1,npar);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   } /* End age */                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                 }
   free_vector(xp,1,npar);                
   free_matrix(doldm,1,nlstate,1,npar);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   free_matrix(dnewm,1,nlstate,1,nlstate);                  dateintsum=dateintsum+k2;
                   k2cpt++;
 }                }
                 /*}*/
 /************ 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)          }
 {        }
   int i, j=0,  i1, k1, l1, t, tj;         
   int k2, l2, j1,  z1;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   int k=0,l, cptcode;        pstamp(ficresp);
   int first=1, first1;        if  (cptcovn>0) {
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;          fprintf(ficresp, "\n#********** Variable "); 
   double **dnewm,**doldm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double *xp;          fprintf(ficresp, "**********\n#");
   double *gp, *gm;        }
   double **gradg, **trgradg;        for(i=1; i<=nlstate;i++) 
   double **mu;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double age,agelim, cov[NCOVMAX];        fprintf(ficresp, "\n");
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */        
   int theta;        for(i=iagemin; i <= iagemax+3; i++){
   char fileresprob[FILENAMELENGTH];          if(i==iagemax+3){
   char fileresprobcov[FILENAMELENGTH];            fprintf(ficlog,"Total");
   char fileresprobcor[FILENAMELENGTH];          }else{
             if(first==1){
   double ***varpij;              first=0;
               printf("See log file for details...\n");
   strcpy(fileresprob,"prob");            }
   strcat(fileresprob,fileres);            fprintf(ficlog,"Age %d", i);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          }
     printf("Problem with resultfile: %s\n", fileresprob);          for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   }              pp[jk] += freq[jk][m][i]; 
   strcpy(fileresprobcov,"probcov");          }
   strcat(fileresprobcov,fileres);          for(jk=1; jk <=nlstate ; jk++){
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {            for(m=-1, pos=0; m <=0 ; m++)
     printf("Problem with resultfile: %s\n", fileresprobcov);              pos += freq[jk][m][i];
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);            if(pp[jk]>=1.e-10){
   }              if(first==1){
   strcpy(fileresprobcor,"probcor");                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   strcat(fileresprobcor,fileres);              }
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     printf("Problem with resultfile: %s\n", fileresprobcor);            }else{
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);              if(first==1)
   }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);            }
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);          }
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);          for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                pp[jk] += freq[jk][m][i];
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");          }       
   fprintf(ficresprob,"# Age");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");            pos += pp[jk];
   fprintf(ficresprobcov,"# Age");            posprop += prop[jk][i];
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");          }
   fprintf(ficresprobcov,"# Age");          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
               if(first==1)
   for(i=1; i<=nlstate;i++)                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(j=1; j<=(nlstate+ndeath);j++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);            }else{
       fprintf(ficresprobcov," p%1d-%1d ",i,j);              if(first==1)
       fprintf(ficresprobcor," p%1d-%1d ",i,j);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }                fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficresprob,"\n");            }
   fprintf(ficresprobcov,"\n");            if( i <= iagemax){
   fprintf(ficresprobcor,"\n");              if(pos>=1.e-5){
   xp=vector(1,npar);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);                /*probs[i][jk][j1]= pp[jk]/pos;*/
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);              }
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);              else
   first=1;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            }
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          }
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);          
     exit(0);          for(jk=-1; jk <=nlstate+ndeath; jk++)
   }            for(m=-1; m <=nlstate+ndeath; m++)
   else{              if(freq[jk][m][i] !=0 ) {
     fprintf(ficgp,"\n# Routine varprob");              if(first==1)
   }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     printf("Problem with html file: %s\n", optionfilehtm);              }
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);          if(i <= iagemax)
     exit(0);            fprintf(ficresp,"\n");
   }          if(first==1)
   else{            printf("Others in log...\n");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");          fprintf(ficlog,"\n");
     fprintf(fichtm,"\n");        }
       }
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");    }
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");    dateintmean=dateintsum/k2cpt; 
     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");   
     fclose(ficresp);
   }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
      free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   cov[1]=1;    /* End of Freq */
   tj=cptcoveff;  }
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}  
   j1=0;  /************ Prevalence ********************/
   for(t=1; t<=tj;t++){  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)
     for(i1=1; i1<=ncodemax[t];i1++){  {  
       j1++;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
             in each health status at the date of interview (if between dateprev1 and dateprev2).
       if  (cptcovn>0) {       We still use firstpass and lastpass as another selection.
         fprintf(ficresprob, "\n#********** Variable ");    */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);   
         fprintf(ficresprob, "**********\n#");    int i, m, jk, k1, i1, j1, bool, z1,j;
         fprintf(ficresprobcov, "\n#********** Variable ");    double ***freq; /* Frequencies */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double *pp, **prop;
         fprintf(ficresprobcov, "**********\n#");    double pos,posprop; 
            double  y2; /* in fractional years */
         fprintf(ficgp, "\n#********** Variable ");    int iagemin, iagemax;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficgp, "**********\n#");    iagemin= (int) agemin;
            iagemax= (int) agemax;
            /*pp=vector(1,nlstate);*/
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");    j1=0;
            
         fprintf(ficresprobcor, "\n#********** Variable ");        j=cptcoveff;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         fprintf(ficgp, "**********\n#");        
       }    for(k1=1; k1<=j;k1++){
            for(i1=1; i1<=ncodemax[k1];i1++){
       for (age=bage; age<=fage; age ++){        j1++;
         cov[2]=age;        
         for (k=1; k<=cptcovn;k++) {        for (i=1; i<=nlstate; i++)  
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          for(m=iagemin; m <= iagemax+3; m++)
         }            prop[i][m]=0.0;
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       
         for (k=1; k<=cptcovprod;k++)        for (i=1; i<=imx; i++) { /* Each individual */
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          bool=1;
                  if  (cptcovn>0) {
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));            for (z1=1; z1<=cptcoveff; z1++) 
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         gp=vector(1,(nlstate)*(nlstate+ndeath));                bool=0;
         gm=vector(1,(nlstate)*(nlstate+ndeath));          } 
              if (bool==1) { 
         for(theta=1; theta <=npar; theta++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           for(i=1; i<=npar; i++)              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
             xp[i] = x[i] + (i==theta ?delti[theta]:0);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                          if(agev[m][i]==0) agev[m][i]=iagemax+1;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                          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); 
           k=0;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           for(i=1; i<= (nlstate); i++){                  /*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]]);*/
             for(j=1; j<=(nlstate+ndeath);j++){                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
               k=k+1;                  prop[s[m][i]][iagemax+3] += weight[i]; 
               gp[k]=pmmij[i][j];                } 
             }              }
           }            } /* end selection of waves */
                    }
           for(i=1; i<=npar; i++)        }
             xp[i] = x[i] - (i==theta ?delti[theta]:0);        for(i=iagemin; i <= iagemax+3; i++){  
              
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           k=0;            posprop += prop[jk][i]; 
           for(i=1; i<=(nlstate); i++){          } 
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;          for(jk=1; jk <=nlstate ; jk++){     
               gm[k]=pmmij[i][j];            if( i <=  iagemax){ 
             }              if(posprop>=1.e-5){ 
           }                probs[i][jk][j1]= prop[jk][i]/posprop;
                    } else
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              } 
         }          }/* end jk */ 
         }/* end i */ 
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)      } /* end i1 */
           for(theta=1; theta <=npar; theta++)    } /* end k1 */
             trgradg[j][theta]=gradg[theta][j];    
            /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    /*free_vector(pp,1,nlstate);*/
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
          }  /* End of prevalence */
         pmij(pmmij,cov,ncovmodel,x,nlstate);  
          /************* Waves Concatenation ***************/
         k=0;  
         for(i=1; i<=(nlstate); i++){  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
           for(j=1; j<=(nlstate+ndeath);j++){  {
             k=k+1;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
             mu[k][(int) age]=pmmij[i][j];       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
         }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)       and mw[mi+1][i]. dh depends on stepm.
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)       */
             varpij[i][j][(int)age] = doldm[i][j];  
     int i, mi, m;
         /*printf("\n%d ",(int)age);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){       double sum=0., jmean=0.;*/
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    int first;
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    int j, k=0,jk, ju, jl;
      }*/    double sum=0.;
     first=0;
         fprintf(ficresprob,"\n%d ",(int)age);    jmin=1e+5;
         fprintf(ficresprobcov,"\n%d ",(int)age);    jmax=-1;
         fprintf(ficresprobcor,"\n%d ",(int)age);    jmean=0.;
     for(i=1; i<=imx; i++){
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)      mi=0;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));      m=firstpass;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){      while(s[m][i] <= nlstate){
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);          mw[++mi][i]=m;
         }        if(m >=lastpass)
         i=0;          break;
         for (k=1; k<=(nlstate);k++){        else
           for (l=1; l<=(nlstate+ndeath);l++){          m++;
             i=i++;      }/* end while */
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);      if (s[m][i] > nlstate){
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);        mi++;     /* Death is another wave */
             for (j=1; j<=i;j++){        /* if(mi==0)  never been interviewed correctly before death */
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);           /* Only death is a correct wave */
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));        mw[mi][i]=m;
             }      }
           }  
         }/* end of loop for state */      wav[i]=mi;
       } /* end of loop for age */      if(mi==0){
         nbwarn++;
       /* Confidence intervalle of pij  */        if(first==0){
       /*          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       fprintf(ficgp,"\nset noparametric;unset label");          first=1;
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");        }
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        if(first==1){
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);        }
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);      } /* end mi==0 */
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);    } /* End individuals */
       */  
     for(i=1; i<=imx; i++){
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/      for(mi=1; mi<wav[i];mi++){
       first1=1;        if (stepm <=0)
       for (k2=1; k2<=(nlstate);k2++){          dh[mi][i]=1;
         for (l2=1; l2<=(nlstate+ndeath);l2++){        else{
           if(l2==k2) continue;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           j=(k2-1)*(nlstate+ndeath)+l2;            if (agedc[i] < 2*AGESUP) {
           for (k1=1; k1<=(nlstate);k1++){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             for (l1=1; l1<=(nlstate+ndeath);l1++){              if(j==0) j=1;  /* Survives at least one month after exam */
               if(l1==k1) continue;              else if(j<0){
               i=(k1-1)*(nlstate+ndeath)+l1;                nberr++;
               if(i<=j) continue;                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               for (age=bage; age<=fage; age ++){                j=1; /* Temporary Dangerous patch */
                 if ((int)age %5==0){                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);
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;                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]);
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;                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);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;              }
                   mu1=mu[i][(int) age]/stepm*YEARM ;              k=k+1;
                   mu2=mu[j][(int) age]/stepm*YEARM;              if (j >= jmax){
                   c12=cv12/sqrt(v1*v2);                jmax=j;
                   /* Computing eigen value of matrix of covariance */                ijmax=i;
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;              }
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;              if (j <= jmin){
                   /* Eigen vectors */                jmin=j;
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));                ijmin=i;
                   /*v21=sqrt(1.-v11*v11); *//* error */              }
                   v21=(lc1-v1)/cv12*v11;              sum=sum+j;
                   v12=-v21;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                   v22=v11;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                   tnalp=v21/v11;            }
                   if(first1==1){          }
                     first1=0;          else{
                     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);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
                   }  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
                   fprintf(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);  
                   /*printf(fignu*/            k=k+1;
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */            if (j >= jmax) {
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */              jmax=j;
                   if(first==1){              ijmax=i;
                     first=0;            }
                     fprintf(ficgp,"\nset parametric;unset label");            else if (j <= jmin){
                     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);              jmin=j;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");              ijmin=i;
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);            }
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);            if(j<0){
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);              nberr++;
                     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",\              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]);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));            }
                   }else{            sum=sum+j;
                     first=0;          }
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);          jk= j/stepm;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);          jl= j -jk*stepm;
                     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",\          ju= j -(jk+1)*stepm;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));            if(jl==0){
                   }/* if first */              dh[mi][i]=jk;
                 } /* age mod 5 */              bh[mi][i]=0;
               } /* end loop age */            }else{ /* We want a negative bias in order to only have interpolation ie
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);                    * at the price of an extra matrix product in likelihood */
               first=1;              dh[mi][i]=jk+1;
             } /*l12 */              bh[mi][i]=ju;
           } /* k12 */            }
         } /*l1 */          }else{
       }/* k1 */            if(jl <= -ju){
     } /* loop covariates */              dh[mi][i]=jk;
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);              bh[mi][i]=jl;       /* bias is positive if real duration
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));                                   * is higher than the multiple of stepm and negative otherwise.
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));                                   */
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);            }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            else{
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              dh[mi][i]=jk+1;
   }              bh[mi][i]=ju;
   free_vector(xp,1,npar);            }
   fclose(ficresprob);            if(dh[mi][i]==0){
   fclose(ficresprobcov);              dh[mi][i]=1; /* At least one step */
   fclose(ficresprobcor);              bh[mi][i]=ju; /* At least one step */
   fclose(ficgp);              /*  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);*/
   fclose(fichtm);            }
 }          } /* end if mle */
         }
       } /* end wave */
 /******************* Printing html file ***********/    }
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    jmean=sum/k;
                   int lastpass, int stepm, int weightopt, char model[],\    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    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);
                   int popforecast, int estepm ,\   }
                   double jprev1, double mprev1,double anprev1, \  
                   double jprev2, double mprev2,double anprev2){  /*********** Tricode ****************************/
   int jj1, k1, i1, cpt;  void tricode(int *Tvar, int **nbcode, int imx)
   /*char optionfilehtm[FILENAMELENGTH];*/  {
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    
     printf("Problem with %s \n",optionfilehtm), exit(0);    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);  
   }    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     int cptcode=0;
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n    cptcoveff=0; 
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n   
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    for (k=0; k<maxncov; k++) Ndum[k]=0;
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
  - Life expectancies by age and initial health status (estepm=%2d months):  
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
         Ndum[ij]++; /*counts the occurence of this modality */
  m=cptcoveff;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        if (ij > cptcode) cptcode=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 0 and 
  jj1=0;                                         female is 1, then  cptcode=1.*/
  for(k1=1; k1<=m;k1++){      }
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;      for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
      if (cptcovn > 0) {        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                                         th covariate. In fact
        for (cpt=1; cpt<=cptcoveff;cpt++)                                         ncodemax[j]=2
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);                                         (dichotom. variables only) but
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                                         it can be more */
      }      } /* Ndum[-1] number of undefined modalities */
      /* 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>      ij=1; 
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
      /* Quasi-incidences */        for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
      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>          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
        /* Stable prevalence in each health state */                                       k is a modality. If we have model=V1+V1*sex 
        for(cpt=1; cpt<nlstate;cpt++){                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>            ij++;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          }
        }          if (ij > ncodemax[j]) break; 
      for(cpt=1; cpt<=nlstate;cpt++) {        }  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>      } 
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    }  
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and   for (k=0; k< maxncov; k++) Ndum[k]=0;
 health expectancies in states (1) and (2): e%s%d.png<br>  
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
    } /* end i1 */     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
  }/* End k1 */     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
  fprintf(fichtm,"</ul>");     Ndum[ij]++;
    }
   
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n   ij=1;
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n   for (i=1; i<= maxncov; i++) {
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n     if((Ndum[i]!=0) && (i<=ncovcol)){
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n       Tvaraff[ij]=i; /*For printing */
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n       ij++;
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n     }
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n   }
  - 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);   ij--;
    cptcoveff=ij; /*Number of simple covariates*/
  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  /*********** Health Expectancies ****************/
         <br>",fileres,fileres,fileres,fileres);  
  else  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);  
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");  {
     /* Health expectancies, no variances */
  m=cptcoveff;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
  jj1=0;    double ***p3mat;
  for(k1=1; k1<=m;k1++){    double eip;
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;    pstamp(ficreseij);
      if (cptcovn > 0) {    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    fprintf(ficreseij,"# Age");
        for (cpt=1; cpt<=cptcoveff;cpt++)    for(i=1; i<=nlstate;i++){
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      for(j=1; j<=nlstate;j++){
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        fprintf(ficreseij," e%1d%1d ",i,j);
      }      }
      for(cpt=1; cpt<=nlstate;cpt++) {      fprintf(ficreseij," e%1d. ",i);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    }
 interval) in state (%d): v%s%d%d.png <br>    fprintf(ficreseij,"\n");
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
      }    
    } /* end i1 */    if(estepm < stepm){
  }/* End k1 */      printf ("Problem %d lower than %d\n",estepm, stepm);
  fprintf(fichtm,"</ul>");    }
 fclose(fichtm);    else  hstepm=estepm;   
 }    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
 /******************* Gnuplot file **************/     * if stepm=24 months pijx are given only every 2 years and by summing them
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;     * to the curvature of the survival function. If, for the same date, we 
   int ng;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {     * to compare the new estimate of Life expectancy with the same linear 
     printf("Problem with file %s",optionfilegnuplot);     * hypothesis. A more precise result, taking into account a more precise
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);     * curvature will be obtained if estepm is as small as stepm. */
   }  
     /* For example we decided to compute the life expectancy with the smallest unit */
 #ifdef windows    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     fprintf(ficgp,"cd \"%s\" \n",pathc);       nhstepm is the number of hstepm from age to agelim 
 #endif       nstepm is the number of stepm from age to agelin. 
 m=pow(2,cptcoveff);       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like estepm months */
  /* 1eme*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   for (cpt=1; cpt<= nlstate ; cpt ++) {       survival function given by stepm (the optimization length). Unfortunately it
    for (k1=1; k1<= m ; k1 ++) {       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 
 #ifdef windows       results. So we changed our mind and took the option of the best precision.
      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);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 #endif  
 #ifdef unix    agelim=AGESUP;
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    /* If stepm=6 months */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 #endif         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
 for (i=1; i<= nlstate ; i ++) {  /* nhstepm age range expressed in number of stepm */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 }    /* if (stepm >= YEARM) hstepm=1;*/
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for (i=1; i<= nlstate ; i ++) {    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (age=bage; age<=fage; age ++){ 
 }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      for (i=1; i<= nlstate ; i ++) {      /* if (stepm >= YEARM) hstepm=1;*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        /* If stepm=6 months */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      /* Computed by stepm unit matrices, product of hstepma matrices, stored
 #ifdef unix         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");      
 #endif      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
    }      
   }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   /*2 eme*/      
       printf("%d|",(int)age);fflush(stdout);
   for (k1=1; k1<= m ; k1 ++) {      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      /* Computing expectancies */
          for(i=1; i<=nlstate;i++)
     for (i=1; i<= nlstate+1 ; i ++) {        for(j=1; j<=nlstate;j++)
       k=2*i;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       for (j=1; j<= nlstate+1 ; j ++) {            
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            /* 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]);*/
   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(ficreseij,"%3.0f",age );
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(i=1; i<=nlstate;i++){
       for (j=1; j<= nlstate+1 ; j ++) {        eip=0;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<=nlstate;j++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");          eip +=eij[i][j][(int)age];
 }            fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
       fprintf(ficgp,"\" t\"\" w l 0,");        }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficreseij,"%9.4f", eip );
       for (j=1; j<= nlstate+1 ; j ++) {      }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficreseij,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");      
 }      }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       else fprintf(ficgp,"\" t\"\" w l 0,");    printf("\n");
     }    fprintf(ficlog,"\n");
   }    
    }
   /*3eme*/  
   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {  {
       k=2+nlstate*(2*cpt-2);    /* Covariances of health expectancies eij and of total life expectancies according
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);     to initial status i, ei. .
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    */
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    int nhstepma, nstepma; /* Decreasing with age */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    double age, agelim, hf;
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    double ***p3matp, ***p3matm, ***varhe;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    double **dnewm,**doldm;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    double *xp, *xm;
     double **gp, **gm;
 */    double ***gradg, ***trgradg;
       for (i=1; i< nlstate ; i ++) {    int theta;
         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);  
     double eip, vip;
       }  
     }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   }    xp=vector(1,npar);
      xm=vector(1,npar);
   /* CV preval stat */    dnewm=matrix(1,nlstate*nlstate,1,npar);
     for (k1=1; k1<= m ; k1 ++) {    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     for (cpt=1; cpt<nlstate ; cpt ++) {    
       k=3;    pstamp(ficresstdeij);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for (i=1; i< nlstate ; i ++)      for(j=1; j<=nlstate;j++)
         fprintf(ficgp,"+$%d",k+i+1);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      fprintf(ficresstdeij," e%1d. ",i);
          }
       l=3+(nlstate+ndeath)*cpt;    fprintf(ficresstdeij,"\n");
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {    pstamp(ficrescveij);
         l=3+(nlstate+ndeath)*cpt;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
         fprintf(ficgp,"+$%d",l+i+1);    fprintf(ficrescveij,"# Age");
       }    for(i=1; i<=nlstate;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        for(j=1; j<=nlstate;j++){
     }        cptj= (j-1)*nlstate+i;
   }          for(i2=1; i2<=nlstate;i2++)
            for(j2=1; j2<=nlstate;j2++){
   /* proba elementaires */            cptj2= (j2-1)*nlstate+i2;
    for(i=1,jk=1; i <=nlstate; i++){            if(cptj2 <= cptj)
     for(k=1; k <=(nlstate+ndeath); k++){              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
       if (k != i) {          }
         for(j=1; j <=ncovmodel; j++){      }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(ficrescveij,"\n");
           jk++;    
           fprintf(ficgp,"\n");    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
       }    }
     }    else  hstepm=estepm;   
    }    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/     * if stepm=24 months pijx are given only every 2 years and by summing them
      for(jk=1; jk <=m; jk++) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);     * progression in between and thus overestimating or underestimating according
        if (ng==2)     * to the curvature of the survival function. If, for the same date, we 
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
        else     * to compare the new estimate of Life expectancy with the same linear 
          fprintf(ficgp,"\nset title \"Probability\"\n");     * hypothesis. A more precise result, taking into account a more precise
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);     * curvature will be obtained if estepm is as small as stepm. */
        i=1;  
        for(k2=1; k2<=nlstate; k2++) {    /* For example we decided to compute the life expectancy with the smallest unit */
          k3=i;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
          for(k=1; k<=(nlstate+ndeath); k++) {       nhstepm is the number of hstepm from age to agelim 
            if (k != k2){       nstepm is the number of stepm from age to agelin. 
              if(ng==2)       Look at hpijx to understand the reason of that which relies in memory size
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);       and note for a fixed period like estepm months */
              else    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);       survival function given by stepm (the optimization length). Unfortunately it
              ij=1;       means that if the survival funtion is printed only each two years of age and if
              for(j=3; j <=ncovmodel; j++) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       results. So we changed our mind and took the option of the best precision.
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    */
                  ij++;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                }  
                else    /* If stepm=6 months */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* nhstepm age range expressed in number of stepm */
              }    agelim=AGESUP;
              fprintf(ficgp,")/(1");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
                  /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
              for(k1=1; k1 <=nlstate; k1++){      /* if (stepm >= YEARM) hstepm=1;*/
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                ij=1;    
                for(j=3; j <=ncovmodel; j++){    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                    ij++;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
                  }    gp=matrix(0,nhstepm,1,nlstate*nlstate);
                  else    gm=matrix(0,nhstepm,1,nlstate*nlstate);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
                }    for (age=bage; age<=fage; age ++){ 
                fprintf(ficgp,")");      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
              }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      /* if (stepm >= YEARM) hstepm=1;*/
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
              i=i+ncovmodel;  
            }      /* If stepm=6 months */
          } /* end k */      /* Computed by stepm unit matrices, product of hstepma matrices, stored
        } /* end k2 */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      } /* end jk */      
    } /* end ng */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    fclose(ficgp);  
 }  /* end gnuplot */      /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
 /*************** Moving average **************/      for(theta=1; theta <=npar; theta++){
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   int i, cpt, cptcod;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        }
       for (i=1; i<=nlstate;i++)        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
           mobaverage[(int)agedeb][i][cptcod]=0.;    
            for(j=1; j<= nlstate; j++){
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          for(i=1; i<=nlstate; i++){
       for (i=1; i<=nlstate;i++){            for(h=0; h<=nhstepm-1; h++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
           for (cpt=0;cpt<=4;cpt++){              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            }
           }          }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        }
         }       
       }        for(ij=1; ij<= nlstate*nlstate; ij++)
     }          for(h=0; h<=nhstepm-1; h++){
                gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
 }          }
       }/* End theta */
       
 /************** Forecasting ******************/      
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){      for(h=0; h<=nhstepm-1; h++)
          for(j=1; j<=nlstate*nlstate;j++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          for(theta=1; theta <=npar; theta++)
   int *popage;            trgradg[h][j][theta]=gradg[h][theta][j];
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      
   double *popeffectif,*popcount;  
   double ***p3mat;       for(ij=1;ij<=nlstate*nlstate;ij++)
   char fileresf[FILENAMELENGTH];        for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
  agelim=AGESUP;  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);       for(h=0;h<=nhstepm-1;h++){
          for(k=0;k<=nhstepm-1;k++){
            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   strcpy(fileresf,"f");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   strcat(fileresf,fileres);          for(ij=1;ij<=nlstate*nlstate;ij++)
   if((ficresf=fopen(fileresf,"w"))==NULL) {            for(ji=1;ji<=nlstate*nlstate;ji++)
     printf("Problem with forecast resultfile: %s\n", fileresf);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     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);      /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   if (mobilav==1) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     movingaverage(agedeb, fage, ageminpar, mobaverage);            
   }            /* 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]);*/
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;          }
   if (stepm<=12) stepsize=1;  
        fprintf(ficresstdeij,"%3.0f",age );
   agelim=AGESUP;      for(i=1; i<=nlstate;i++){
          eip=0.;
   hstepm=1;        vip=0.;
   hstepm=hstepm/stepm;        for(j=1; j<=nlstate;j++){
   yp1=modf(dateintmean,&yp);          eip += eij[i][j][(int)age];
   anprojmean=yp;          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   yp2=modf((yp1*12),&yp);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   mprojmean=yp;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   yp1=modf((yp2*30.5),&yp);        }
   jprojmean=yp;        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   if(jprojmean==0) jprojmean=1;      }
   if(mprojmean==0) jprojmean=1;      fprintf(ficresstdeij,"\n");
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      fprintf(ficrescveij,"%3.0f",age );
        for(i=1; i<=nlstate;i++)
   for(cptcov=1;cptcov<=i2;cptcov++){        for(j=1; j<=nlstate;j++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          cptj= (j-1)*nlstate+i;
       k=k+1;          for(i2=1; i2<=nlstate;i2++)
       fprintf(ficresf,"\n#******");            for(j2=1; j2<=nlstate;j2++){
       for(j=1;j<=cptcoveff;j++) {              cptj2= (j2-1)*nlstate+i2;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              if(cptj2 <= cptj)
       }                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
       fprintf(ficresf,"******\n");            }
       fprintf(ficresf,"# StartingAge FinalAge");        }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      fprintf(ficrescveij,"\n");
           
          }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         fprintf(ficresf,"\n");    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           nhstepm = nhstepm/hstepm;    printf("\n");
              fprintf(ficlog,"\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    free_vector(xm,1,npar);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      free_vector(xp,1,npar);
            free_matrix(dnewm,1,nlstate*nlstate,1,npar);
           for (h=0; h<=nhstepm; h++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
             if (h==(int) (calagedate+YEARM*cpt)) {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  }
             }  
             for(j=1; j<=nlstate+ndeath;j++) {  /************ Variance ******************/
               kk1=0.;kk2=0;  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
               for(i=1; i<=nlstate;i++) {                {
                 if (mobilav==1)    /* Variance of health expectancies */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                 else {    /* double **newm;*/
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double **dnewm,**doldm;
                 }    double **dnewmp,**doldmp;
                    int i, j, nhstepm, hstepm, h, nstepm ;
               }    int k, cptcode;
               if (h==(int)(calagedate+12*cpt)){    double *xp;
                 fprintf(ficresf," %.3f", kk1);    double **gp, **gm;  /* for var eij */
                            double ***gradg, ***trgradg; /*for var eij */
               }    double **gradgp, **trgradgp; /* for var p point j */
             }    double *gpp, *gmp; /* for var p point j */
           }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double ***p3mat;
         }    double age,agelim, hf;
       }    double ***mobaverage;
     }    int theta;
   }    char digit[4];
            char digitp[25];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     char fileresprobmorprev[FILENAMELENGTH];
   fclose(ficresf);  
 }    if(popbased==1){
 /************** Forecasting ******************/      if(mobilav!=0)
 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){        strcpy(digitp,"-populbased-mobilav-");
        else strcpy(digitp,"-populbased-nomobil-");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    }
   int *popage;    else 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      strcpy(digitp,"-stablbased-");
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;    if (mobilav!=0) {
   char filerespop[FILENAMELENGTH];      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   agelim=AGESUP;      }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    }
    
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    strcpy(fileresprobmorprev,"prmorprev"); 
      sprintf(digit,"%-d",ij);
      /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   strcpy(filerespop,"pop");    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   strcat(filerespop,fileres);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    strcat(fileresprobmorprev,fileres);
     printf("Problem with forecast resultfile: %s\n", filerespop);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   printf("Computing forecasting: result on file '%s' \n", filerespop);    }
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
   if (mobilav==1) {    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   }      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   if (stepm<=12) stepsize=1;    }  
      fprintf(ficresprobmorprev,"\n");
   agelim=AGESUP;    fprintf(ficgp,"\n# Routine varevsij");
      /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   hstepm=1;    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");
   hstepm=hstepm/stepm;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
    /*   } */
   if (popforecast==1) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if((ficpop=fopen(popfile,"r"))==NULL) {    pstamp(ficresvij);
       printf("Problem with population file : %s\n",popfile);exit(0);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);    if(popbased==1)
     }      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     popage=ivector(0,AGESUP);    else
     popeffectif=vector(0,AGESUP);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     popcount=vector(0,AGESUP);    fprintf(ficresvij,"# Age");
        for(i=1; i<=nlstate;i++)
     i=1;        for(j=1; j<=nlstate;j++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
        fprintf(ficresvij,"\n");
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    xp=vector(1,npar);
   }    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   for(cptcov=1;cptcov<=i2;cptcov++){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       k=k+1;  
       fprintf(ficrespop,"\n#******");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       for(j=1;j<=cptcoveff;j++) {    gpp=vector(nlstate+1,nlstate+ndeath);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    gmp=vector(nlstate+1,nlstate+ndeath);
       }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       fprintf(ficrespop,"******\n");    
       fprintf(ficrespop,"# Age");    if(estepm < stepm){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      printf ("Problem %d lower than %d\n",estepm, stepm);
       if (popforecast==1)  fprintf(ficrespop," [Population]");    }
          else  hstepm=estepm;   
       for (cpt=0; cpt<=0;cpt++) {    /* For example we decided to compute the life expectancy with the smallest unit */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
               nhstepm is the number of hstepm from age to agelim 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       nstepm is the number of stepm from age to agelin. 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       Look at function hpijx to understand why (it is linked to memory size questions) */
           nhstepm = nhstepm/hstepm;    /* 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
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       means that if the survival funtion is printed every two years of age and if
           oldm=oldms;savm=savms;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         results. So we changed our mind and took the option of the best precision.
            */
           for (h=0; h<=nhstepm; h++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             if (h==(int) (calagedate+YEARM*cpt)) {    agelim = AGESUP;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             for(j=1; j<=nlstate+ndeath;j++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               kk1=0.;kk2=0;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               for(i=1; i<=nlstate;i++) {                    gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                 if (mobilav==1)      gp=matrix(0,nhstepm,1,nlstate);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      gm=matrix(0,nhstepm,1,nlstate);
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }      for(theta=1; theta <=npar; theta++){
               }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
               if (h==(int)(calagedate+12*cpt)){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;        }
                   /*fprintf(ficrespop," %.3f", kk1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               }  
             }        if (popbased==1) {
             for(i=1; i<=nlstate;i++){          if(mobilav ==0){
               kk1=0.;            for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate;j++){              prlim[i][i]=probs[(int)age][i][ij];
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          }else{ /* mobilav */ 
                 }            for(i=1; i<=nlstate;i++)
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];              prlim[i][i]=mobaverage[(int)age][i][ij];
             }          }
         }
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        for(j=1; j<= nlstate; j++){
           }          for(h=0; h<=nhstepm; h++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       }          }
          }
   /******/        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {           as a weighted average of prlim.
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
           nhstepm = nhstepm/hstepm;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
                  }    
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* end probability of death */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           for (h=0; h<=nhstepm; h++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             if (h==(int) (calagedate+YEARM*cpt)) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             }   
             for(j=1; j<=nlstate+ndeath;j++) {        if (popbased==1) {
               kk1=0.;kk2=0;          if(mobilav ==0){
               for(i=1; i<=nlstate;i++) {                          for(i=1; i<=nlstate;i++)
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  prlim[i][i]=probs[(int)age][i][ij];
               }          }else{ /* mobilav */ 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            for(i=1; i<=nlstate;i++)
             }              prlim[i][i]=mobaverage[(int)age][i][ij];
           }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }  
       }        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
    }          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
         }
   if (popforecast==1) {        /* This for computing probability of death (h=1 means
     free_ivector(popage,0,AGESUP);           computed over hstepm matrices product = hstepm*stepm months) 
     free_vector(popeffectif,0,AGESUP);           as a weighted average of prlim.
     free_vector(popcount,0,AGESUP);        */
   }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   fclose(ficrespop);        }    
 }        /* end probability of death */
   
 /***********************************************/        for(j=1; j<= nlstate; j++) /* vareij */
 /**************** Main Program *****************/          for(h=0; h<=nhstepm; h++){
 /***********************************************/            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
 int main(int argc, char *argv[])  
 {        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        }
   double agedeb, agefin,hf;  
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      } /* End theta */
   
   double fret;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   double **xi,tmp,delta;  
       for(h=0; h<=nhstepm; h++) /* veij */
   double dum; /* Dummy variable */        for(j=1; j<=nlstate;j++)
   double ***p3mat;          for(theta=1; theta <=npar; theta++)
   int *indx;            trgradg[h][j][theta]=gradg[h][theta][j];
   char line[MAXLINE], linepar[MAXLINE];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   int firstobs=1, lastobs=10;        for(theta=1; theta <=npar; theta++)
   int sdeb, sfin; /* Status at beginning and end */          trgradgp[j][theta]=gradgp[theta][j];
   int c,  h , cpt,l;    
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      for(i=1;i<=nlstate;i++)
   int mobilav=0,popforecast=0;        for(j=1;j<=nlstate;j++)
   int hstepm, nhstepm;          vareij[i][j][(int)age] =0.;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  
       for(h=0;h<=nhstepm;h++){
   double bage, fage, age, agelim, agebase;        for(k=0;k<=nhstepm;k++){
   double ftolpl=FTOL;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   double **prlim;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   double *severity;          for(i=1;i<=nlstate;i++)
   double ***param; /* Matrix of parameters */            for(j=1;j<=nlstate;j++)
   double  *p;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   double **matcov; /* Matrix of covariance */        }
   double ***delti3; /* Scale */      }
   double *delti; /* Scale */    
   double ***eij, ***vareij;      /* pptj */
   double **varpl; /* Variances of prevalence limits by age */      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   double *epj, vepp;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   double kk1, kk2;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
            varppt[j][i]=doldmp[j][i];
       /* end ppptj */
   char *alph[]={"a","a","b","c","d","e"}, str[4];      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   char z[1]="c", occ;   
 #include <sys/time.h>      if (popbased==1) {
 #include <time.h>        if(mobilav ==0){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          for(i=1; i<=nlstate;i++)
              prlim[i][i]=probs[(int)age][i][ij];
   /* long total_usecs;        }else{ /* mobilav */ 
   struct timeval start_time, end_time;          for(i=1; i<=nlstate;i++)
              prlim[i][i]=mobaverage[(int)age][i][ij];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        }
   getcwd(pathcd, size);      }
                
   printf("\n%s",version);      /* This for computing probability of death (h=1 means
   if(argc <=1){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     printf("\nEnter the parameter file name: ");         as a weighted average of prlim.
     scanf("%s",pathtot);      */
   }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   else{        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     strcpy(pathtot,argv[1]);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   }      }    
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      /* end probability of death */
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   /* cutv(path,optionfile,pathtot,'\\');*/      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        for(i=1; i<=nlstate;i++){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   chdir(path);        }
   replace(pathc,path);      } 
       fprintf(ficresprobmorprev,"\n");
 /*-------- arguments in the command line --------*/  
       fprintf(ficresvij,"%.0f ",age );
   /* Log file */      for(i=1; i<=nlstate;i++)
   strcat(filelog, optionfilefiname);        for(j=1; j<=nlstate;j++){
   strcat(filelog,".log");    /* */          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   if((ficlog=fopen(filelog,"w"))==NULL)    {        }
     printf("Problem with logfile %s\n",filelog);      fprintf(ficresvij,"\n");
     goto end;      free_matrix(gp,0,nhstepm,1,nlstate);
   }      free_matrix(gm,0,nhstepm,1,nlstate);
   fprintf(ficlog,"Log filename:%s\n",filelog);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   fprintf(ficlog,"\n%s",version);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   fprintf(ficlog,"\nEnter the parameter file name: ");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    } /* End age */
   fflush(ficlog);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
   /* */    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   strcpy(fileres,"r");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   strcat(fileres, optionfilefiname);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
   strcat(fileres,".txt");    /* Other files have txt extension */    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*---------arguments file --------*/  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     printf("Problem with optionfile %s\n",optionfile);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     goto end;    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));
     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);
   strcpy(filereso,"o");    /*  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);
   strcat(filereso,fileres);  */
   if((ficparo=fopen(filereso,"w"))==NULL) {  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     printf("Problem with Output resultfile: %s\n", filereso);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);  
     goto end;    free_vector(xp,1,npar);
   }    free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
   /* Reads comments: lines beginning with '#' */    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     ungetc(c,ficpar);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fgets(line, MAXLINE, ficpar);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     puts(line);    fclose(ficresprobmorprev);
     fputs(line,ficparo);    fflush(ficgp);
   }    fflush(fichtm); 
   ungetc(c,ficpar);  }  /* end varevsij */
   
   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);  /************ Variance of prevlim ******************/
   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);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);  {
 while((c=getc(ficpar))=='#' && c!= EOF){    /* Variance of prevalence limit */
     ungetc(c,ficpar);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     fgets(line, MAXLINE, ficpar);    double **newm;
     puts(line);    double **dnewm,**doldm;
     fputs(line,ficparo);    int i, j, nhstepm, hstepm;
   }    int k, cptcode;
   ungetc(c,ficpar);    double *xp;
      double *gp, *gm;
        double **gradg, **trgradg;
   covar=matrix(0,NCOVMAX,1,n);    double age,agelim;
   cptcovn=0;    int theta;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    
     pstamp(ficresvpl);
   ncovmodel=2+cptcovn;    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    fprintf(ficresvpl,"# Age");
      for(i=1; i<=nlstate;i++)
   /* Read guess parameters */        fprintf(ficresvpl," %1d-%1d",i,i);
   /* Reads comments: lines beginning with '#' */    fprintf(ficresvpl,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    xp=vector(1,npar);
     fgets(line, MAXLINE, ficpar);    dnewm=matrix(1,nlstate,1,npar);
     puts(line);    doldm=matrix(1,nlstate,1,nlstate);
     fputs(line,ficparo);    
   }    hstepm=1*YEARM; /* Every year of age */
   ungetc(c,ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
      agelim = AGESUP;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     for(i=1; i <=nlstate; i++)      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     for(j=1; j <=nlstate+ndeath-1; j++){      if (stepm >= YEARM) hstepm=1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       fprintf(ficparo,"%1d%1d",i1,j1);      gradg=matrix(1,npar,1,nlstate);
       if(mle==1)      gp=vector(1,nlstate);
         printf("%1d%1d",i,j);      gm=vector(1,nlstate);
       fprintf(ficlog,"%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){      for(theta=1; theta <=npar; theta++){
         fscanf(ficpar," %lf",&param[i][j][k]);        for(i=1; i<=npar; i++){ /* Computes gradient */
         if(mle==1){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           printf(" %lf",param[i][j][k]);        }
           fprintf(ficlog," %lf",param[i][j][k]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         }        for(i=1;i<=nlstate;i++)
         else          gp[i] = prlim[i][i];
           fprintf(ficlog," %lf",param[i][j][k]);      
         fprintf(ficparo," %lf",param[i][j][k]);        for(i=1; i<=npar; i++) /* Computes gradient */
       }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fscanf(ficpar,"\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       if(mle==1)        for(i=1;i<=nlstate;i++)
         printf("\n");          gm[i] = prlim[i][i];
       fprintf(ficlog,"\n");  
       fprintf(ficparo,"\n");        for(i=1;i<=nlstate;i++)
     }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
        } /* End theta */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
       trgradg =matrix(1,nlstate,1,npar);
   p=param[1][1];  
        for(j=1; j<=nlstate;j++)
   /* Reads comments: lines beginning with '#' */        for(theta=1; theta <=npar; theta++)
   while((c=getc(ficpar))=='#' && c!= EOF){          trgradg[j][theta]=gradg[theta][j];
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      for(i=1;i<=nlstate;i++)
     puts(line);        varpl[i][(int)age] =0.;
     fputs(line,ficparo);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   ungetc(c,ficpar);      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      fprintf(ficresvpl,"%.0f ",age );
   for(i=1; i <=nlstate; i++){      for(i=1; i<=nlstate;i++)
     for(j=1; j <=nlstate+ndeath-1; j++){        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fscanf(ficpar,"%1d%1d",&i1,&j1);      fprintf(ficresvpl,"\n");
       printf("%1d%1d",i,j);      free_vector(gp,1,nlstate);
       fprintf(ficparo,"%1d%1d",i1,j1);      free_vector(gm,1,nlstate);
       for(k=1; k<=ncovmodel;k++){      free_matrix(gradg,1,npar,1,nlstate);
         fscanf(ficpar,"%le",&delti3[i][j][k]);      free_matrix(trgradg,1,nlstate,1,npar);
         printf(" %le",delti3[i][j][k]);    } /* End age */
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }    free_vector(xp,1,npar);
       fscanf(ficpar,"\n");    free_matrix(doldm,1,nlstate,1,npar);
       printf("\n");    free_matrix(dnewm,1,nlstate,1,nlstate);
       fprintf(ficparo,"\n");  
     }  }
   }  
   delti=delti3[1][1];  /************ 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[])
   /* Reads comments: lines beginning with '#' */  {
   while((c=getc(ficpar))=='#' && c!= EOF){    int i, j=0,  i1, k1, l1, t, tj;
     ungetc(c,ficpar);    int k2, l2, j1,  z1;
     fgets(line, MAXLINE, ficpar);    int k=0,l, cptcode;
     puts(line);    int first=1, first1;
     fputs(line,ficparo);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   }    double **dnewm,**doldm;
   ungetc(c,ficpar);    double *xp;
      double *gp, *gm;
   matcov=matrix(1,npar,1,npar);    double **gradg, **trgradg;
   for(i=1; i <=npar; i++){    double **mu;
     fscanf(ficpar,"%s",&str);    double age,agelim, cov[NCOVMAX];
     if(mle==1)    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       printf("%s",str);    int theta;
     fprintf(ficlog,"%s",str);    char fileresprob[FILENAMELENGTH];
     fprintf(ficparo,"%s",str);    char fileresprobcov[FILENAMELENGTH];
     for(j=1; j <=i; j++){    char fileresprobcor[FILENAMELENGTH];
       fscanf(ficpar," %le",&matcov[i][j]);  
       if(mle==1){    double ***varpij;
         printf(" %.5le",matcov[i][j]);  
         fprintf(ficlog," %.5le",matcov[i][j]);    strcpy(fileresprob,"prob"); 
       }    strcat(fileresprob,fileres);
       else    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
         fprintf(ficlog," %.5le",matcov[i][j]);      printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficparo," %.5le",matcov[i][j]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }    }
     fscanf(ficpar,"\n");    strcpy(fileresprobcov,"probcov"); 
     if(mle==1)    strcat(fileresprobcov,fileres);
       printf("\n");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     fprintf(ficlog,"\n");      printf("Problem with resultfile: %s\n", fileresprobcov);
     fprintf(ficparo,"\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   }    }
   for(i=1; i <=npar; i++)    strcpy(fileresprobcor,"probcor"); 
     for(j=i+1;j<=npar;j++)    strcat(fileresprobcor,fileres);
       matcov[i][j]=matcov[j][i];    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresprobcor);
   if(mle==1)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     printf("\n");    }
   fprintf(ficlog,"\n");    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     /*-------- Rewriting paramater file ----------*/    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      strcpy(rfileres,"r");    /* "Rparameterfile */    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      strcat(rfileres,".");    /* */    pstamp(ficresprob);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     if((ficres =fopen(rfileres,"w"))==NULL) {    fprintf(ficresprob,"# Age");
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    pstamp(ficresprobcov);
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     }    fprintf(ficresprobcov,"# Age");
     fprintf(ficres,"#%s\n",version);    pstamp(ficresprobcor);
        fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     /*-------- data file ----------*/    fprintf(ficresprobcor,"# Age");
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;  
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     n= lastobs;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     severity = vector(1,maxwav);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     outcome=imatrix(1,maxwav+1,1,n);      }  
     num=ivector(1,n);   /* fprintf(ficresprob,"\n");
     moisnais=vector(1,n);    fprintf(ficresprobcov,"\n");
     annais=vector(1,n);    fprintf(ficresprobcor,"\n");
     moisdc=vector(1,n);   */
     andc=vector(1,n);    xp=vector(1,npar);
     agedc=vector(1,n);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     cod=ivector(1,n);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     weight=vector(1,n);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     mint=matrix(1,maxwav,1,n);    first=1;
     anint=matrix(1,maxwav,1,n);    fprintf(ficgp,"\n# Routine varprob");
     s=imatrix(1,maxwav+1,1,n);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     adl=imatrix(1,maxwav+1,1,n);        fprintf(fichtm,"\n");
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);    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\
     i=1;    file %s<br>\n",optionfilehtmcov);
     while (fgets(line, MAXLINE, fic) != NULL)    {    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
       if ((i >= firstobs) && (i <=lastobs)) {  and drawn. It helps understanding how is the covariance between two incidences.\
           They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
         for (j=maxwav;j>=1;j--){    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
           strcpy(line,stra);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  standard deviations wide on each axis. <br>\
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
         }   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
          To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    cov[1]=1;
     tj=cptcoveff;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    j1=0;
     for(t=1; t<=tj;t++){
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      for(i1=1; i1<=ncodemax[t];i1++){ 
         for (j=ncovcol;j>=1;j--){        j1++;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        if  (cptcovn>0) {
         }          fprintf(ficresprob, "\n#********** Variable "); 
         num[i]=atol(stra);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(ficresprob, "**********\n#\n");
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          fprintf(ficresprobcov, "\n#********** Variable "); 
           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;}*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
         i=i+1;          
       }          fprintf(ficgp, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     /* printf("ii=%d", ij);          fprintf(ficgp, "**********\n#\n");
        scanf("%d",i);*/          
   imx=i-1; /* Number of individuals */          
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   /* for (i=1; i<=imx; i++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          fprintf(ficresprobcor, "\n#********** Variable ");    
     }*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    /*  for (i=1; i<=imx; i++){          fprintf(ficresprobcor, "**********\n#");    
      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 (age=bage; age<=fage; age ++){ 
            cov[2]=age;
   /* Calculation of the number of parameter from char model*/          for (k=1; k<=cptcovn;k++) {
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   Tprod=ivector(1,15);          }
   Tvaraff=ivector(1,15);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   Tvard=imatrix(1,15,1,2);          for (k=1; k<=cptcovprod;k++)
   Tage=ivector(1,15);                  cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
              
   if (strlen(model) >1){          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     j=0, j1=0, k1=1, k2=1;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     j=nbocc(model,'+');          gp=vector(1,(nlstate)*(nlstate+ndeath));
     j1=nbocc(model,'*');          gm=vector(1,(nlstate)*(nlstate+ndeath));
     cptcovn=j+1;      
     cptcovprod=j1;          for(theta=1; theta <=npar; theta++){
                for(i=1; i<=npar; i++)
     strcpy(modelsav,model);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            
       printf("Error. Non available option model=%s ",model);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fprintf(ficlog,"Error. Non available option model=%s ",model);            
       goto end;            k=0;
     }            for(i=1; i<= (nlstate); i++){
                  for(j=1; j<=(nlstate+ndeath);j++){
     for(i=(j+1); i>=1;i--){                k=k+1;
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */                gp[k]=pmmij[i][j];
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze 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 */            for(i=1; i<=npar; i++)
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
         if (strcmp(strc,"age")==0) { /* Vn*age */      
           cptcovprod--;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           cutv(strb,stre,strd,'V');            k=0;
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/            for(i=1; i<=(nlstate); i++){
           cptcovage++;              for(j=1; j<=(nlstate+ndeath);j++){
             Tage[cptcovage]=i;                k=k+1;
             /*printf("stre=%s ", stre);*/                gm[k]=pmmij[i][j];
         }              }
         else if (strcmp(strd,"age")==0) { /* or age*Vn */            }
           cptcovprod--;       
           cutv(strb,stre,strc,'V');            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
           Tvar[i]=atoi(stre);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           cptcovage++;          }
           Tage[cptcovage]=i;  
         }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
         else {  /* Age is not in the model */            for(theta=1; theta <=npar; theta++)
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/              trgradg[j][theta]=gradg[theta][j];
           Tvar[i]=ncovcol+k1;          
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           Tprod[k1]=i;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           Tvard[k1][1]=atoi(strc); /* m*/          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           Tvard[k1][2]=atoi(stre); /* n */          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           Tvar[cptcovn+k2]=Tvard[k1][1];          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           for (k=1; k<=lastobs;k++)  
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          pmij(pmmij,cov,ncovmodel,x,nlstate);
           k1++;          
           k2=k2+2;          k=0;
         }          for(i=1; i<=(nlstate); i++){
       }            for(j=1; j<=(nlstate+ndeath);j++){
       else { /* no more sum */              k=k+1;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/              mu[k][(int) age]=pmmij[i][j];
        /*  scanf("%d",i);*/            }
       cutv(strd,strc,strb,'V');          }
       Tvar[i]=atoi(strc);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       strcpy(modelsav,stra);                varpij[i][j][(int)age] = doldm[i][j];
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/          /*printf("\n%d ",(int)age);
     } /* end of loop + */            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   } /* end model */            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   /* printf("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);          fprintf(ficresprob,"\n%d ",(int)age);
   scanf("%d ",i);*/          fprintf(ficresprobcov,"\n%d ",(int)age);
     fclose(fic);          fprintf(ficresprobcor,"\n%d ",(int)age);
   
     /*  if(mle==1){*/          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     if (weightopt != 1) { /* Maximisation without weights*/            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       for(i=1;i<=n;i++) weight[i]=1.0;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     /*-calculation of age at interview from date of interview and age at death -*/            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     agev=matrix(1,maxwav,1,imx);          }
           i=0;
     for (i=1; i<=imx; i++) {          for (k=1; k<=(nlstate);k++){
       for(m=2; (m<= maxwav); m++) {            for (l=1; l<=(nlstate+ndeath);l++){ 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){              i=i++;
          anint[m][i]=9999;              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
          s[m][i]=-1;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
        }              for (j=1; j<=i;j++){
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;                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<=imx; i++)  {          }/* end of loop for state */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        } /* end of loop for age */
       for(m=1; (m<= maxwav); m++){  
         if(s[m][i] >0){        /* Confidence intervalle of pij  */
           if (s[m][i] >= nlstate+1) {        /*
             if(agedc[i]>0)          fprintf(ficgp,"\nunset parametric;unset label");
               if(moisdc[i]!=99 && andc[i]!=9999)          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
                 agev[m][i]=agedc[i];          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/          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);
            else {          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
               if (andc[i]!=9999){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);        */
               agev[m][i]=-1;  
               }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
             }        first1=1;
           }        for (k2=1; k2<=(nlstate);k2++){
           else if(s[m][i] !=9){ /* Should no more exist */          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            if(l2==k2) continue;
             if(mint[m][i]==99 || anint[m][i]==9999)            j=(k2-1)*(nlstate+ndeath)+l2;
               agev[m][i]=1;            for (k1=1; k1<=(nlstate);k1++){
             else if(agev[m][i] <agemin){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
               agemin=agev[m][i];                if(l1==k1) continue;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/                i=(k1-1)*(nlstate+ndeath)+l1;
             }                if(i<=j) continue;
             else if(agev[m][i] >agemax){                for (age=bage; age<=fage; age ++){ 
               agemax=agev[m][i];                  if ((int)age %5==0){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
             }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
             /*agev[m][i]=anint[m][i]-annais[i];*/                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
             /*   agev[m][i] = age[i]+2*m;*/                    mu1=mu[i][(int) age]/stepm*YEARM ;
           }                    mu2=mu[j][(int) age]/stepm*YEARM;
           else { /* =9 */                    c12=cv12/sqrt(v1*v2);
             agev[m][i]=1;                    /* Computing eigen value of matrix of covariance */
             s[m][i]=-1;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         }                    if ((lc2 <0) || (lc1 <0) ){
         else /*= 0 Unknown */                      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);
           agev[m][i]=1;                      fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
       }                      lc1=fabs(lc1);
                          lc2=fabs(lc2);
     }                    }
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){                    /* Eigen vectors */
         if (s[m][i] > (nlstate+ndeath)) {                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           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);                      /*v21=sqrt(1.-v11*v11); *//* error */
           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);                      v21=(lc1-v1)/cv12*v11;
           goto end;                    v12=-v21;
         }                    v22=v11;
       }                    tnalp=v21/v11;
     }                    if(first1==1){
                       first1=0;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                    }
                     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);
     free_vector(severity,1,maxwav);                    /*printf(fignu*/
     free_imatrix(outcome,1,maxwav+1,1,n);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     free_vector(moisnais,1,n);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     free_vector(annais,1,n);                    if(first==1){
     /* free_matrix(mint,1,maxwav,1,n);                      first=0;
        free_matrix(anint,1,maxwav,1,n);*/                      fprintf(ficgp,"\nset parametric;unset label");
     free_vector(moisdc,1,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);
     free_vector(andc,1,n);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
       :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
     wav=ivector(1,imx);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
     dh=imatrix(1,lastpass-firstpass+1,1,imx);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                          fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     /* Concatenates waves */                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);                      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);
       Tcode=ivector(1,100);                      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",\
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       ncodemax[1]=1;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                    }else{
                            first=0;
    codtab=imatrix(1,100,1,10);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
    h=0;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
    m=pow(2,cptcoveff);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                        fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
    for(k=1;k<=cptcoveff; k++){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
      for(i=1; i <=(m/pow(2,k));i++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
        for(j=1; j <= ncodemax[k]; j++){                    }/* if first */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                  } /* age mod 5 */
            h++;                } /* end loop age */
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                first=1;
          }              } /*l12 */
        }            } /* k12 */
      }          } /*l1 */
    }        }/* k1 */
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      } /* loop covariates */
       codtab[1][2]=1;codtab[2][2]=2; */    }
    /* for(i=1; i <=m ;i++){    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       for(k=1; k <=cptcovn; k++){    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       }    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
       printf("\n");    free_vector(xp,1,npar);
       }    fclose(ficresprob);
       scanf("%d",i);*/    fclose(ficresprobcov);
        fclose(ficresprobcor);
    /* Calculates basic frequencies. Computes observed prevalence at single age    fflush(ficgp);
        and prints on file fileres'p'. */    fflush(fichtmcov);
   }
      
      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /******************* Printing html file ***********/
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    int lastpass, int stepm, int weightopt, char model[],\
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                    int popforecast, int estepm ,\
                          double jprev1, double mprev1,double anprev1, \
     /* For Powell, parameters are in a vector p[] starting at p[1]                    double jprev2, double mprev2,double anprev2){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    int jj1, k1, i1, cpt;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     if(mle==1){     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  </ul>");
     }     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 ",
     /*--------- results files --------------*/             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);     fprintf(fichtm,"\
     - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
    jk=1;     fprintf(fichtm,"\
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");     fprintf(fichtm,"\
    for(i=1,jk=1; i <=nlstate; i++){   - (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): \
      for(k=1; k <=(nlstate+ndeath); k++){     <a href=\"%s\">%s</a> <br>\n",
        if (k != i)             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
          {     fprintf(fichtm,"\
            printf("%d%d ",i,k);   - Population projections by age and states: \
            fprintf(ficlog,"%d%d ",i,k);     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
              printf("%f ",p[jk]);  
              fprintf(ficlog,"%f ",p[jk]);   m=cptcoveff;
              fprintf(ficres,"%f ",p[jk]);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
              jk++;  
            }   jj1=0;
            printf("\n");   for(k1=1; k1<=m;k1++){
            fprintf(ficlog,"\n");     for(i1=1; i1<=ncodemax[k1];i1++){
            fprintf(ficres,"\n");       jj1++;
          }       if (cptcovn > 0) {
      }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
    }         for (cpt=1; cpt<=cptcoveff;cpt++) 
    if(mle==1){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
      /* Computing hessian and covariance matrix */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      ftolhess=ftol; /* Usually correct */       }
      hesscov(matcov, p, npar, delti, ftolhess, func);       /* Pij */
    }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
    printf("# Scales (for hessian or gradient estimation)\n");       /* Quasi-incidences */
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    for(i=1,jk=1; i <=nlstate; i++){   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> \
      for(j=1; j <=nlstate+ndeath; j++){  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        if (j!=i) {         /* Period (stable) prevalence in each health state */
          fprintf(ficres,"%1d%1d",i,j);         for(cpt=1; cpt<nlstate;cpt++){
          printf("%1d%1d",i,j);           fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
          fprintf(ficlog,"%1d%1d",i,j);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          for(k=1; k<=ncovmodel;k++){         }
            printf(" %.5e",delti[jk]);       for(cpt=1; cpt<=nlstate;cpt++) {
            fprintf(ficlog," %.5e",delti[jk]);          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> \
            fprintf(ficres," %.5e",delti[jk]);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
            jk++;       }
          }     } /* end i1 */
          printf("\n");   }/* End k1 */
          fprintf(ficlog,"\n");   fprintf(fichtm,"</ul>");
          fprintf(ficres,"\n");  
        }  
      }   fprintf(fichtm,"\
    }  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
       - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
    k=1;  
    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
    if(mle==1)           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
      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(fichtm,"\
    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");   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
    for(i=1;i<=npar;i++){           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
      /*  if (k>nlstate) k=1;  
          i1=(i-1)/(ncovmodel*nlstate)+1;   fprintf(fichtm,"\
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          printf("%s%d%d",alph[k],i1,tab[i]);*/           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
      fprintf(ficres,"%3d",i);   fprintf(fichtm,"\
      if(mle==1)   - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
        printf("%3d",i);     <a href=\"%s\">%s</a> <br>\n</li>",
      fprintf(ficlog,"%3d",i);             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
      for(j=1; j<=i;j++){   fprintf(fichtm,"\
        fprintf(ficres," %.5e",matcov[i][j]);   - (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): \
        if(mle==1)     <a href=\"%s\">%s</a> <br>\n</li>",
          printf(" %.5e",matcov[i][j]);             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
        fprintf(ficlog," %.5e",matcov[i][j]);   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",
      fprintf(ficres,"\n");           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
      if(mle==1)   fprintf(fichtm,"\
        printf("\n");   - 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",
      fprintf(ficlog,"\n");           estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
      k++;   fprintf(fichtm,"\
    }   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
               subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
    while((c=getc(ficpar))=='#' && c!= EOF){  
      ungetc(c,ficpar);  /*  if(popforecast==1) fprintf(fichtm,"\n */
      fgets(line, MAXLINE, ficpar);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
      puts(line);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
      fputs(line,ficparo);  /*      <br>",fileres,fileres,fileres,fileres); */
    }  /*  else  */
    ungetc(c,ficpar);  /*    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); */
    estepm=0;   fflush(fichtm);
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
    if (estepm==0 || estepm < stepm) estepm=stepm;  
    if (fage <= 2) {   m=cptcoveff;
      bage = ageminpar;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
      fage = agemaxpar;  
    }   jj1=0;
       for(k1=1; k1<=m;k1++){
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");     for(i1=1; i1<=ncodemax[k1];i1++){
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);       jj1++;
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);       if (cptcovn > 0) {
             fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
    while((c=getc(ficpar))=='#' && c!= EOF){         for (cpt=1; cpt<=cptcoveff;cpt++) 
      ungetc(c,ficpar);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
      fgets(line, MAXLINE, ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      puts(line);       }
      fputs(line,ficparo);       for(cpt=1; cpt<=nlstate;cpt++) {
    }         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
    ungetc(c,ficpar);  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);  
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);       }
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  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\
    while((c=getc(ficpar))=='#' && c!= EOF){   drawn in addition to the population based expectancies computed using\
      ungetc(c,ficpar);   observed and cahotic prevalences: %s%d.png<br>\
      fgets(line, MAXLINE, ficpar);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      puts(line);     } /* end i1 */
      fputs(line,ficparo);   }/* End k1 */
    }   fprintf(fichtm,"</ul>");
    ungetc(c,ficpar);   fflush(fichtm);
    }
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  /******************* Gnuplot file **************/
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    char dirfileres[132],optfileres[132];
   fprintf(ficparo,"pop_based=%d\n",popbased);      int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   fprintf(ficres,"pop_based=%d\n",popbased);      int ng=0;
    /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   while((c=getc(ficpar))=='#' && c!= EOF){  /*     printf("Problem with file %s",optionfilegnuplot); */
     ungetc(c,ficpar);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
     fgets(line, MAXLINE, ficpar);  /*   } */
     puts(line);  
     fputs(line,ficparo);    /*#ifdef windows */
   }    fprintf(ficgp,"cd \"%s\" \n",pathc);
   ungetc(c,ficpar);      /*#endif */
     m=pow(2,cptcoveff);
   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);    strcpy(dirfileres,optionfilefiname);
 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);    strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
 while((c=getc(ficpar))=='#' && c!= EOF){     for (k1=1; k1<= m ; k1 ++) {
     ungetc(c,ficpar);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
     fgets(line, MAXLINE, ficpar);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
     puts(line);       fprintf(ficgp,"set xlabel \"Age\" \n\
     fputs(line,ficparo);  set ylabel \"Probability\" \n\
   }  set ter png small\n\
   ungetc(c,ficpar);  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);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);       for (i=1; i<= nlstate ; i ++) {
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       }
        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);
 /*------------ gnuplot -------------*/       for (i=1; i<= nlstate ; i ++) {
   strcpy(optionfilegnuplot,optionfilefiname);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   strcat(optionfilegnuplot,".gp");         else fprintf(ficgp," \%%*lf (\%%*lf)");
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {       } 
     printf("Problem with file %s",optionfilegnuplot);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
   }       for (i=1; i<= nlstate ; i ++) {
   fclose(ficgp);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);         else fprintf(ficgp," \%%*lf (\%%*lf)");
 /*--------- index.htm --------*/       }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
   strcpy(optionfilehtm,optionfile);     }
   strcat(optionfilehtm,".htm");    }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    /*2 eme*/
     printf("Problem with %s \n",optionfilehtm), exit(0);    
   }    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      
 \n      for (i=1; i<= nlstate+1 ; i ++) {
 Total number of observations=%d <br>\n        k=2*i;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
 <hr  size=\"2\" color=\"#EC5E5E\">        for (j=1; j<= nlstate+1 ; j ++) {
  <ul><li><h4>Parameter files</h4>\n          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          else fprintf(ficgp," \%%*lf (\%%*lf)");
  - Log file of the run: <a href=\"%s\">%s</a><br>\n        }   
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   fclose(fichtm);        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);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);        for (j=1; j<= nlstate+1 ; j ++) {
            if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 /*------------ free_vector  -------------*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
  chdir(path);        }   
          fprintf(ficgp,"\" t\"\" w l 0,");
  free_ivector(wav,1,imx);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        for (j=1; j<= nlstate+1 ; j ++) {
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  free_ivector(num,1,n);          else fprintf(ficgp," \%%*lf (\%%*lf)");
  free_vector(agedc,1,n);        }   
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
  fclose(ficparo);        else fprintf(ficgp,"\" t\"\" w l 0,");
  fclose(ficres);      }
     }
     
   /*--------------- Prevalence limit --------------*/    /*3eme*/
      
   strcpy(filerespl,"pl");    for (k1=1; k1<= m ; k1 ++) { 
   strcat(filerespl,fileres);      for (cpt=1; cpt<= nlstate ; cpt ++) {
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        /*       k=2+nlstate*(2*cpt-2); */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        k=2+(nlstate+1)*(cpt-1);
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
   }        fprintf(ficgp,"set ter png small\n\
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  set size 0.65,0.65\n\
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);  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(ficrespl,"#Prevalence limit\n");        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   fprintf(ficrespl,"#Age ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   fprintf(ficrespl,"\n");          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) ");
   prlim=matrix(1,nlstate,1,nlstate);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   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 */        for (i=1; i< nlstate ; i ++) {
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          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);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          /*      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);*/
   k=0;          
   agebase=ageminpar;        } 
   agelim=agemaxpar;        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
   ftolpl=1.e-10;      }
   i1=cptcoveff;    }
   if (cptcovn < 1){i1=1;}    
     /* CV preval stable (period) */
   for(cptcov=1;cptcov<=i1;cptcov++){    for (k1=1; k1<= m ; k1 ++) { 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=k+1;        k=3;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficrespl,"\n#******");        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
         printf("\n#******");  set ter png small\nset size 0.65,0.65\n\
         fprintf(ficlog,"\n#******");  unset log y\n\
         for(j=1;j<=cptcoveff;j++) {  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for (i=1; i< nlstate ; i ++)
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"+$%d",k+i+1);
         }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         fprintf(ficrespl,"******\n");        
         printf("******\n");        l=3+(nlstate+ndeath)*cpt;
         fprintf(ficlog,"******\n");        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
                for (i=1; i< nlstate ; i ++) {
         for (age=agebase; age<=agelim; age++){          l=3+(nlstate+ndeath)*cpt;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          fprintf(ficgp,"+$%d",l+i+1);
           fprintf(ficrespl,"%.0f",age );        }
           for(i=1; i<=nlstate;i++)        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
           fprintf(ficrespl," %.5f", prlim[i][i]);      } 
           fprintf(ficrespl,"\n");    }  
         }    
       }    /* proba elementaires */
     }    for(i=1,jk=1; i <=nlstate; i++){
   fclose(ficrespl);      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
   /*------------- h Pij x at various ages ------------*/          for(j=1; j <=ncovmodel; j++){
              fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);            jk++; 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            fprintf(ficgp,"\n");
     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);  
       for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;       for(jk=1; jk <=m; jk++) {
   /*if (stepm<=24) stepsize=2;*/         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
   agelim=AGESUP;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   hstepm=stepsize*YEARM; /* Every year of age */         else
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */           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);
   /* hstepm=1;   aff par mois*/         i=1;
          for(k2=1; k2<=nlstate; k2++) {
   k=0;           k3=i;
   for(cptcov=1;cptcov<=i1;cptcov++){           for(k=1; k<=(nlstate+ndeath); k++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){             if (k != k2){
       k=k+1;               if(ng==2)
         fprintf(ficrespij,"\n#****** ");                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
         for(j=1;j<=cptcoveff;j++)               else
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
         fprintf(ficrespij,"******\n");               ij=1;
                       for(j=3; j <=ncovmodel; j++) {
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                   ij++;
                  }
           /*      nhstepm=nhstepm*YEARM; aff par mois*/                 else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);               }
           oldm=oldms;savm=savms;               fprintf(ficgp,")/(1");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                 
           fprintf(ficrespij,"# Age");               for(k1=1; k1 <=nlstate; k1++){   
           for(i=1; i<=nlstate;i++)                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
             for(j=1; j<=nlstate+ndeath;j++)                 ij=1;
               fprintf(ficrespij," %1d-%1d",i,j);                 for(j=3; j <=ncovmodel; j++){
           fprintf(ficrespij,"\n");                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
            for (h=0; h<=nhstepm; h++){                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                     ij++;
             for(i=1; i<=nlstate;i++)                   }
               for(j=1; j<=nlstate+ndeath;j++)                   else
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
             fprintf(ficrespij,"\n");                 }
              }                 fprintf(ficgp,")");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);               }
           fprintf(ficrespij,"\n");               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
         }               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     }               i=i+ncovmodel;
   }             }
            } /* end k */
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);         } /* end k2 */
        } /* end jk */
   fclose(ficrespij);     } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   /*---------- Forecasting ------------------*/  
   if((stepm == 1) && (strcmp(model,".")==0)){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  /*************** Moving average **************/
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   }  
   else{    int i, cpt, cptcod;
     erreur=108;    int modcovmax =1;
     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);    int mobilavrange, mob;
     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);    double age;
   }  
      modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
   /*---------- Health expectancies and variances ------------*/    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   strcpy(filerest,"t");    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   strcat(filerest,fileres);      if(mobilav==1) mobilavrange=5; /* default */
   if((ficrest=fopen(filerest,"w"))==NULL) {      else mobilavrange=mobilav;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      for (age=bage; age<=fage; age++)
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;        for (i=1; i<=nlstate;i++)
   }          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   printf("Computing Total LEs with variances: file '%s' \n", filerest);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);      /* 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. 
   strcpy(filerese,"e");      */ 
   strcat(filerese,fileres);      for (mob=3;mob <=mobilavrange;mob=mob+2){
   if((ficreseij=fopen(filerese,"w"))==NULL) {        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          for (i=1; i<=nlstate;i++){
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   strcpy(fileresv,"v");                }
   strcat(fileresv,fileres);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   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);        }/* end age */
   }      }/* end mob */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    }else return -1;
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    return 0;
   calagedate=-1;  }/* End movingaverage */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
   
   k=0;  /************** Forecasting ******************/
   for(cptcov=1;cptcov<=i1;cptcov++){  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* proj1, year, month, day of starting projection 
       k=k+1;       agemin, agemax range of age
       fprintf(ficrest,"\n#****** ");       dateprev1 dateprev2 range of dates during which prevalence is computed
       for(j=1;j<=cptcoveff;j++)       anproj2 year of en of projection (same day and month as proj1).
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    */
       fprintf(ficrest,"******\n");    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
       fprintf(ficreseij,"\n#****** ");    double agec; /* generic age */
       for(j=1;j<=cptcoveff;j++)    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double *popeffectif,*popcount;
       fprintf(ficreseij,"******\n");    double ***p3mat;
     double ***mobaverage;
       fprintf(ficresvij,"\n#****** ");    char fileresf[FILENAMELENGTH];
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    agelim=AGESUP;
       fprintf(ficresvij,"******\n");    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    strcpy(fileresf,"f"); 
       oldm=oldms;savm=savms;    strcat(fileresf,fileres);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      if((ficresf=fopen(fileresf,"w"))==NULL) {
        printf("Problem with forecast resultfile: %s\n", fileresf);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
       oldm=oldms;savm=savms;    }
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);    printf("Computing forecasting: result on file '%s' \n", fileresf);
       if(popbased==1){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);  
        }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
      if (mobilav!=0) {
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       fprintf(ficrest,"\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       epj=vector(1,nlstate+1);      }
       for(age=bage; age <=fage ;age++){    }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==1) {    stepsize=(int) (stepm+YEARM-1)/YEARM;
           for(i=1; i<=nlstate;i++)    if (stepm<=12) stepsize=1;
             prlim[i][i]=probs[(int)age][i][k];    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
            }
         fprintf(ficrest," %4.0f",age);    else  hstepm=estepm;   
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    hstepm=hstepm/stepm; 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                                 fractional in yp1 */
           }    anprojmean=yp;
           epj[nlstate+1] +=epj[j];    yp2=modf((yp1*12),&yp);
         }    mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
         for(i=1, vepp=0.;i <=nlstate;i++)    jprojmean=yp;
           for(j=1;j <=nlstate;j++)    if(jprojmean==0) jprojmean=1;
             vepp += vareij[i][j][(int)age];    if(mprojmean==0) jprojmean=1;
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));  
         for(j=1;j <=nlstate;j++){    i1=cptcoveff;
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    if (cptcovn < 1){i1=1;}
         }    
         fprintf(ficrest,"\n");    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");
   }  
 free_matrix(mint,1,maxwav,1,n);  /*            if (h==(int)(YEARM*yearp)){ */
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     free_vector(weight,1,n);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   fclose(ficreseij);        k=k+1;
   fclose(ficresvij);        fprintf(ficresf,"\n#******");
   fclose(ficrest);        for(j=1;j<=cptcoveff;j++) {
   fclose(ficpar);          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]]);
   free_vector(epj,1,nlstate+1);        }
          fprintf(ficresf,"******\n");
   /*------- Variance limit prevalence------*/          fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
   strcpy(fileresvpl,"vpl");          for(i=1; i<=nlstate;i++)              
   strcat(fileresvpl,fileres);            fprintf(ficresf," p%d%d",i,j);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          fprintf(ficresf," p.%d",j);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        }
     exit(0);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
   }          fprintf(ficresf,"\n");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
   k=0;          for (agec=fage; agec>=(ageminpar-1); agec--){ 
   for(cptcov=1;cptcov<=i1;cptcov++){            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            nhstepm = nhstepm/hstepm; 
       k=k+1;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficresvpl,"\n#****** ");            oldm=oldms;savm=savms;
       for(j=1;j<=cptcoveff;j++)            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          
       fprintf(ficresvpl,"******\n");            for (h=0; h<=nhstepm; h++){
                    if (h*hstepm/YEARM*stepm ==yearp) {
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                fprintf(ficresf,"\n");
       oldm=oldms;savm=savms;                for(j=1;j<=cptcoveff;j++) 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                  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++) {
   fclose(ficresvpl);                ppij=0.;
                 for(i=1; i<=nlstate;i++) {
   /*---------- End : free ----------------*/                  if (mobilav==1) 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                    else {
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                  }
                    if (h*hstepm/YEARM*stepm== yearp) {
                      fprintf(ficresf," %.3f", p3mat[i][j][h]);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                  }
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                } /* end i */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                if (h*hstepm/YEARM*stepm==yearp) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                  fprintf(ficresf," %.3f", ppij);
                  }
   free_matrix(matcov,1,npar,1,npar);              }/* end j */
   free_vector(delti,1,npar);            } /* end h */
   free_matrix(agev,1,maxwav,1,imx);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          } /* end agec */
         } /* end yearp */
   fprintf(fichtm,"\n</body>");      } /* end cptcod */
   fclose(fichtm);    } /* end  cptcov */
   fclose(ficgp);         
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   if(erreur >0){    fclose(ficresf);
     printf("End of Imach with error or warning %d\n",erreur);  }
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);  
   }else{  /************** Forecasting *****not tested NB*************/
    printf("End of Imach\n");  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
    fprintf(ficlog,"End of Imach\n");    
   }    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   printf("See log file on %s\n",filelog);    int *popage;
   fclose(ficlog);    double calagedatem, agelim, kk1, kk2;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    double *popeffectif,*popcount;
      double ***p3mat,***tabpop,***tabpopprev;
   /* 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);*/    double ***mobaverage;
   /*printf("Total time was %d uSec.\n", total_usecs);*/    char filerespop[FILENAMELENGTH];
   /*------ End -----------*/  
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  end:    agelim=AGESUP;
 #ifdef windows    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   /* chdir(pathcd);*/    
 #endif    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
  /*system("wgnuplot graph.plt");*/    
  /*system("../gp37mgw/wgnuplot graph.plt");*/    
  /*system("cd ../gp37mgw");*/    strcpy(filerespop,"pop"); 
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    strcat(filerespop,fileres);
  strcpy(plotcmd,GNUPLOTPROGRAM);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
  strcat(plotcmd," ");      printf("Problem with forecast resultfile: %s\n", filerespop);
  strcat(plotcmd,optionfilegnuplot);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
  system(plotcmd);    }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
 #ifdef windows    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   while (z[0] != 'q') {  
     /* chdir(path); */    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  
     scanf("%s",z);    if (mobilav!=0) {
     if (z[0] == 'c') system("./imach");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     else if (z[0] == 'e') system(optionfilehtm);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     else if (z[0] == 'g') system(plotcmd);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     else if (z[0] == 'q') exit(0);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   }      }
 #endif    }
 }  
     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;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char linetmp[MAXLINE];
       char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
     /* where is ncovprod ?*/
     ncovmodel=2+cptcovn; /*Number of variables = 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 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       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);
             goto end;
           }
         }
         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);
           goto end;
         }
         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);
           goto end;
       }
       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);
           goto end;
       }
       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);
           goto end;
   
       }
       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);
         goto end;
       }
       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);
             goto end;
           }
         }
         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);
           goto end;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (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+V3 =>2+1=3 */
       cptcovprod=j1; /*Number of products  V1*V2 =1 */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
         goto end;
       }
       
       /* 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 */
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 
                                        stra=V2
                                       */ 
         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 V1+V3*age+V2 strb=V3*age*/
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: 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');
             Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
             cptcovage++; /* Sums the number of covariates including age as a product */
             Tage[cptcovage]=i;  /* Tage[1] =2 */
             /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model V1+V3*V2+V2  strb=V3*V2*/
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[i]=ncovcol+k1;  /* find 'n' in Vn and stores in Tvar. 
                                     If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;  /* Tprod[1]  */
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     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);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       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.1.51  
changed lines
  Added in v.1.135


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