Diff for /imach/src/imach.c between versions 1.52 and 1.133

version 1.52, 2002/07/19 18:49:30 version 1.133, 2009/07/06 10:21:25
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.133  2009/07/06 10:21:25  brouard
      just nforces
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.132  2009/07/06 08:22:05  brouard
   first survey ("cross") where individuals from different ages are    Many tings
   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 1.131  2009/06/20 16:22:47  brouard
   second wave of interviews ("longitudinal") which measure each change    Some dimensions resccaled
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.130  2009/05/26 06:44:34  brouard
   model. More health states you consider, more time is necessary to reach the    (Module): Max Covariate is now set to 20 instead of 8. A
   Maximum Likelihood of the parameters involved in the model.  The    lot of cleaning with variables initialized to 0. Trying to make
   simplest model is the multinomial logistic model where pij is the    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.129  2007/08/31 13:49:27  lievre
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.128  2006/06/30 13:02:05  brouard
   where the markup *Covariates have to be included here again* invites    (Module): Clarifications on computing e.j
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
   The advantage of this computer programme, compared to a simple    imach-114 because nhstepm was no more computed in the age
   multinomial logistic model, is clear when the delay between waves is not    loop. Now we define nhstepma in the age loop.
   identical for each individual. Also, if a individual missed an    (Module): In order to speed up (in case of numerous covariates) we
   intermediate interview, the information is lost, but taken into    compute health expectancies (without variances) in a first step
   account using an interpolation or extrapolation.      and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
   hPijx is the probability to be observed in state i at age x+h    computation.
   conditional to the observed state i at age x. The delay 'h' can be    In the future we should be able to stop the program is only health
   split into an exact number (nh*stepm) of unobserved intermediate    expectancies and graph are needed without standard deviations.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.126  2006/04/28 17:23:28  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Yes the sum of survivors was wrong since
   and the contribution of each individual to the likelihood is simply    imach-114 because nhstepm was no more computed in the age
   hPijx.    loop. Now we define nhstepma in the age loop.
     Version 0.98h
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.125  2006/04/04 15:20:31  lievre
      Errors in calculation of health expectancies. Age was not initialized.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Forecasting file added.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.124  2006/03/22 17:13:53  lievre
   from the European Union.    Parameters are printed with %lf instead of %f (more numbers after the comma).
   It is copyrighted identically to a GNU software product, ie programme and    The log-likelihood is printed in the log file
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.123  2006/03/20 10:52:43  brouard
   **********************************************************************/    * imach.c (Module): <title> changed, corresponds to .htm file
      name. <head> headers where missing.
 #include <math.h>  
 #include <stdio.h>    * imach.c (Module): Weights can have a decimal point as for
 #include <stdlib.h>    English (a comma might work with a correct LC_NUMERIC environment,
 #include <unistd.h>    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define MAXLINE 256    1.
 #define GNUPLOTPROGRAM "gnuplot"    Version 0.98g
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.122  2006/03/20 09:45:41  brouard
 /*#define DEBUG*/    (Module): Weights can have a decimal point as for
 #define windows    English (a comma might work with a correct LC_NUMERIC environment,
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    otherwise the weight is truncated).
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Modification of warning when the covariates values are not 0 or
     1.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Version 0.98g
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.121  2006/03/16 17:45:01  lievre
 #define NINTERVMAX 8    * imach.c (Module): Comments concerning covariates added
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    * imach.c (Module): refinements in the computation of lli if
 #define NCOVMAX 8 /* Maximum number of covariates */    status=-2 in order to have more reliable computation if stepm is
 #define MAXN 20000    not 1 month. Version 0.98f
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.120  2006/03/16 15:10:38  lievre
 #define AGEBASE 40    (Module): refinements in the computation of lli if
 #ifdef windows    status=-2 in order to have more reliable computation if stepm is
 #define DIRSEPARATOR '\\'    not 1 month. Version 0.98f
 #define ODIRSEPARATOR '/'  
 #else    Revision 1.119  2006/03/15 17:42:26  brouard
 #define DIRSEPARATOR '/'    (Module): Bug if status = -2, the loglikelihood was
 #define ODIRSEPARATOR '\\'    computed as likelihood omitting the logarithm. Version O.98e
 #endif  
     Revision 1.118  2006/03/14 18:20:07  brouard
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    (Module): varevsij Comments added explaining the second
 int erreur; /* Error number */    table of variances if popbased=1 .
 int nvar;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    (Module): Function pstamp added
 int npar=NPARMAX;    (Module): Version 0.98d
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.117  2006/03/14 17:16:22  brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): varevsij Comments added explaining the second
 int popbased=0;    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Function pstamp added
 int maxwav; /* Maxim number of waves */    (Module): Version 0.98d
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.116  2006/03/06 10:29:27  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Variance-covariance wrong links and
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    varian-covariance of ej. is needed (Saito).
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.115  2006/02/27 12:17:45  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): One freematrix added in mlikeli! 0.98c
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficlog;    Revision 1.114  2006/02/26 12:57:58  brouard
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    (Module): Some improvements in processing parameter
 FILE *ficresprobmorprev;    filename with strsep.
 FILE *fichtm; /* Html File */  
 FILE *ficreseij;    Revision 1.113  2006/02/24 14:20:24  brouard
 char filerese[FILENAMELENGTH];    (Module): Memory leaks checks with valgrind and:
 FILE  *ficresvij;    datafile was not closed, some imatrix were not freed and on matrix
 char fileresv[FILENAMELENGTH];    allocation too.
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    Revision 1.112  2006/01/30 09:55:26  brouard
 char title[MAXLINE];    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    (Module): Comments can be added in data file. Missing date values
 char filelog[FILENAMELENGTH]; /* Log file */    can be a simple dot '.'.
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    Revision 1.110  2006/01/25 00:51:50  brouard
 char popfile[FILENAMELENGTH];    (Module): Lots of cleaning and bugs added (Gompertz)
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.108  2006/01/19 18:05:42  lievre
 #define FTOL 1.0e-10    Gnuplot problem appeared...
     To be fixed
 #define NRANSI  
 #define ITMAX 200    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
 #define TOL 2.0e-4  
     Revision 1.106  2006/01/19 13:24:36  brouard
 #define CGOLD 0.3819660    Some cleaning and links added in html output
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.104  2005/09/30 16:11:43  lievre
 #define TINY 1.0e-20    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 static double maxarg1,maxarg2;    that the person is alive, then we can code his/her status as -2
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (instead of missing=-1 in earlier versions) and his/her
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    contributions to the likelihood is 1 - Prob of dying from last
      health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    the healthy state at last known wave). Version is 0.98
 #define rint(a) floor(a+0.5)  
     Revision 1.103  2005/09/30 15:54:49  lievre
 static double sqrarg;    (Module): sump fixed, loop imx fixed, and simplifications.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
 int imx;  
 int stepm;    Revision 1.101  2004/09/15 10:38:38  brouard
 /* Stepm, step in month: minimum step interpolation*/    Fix on curr_time
   
 int estepm;    Revision 1.100  2004/07/12 18:29:06  brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Add version for Mac OS X. Just define UNIX in Makefile
   
 int m,nb;    Revision 1.99  2004/06/05 08:57:40  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    *** empty log message ***
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.98  2004/05/16 15:05:56  brouard
 double dateintmean=0;    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 double *weight;    state at each age, but using a Gompertz model: log u =a + b*age .
 int **s; /* Status */    This is the basic analysis of mortality and should be done before any
 double *agedc, **covar, idx;    other analysis, in order to test if the mortality estimated from the
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    The same imach parameter file can be used but the option for mle should be -3.
   
 /**************** split *************************/    Agnès, who wrote this part of the code, tried to keep most of the
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    former routines in order to include the new code within the former code.
 {  
    char *s;                             /* pointer */    The output is very simple: only an estimate of the intercept and of
    int  l1, l2;                         /* length counters */    the slope with 95% confident intervals.
   
    l1 = strlen( path );                 /* length of path */    Current limitations:
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    A) Even if you enter covariates, i.e. with the
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    if ( s == NULL ) {                   /* no directory, so use current */    B) There is no computation of Life Expectancy nor Life Table.
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    Revision 1.97  2004/02/20 13:25:42  lievre
 #if     defined(__bsd__)                /* get current working directory */    Version 0.96d. Population forecasting command line is (temporarily)
       extern char       *getwd( );    suppressed.
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.96  2003/07/15 15:38:55  brouard
 #else    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
       extern char       *getcwd( );    rewritten within the same printf. Workaround: many printfs.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.95  2003/07/08 07:54:34  brouard
 #endif    * imach.c (Repository):
          return( GLOCK_ERROR_GETCWD );    (Repository): Using imachwizard code to output a more meaningful covariance
       }    matrix (cov(a12,c31) instead of numbers.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.94  2003/06/27 13:00:02  brouard
       s++;                              /* after this, the filename */    Just cleaning
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.93  2003/06/25 16:33:55  brouard
       strcpy( name, s );                /* save file name */    (Module): On windows (cygwin) function asctime_r doesn't
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    exist so I changed back to asctime which exists.
       dirc[l1-l2] = 0;                  /* add zero */    (Module): Version 0.96b
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.92  2003/06/25 16:30:45  brouard
 #ifdef windows    (Module): On windows (cygwin) function asctime_r doesn't
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    exist so I changed back to asctime which exists.
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.91  2003/06/25 15:30:29  brouard
 #endif    * imach.c (Repository): Duplicated warning errors corrected.
    s = strrchr( name, '.' );            /* find last / */    (Repository): Elapsed time after each iteration is now output. It
    s++;    helps to forecast when convergence will be reached. Elapsed time
    strcpy(ext,s);                       /* save extension */    is stamped in powell.  We created a new html file for the graphs
    l1= strlen( name);    concerning matrix of covariance. It has extension -cov.htm.
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.90  2003/06/24 12:34:15  brouard
    finame[l1-l2]= 0;    (Module): Some bugs corrected for windows. Also, when
    return( 0 );                         /* we're done */    mle=-1 a template is output in file "or"mypar.txt with the design
 }    of the covariance matrix to be input.
   
     Revision 1.89  2003/06/24 12:30:52  brouard
 /******************************************/    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 void replace(char *s, char*t)    of the covariance matrix to be input.
 {  
   int i;    Revision 1.88  2003/06/23 17:54:56  brouard
   int lg=20;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   i=0;  
   lg=strlen(t);    Revision 1.87  2003/06/18 12:26:01  brouard
   for(i=0; i<= lg; i++) {    Version 0.96
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.86  2003/06/17 20:04:08  brouard
   }    (Module): Change position of html and gnuplot routines and added
 }    routine fileappend.
   
 int nbocc(char *s, char occ)    Revision 1.85  2003/06/17 13:12:43  brouard
 {    * imach.c (Repository): Check when date of death was earlier that
   int i,j=0;    current date of interview. It may happen when the death was just
   int lg=20;    prior to the death. In this case, dh was negative and likelihood
   i=0;    was wrong (infinity). We still send an "Error" but patch by
   lg=strlen(s);    assuming that the date of death was just one stepm after the
   for(i=0; i<= lg; i++) {    interview.
   if  (s[i] == occ ) j++;    (Repository): Because some people have very long ID (first column)
   }    we changed int to long in num[] and we added a new lvector for
   return j;    memory allocation. But we also truncated to 8 characters (left
 }    truncation)
     (Repository): No more line truncation errors.
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.84  2003/06/13 21:44:43  brouard
   /* cuts string t into u and v where u is ended by char occ excluding it    * imach.c (Repository): Replace "freqsummary" at a correct
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    place. It differs from routine "prevalence" which may be called
      gives u="abcedf" and v="ghi2j" */    many times. Probs is memory consuming and must be used with
   int i,lg,j,p=0;    parcimony.
   i=0;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.83  2003/06/10 13:39:11  lievre
   }    *** empty log message ***
   
   lg=strlen(t);    Revision 1.82  2003/06/05 15:57:20  brouard
   for(j=0; j<p; j++) {    Add log in  imach.c and  fullversion number is now printed.
     (u[j] = t[j]);  
   }  */
      u[p]='\0';  /*
      Interpolated Markov Chain
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Short summary of the programme:
   }    
 }    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 /********************** nrerror ********************/    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
 void nrerror(char error_text[])    case of a health survey which is our main interest) -2- at least a
 {    second wave of interviews ("longitudinal") which measure each change
   fprintf(stderr,"ERREUR ...\n");    (if any) in individual health status.  Health expectancies are
   fprintf(stderr,"%s\n",error_text);    computed from the time spent in each health state according to a
   exit(1);    model. More health states you consider, more time is necessary to reach the
 }    Maximum Likelihood of the parameters involved in the model.  The
 /*********************** vector *******************/    simplest model is the multinomial logistic model where pij is the
 double *vector(int nl, int nh)    probability to be observed in state j at the second wave
 {    conditional to be observed in state i at the first wave. Therefore
   double *v;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    'age' is age and 'sex' is a covariate. If you want to have a more
   if (!v) nrerror("allocation failure in vector");    complex model than "constant and age", you should modify the program
   return 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.
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    The advantage of this computer programme, compared to a simple
 {    multinomial logistic model, is clear when the delay between waves is not
   free((FREE_ARG)(v+nl-NR_END));    identical for each individual. Also, if a individual missed an
 }    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    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
   int *v;    split into an exact number (nh*stepm) of unobserved intermediate
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    states. This elementary transition (by month, quarter,
   if (!v) nrerror("allocation failure in ivector");    semester or year) is modelled as a multinomial logistic.  The hPx
   return 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.
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Also this programme outputs the covariance matrix of the parameters but also
 {    of the life expectancies. It also computes the period (stable) prevalence. 
   free((FREE_ARG)(v+nl-NR_END));    
 }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 /******************* imatrix *******************************/    This software have been partly granted by Euro-REVES, a concerted action
 int **imatrix(long nrl, long nrh, long ncl, long nch)    from the European Union.
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    It is copyrighted identically to a GNU software product, ie programme and
 {    software can be distributed freely for non commercial use. Latest version
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    can be accessed at http://euroreves.ined.fr/imach .
   int **m;  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   /* allocate pointers to rows */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    
   if (!m) nrerror("allocation failure 1 in matrix()");    **********************************************************************/
   m += NR_END;  /*
   m -= nrl;    main
      read parameterfile
      read datafile
   /* allocate rows and set pointers to them */    concatwav
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    freqsummary
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (mle >= 1)
   m[nrl] += NR_END;      mlikeli
   m[nrl] -= ncl;    print results files
      if mle==1 
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;       computes hessian
      read end of parameter file: agemin, agemax, bage, fage, estepm
   /* return pointer to array of pointers to rows */        begin-prev-date,...
   return m;    open gnuplot file
 }    open html file
     period (stable) prevalence
 /****************** free_imatrix *************************/     for age prevalim()
 void free_imatrix(m,nrl,nrh,ncl,nch)    h Pij x
       int **m;    variance of p varprob
       long nch,ncl,nrh,nrl;    forecasting if prevfcast==1 prevforecast call prevalence()
      /* free an int matrix allocated by imatrix() */    health expectancies
 {    Variance-covariance of DFLE
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    prevalence()
   free((FREE_ARG) (m+nrl-NR_END));     movingaverage()
 }    varevsij() 
     if popbased==1 varevsij(,popbased)
 /******************* matrix *******************************/    total life expectancies
 double **matrix(long nrl, long nrh, long ncl, long nch)    Variance of period (stable) prevalence
 {   end
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  */
   double **m;  
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");   
   m += NR_END;  #include <math.h>
   m -= nrl;  #include <stdio.h>
   #include <stdlib.h>
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <string.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <unistd.h>
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  #include <limits.h>
   #include <sys/types.h>
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <sys/stat.h>
   return m;  #include <errno.h>
 }  extern int errno;
   
 /*************************free matrix ************************/  /* #include <sys/time.h> */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #include <time.h>
 {  #include "timeval.h"
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  /* #include <libintl.h> */
 }  /* #define _(String) gettext (String) */
   
 /******************* ma3x *******************************/  #define MAXLINE 256
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  #define GNUPLOTPROGRAM "gnuplot"
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   double ***m;  #define FILENAMELENGTH 132
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   if (!m) nrerror("allocation failure 1 in matrix()");  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   m += NR_END;  
   m -= nrl;  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define NINTERVMAX 8
   m[nrl] += NR_END;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   m[nrl] -= ncl;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 20 /* Maximum number of covariates */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define AGESUP 130
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define AGEBASE 40
   m[nrl][ncl] += NR_END;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   m[nrl][ncl] -= nll;  #ifdef UNIX
   for (j=ncl+1; j<=nch; j++)  #define DIRSEPARATOR '/'
     m[nrl][j]=m[nrl][j-1]+nlay;  #define CHARSEPARATOR "/"
    #define ODIRSEPARATOR '\\'
   for (i=nrl+1; i<=nrh; i++) {  #else
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define DIRSEPARATOR '\\'
     for (j=ncl+1; j<=nch; j++)  #define CHARSEPARATOR "\\"
       m[i][j]=m[i][j-1]+nlay;  #define ODIRSEPARATOR '/'
   }  #endif
   return m;  
 }  /* $Id$ */
   /* $State$ */
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  char version[]="Imach version 0.98k, June 2009, INED-EUROREVES-Institut de longevite ";
 {  char fullversion[]="$Revision$ $Date$"; 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  char strstart[80];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  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 */
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
 /***************** f1dim *************************/  int npar=NPARMAX;
 extern int ncom;  int nlstate=2; /* Number of live states */
 extern double *pcom,*xicom;  int ndeath=1; /* Number of dead states */
 extern double (*nrfunc)(double []);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    int popbased=0;
 double f1dim(double x)  
 {  int *wav; /* Number of waves for this individuual 0 is possible */
   int j;  int maxwav=0; /* Maxim number of waves */
   double f;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   double *xt;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
    int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   xt=vector(1,ncom);                     to the likelihood and the sum of weights (done by funcone)*/
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int mle=1, weightopt=0;
   f=(*nrfunc)(xt);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   free_vector(xt,1,ncom);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   return f;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean=1; /* Mean space between 2 waves */
 /*****************brent *************************/  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 {  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   int iter;  FILE *ficlog, *ficrespow;
   double a,b,d,etemp;  int globpr=0; /* Global variable for printing or not */
   double fu,fv,fw,fx;  double fretone; /* Only one call to likelihood */
   double ftemp;  long ipmx=0; /* Number of contributions */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  double sw; /* Sum of weights */
   double e=0.0;  char filerespow[FILENAMELENGTH];
    char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   a=(ax < cx ? ax : cx);  FILE *ficresilk;
   b=(ax > cx ? ax : cx);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   x=w=v=bx;  FILE *ficresprobmorprev;
   fw=fv=fx=(*f)(x);  FILE *fichtm, *fichtmcov; /* Html File */
   for (iter=1;iter<=ITMAX;iter++) {  FILE *ficreseij;
     xm=0.5*(a+b);  char filerese[FILENAMELENGTH];
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  FILE *ficresstdeij;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  char fileresstde[FILENAMELENGTH];
     printf(".");fflush(stdout);  FILE *ficrescveij;
     fprintf(ficlog,".");fflush(ficlog);  char filerescve[FILENAMELENGTH];
 #ifdef DEBUG  FILE  *ficresvij;
     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 fileresv[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  *ficresvpl;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  char fileresvpl[FILENAMELENGTH];
 #endif  char title[MAXLINE];
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       *xmin=x;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       return fx;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     }  char command[FILENAMELENGTH];
     ftemp=fu;  int  outcmd=0;
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  char filelog[FILENAMELENGTH]; /* Log file */
       q=2.0*(q-r);  char filerest[FILENAMELENGTH];
       if (q > 0.0) p = -p;  char fileregp[FILENAMELENGTH];
       q=fabs(q);  char popfile[FILENAMELENGTH];
       etemp=e;  
       e=d;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       else {  struct timezone tzp;
         d=p/q;  extern int gettimeofday();
         u=x+d;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
         if (u-a < tol2 || b-u < tol2)  long time_value;
           d=SIGN(tol1,xm-x);  extern long time();
       }  char strcurr[80], strfor[80];
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  char *endptr;
     }  long lval;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  double dval;
     fu=(*f)(u);  
     if (fu <= fx) {  #define NR_END 1
       if (u >= x) a=x; else b=x;  #define FREE_ARG char*
       SHFT(v,w,x,u)  #define FTOL 1.0e-10
         SHFT(fv,fw,fx,fu)  
         } else {  #define NRANSI 
           if (u < x) a=u; else b=u;  #define ITMAX 200 
           if (fu <= fw || w == x) {  
             v=w;  #define TOL 2.0e-4 
             w=u;  
             fv=fw;  #define CGOLD 0.3819660 
             fw=fu;  #define ZEPS 1.0e-10 
           } else if (fu <= fv || v == x || v == w) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
             v=u;  
             fv=fu;  #define GOLD 1.618034 
           }  #define GLIMIT 100.0 
         }  #define TINY 1.0e-20 
   }  
   nrerror("Too many iterations in brent");  static double maxarg1,maxarg2;
   *xmin=x;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   return fx;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 }    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 /****************** mnbrak ***********************/  #define rint(a) floor(a+0.5)
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  static double sqrarg;
             double (*func)(double))  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   double ulim,u,r,q, dum;  int agegomp= AGEGOMP;
   double fu;  
    int imx; 
   *fa=(*func)(*ax);  int stepm=1;
   *fb=(*func)(*bx);  /* Stepm, step in month: minimum step interpolation*/
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)  int estepm;
       SHFT(dum,*fb,*fa,dum)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  int m,nb;
   *fc=(*func)(*cx);  long *num;
   while (*fb > *fc) {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     r=(*bx-*ax)*(*fb-*fc);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     q=(*bx-*cx)*(*fb-*fa);  double **pmmij, ***probs;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  double *ageexmed,*agecens;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  double dateintmean=0;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  double *weight;
       fu=(*func)(u);  int **s; /* Status */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  double *agedc, **covar, idx;
       fu=(*func)(u);  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       if (fu < *fc) {  double *lsurv, *lpop, *tpop;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
           }  double ftolhess; /* Tolerance for computing hessian */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  /**************** split *************************/
       fu=(*func)(u);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       fu=(*func)(u);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     }    */ 
     SHFT(*ax,*bx,*cx,u)    char  *ss;                            /* pointer */
       SHFT(*fa,*fb,*fc,fu)    int   l1, l2;                         /* length counters */
       }  
 }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 /*************** linmin ************************/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so determine current directory */
 int ncom;      strcpy( name, path );               /* we got the fullname name because no directory */
 double *pcom,*xicom;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 double (*nrfunc)(double []);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
        /* get current working directory */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      /*    extern  char* getcwd ( char *buf , int len);*/
 {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   double brent(double ax, double bx, double cx,        return( GLOCK_ERROR_GETCWD );
                double (*f)(double), double tol, double *xmin);      }
   double f1dim(double x);      /* got dirc from getcwd*/
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      printf(" DIRC = %s \n",dirc);
               double *fc, double (*func)(double));    } else {                              /* strip direcotry from path */
   int j;      ss++;                               /* after this, the filename */
   double xx,xmin,bx,ax;      l2 = strlen( ss );                  /* length of filename */
   double fx,fb,fa;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
        strcpy( name, ss );         /* save file name */
   ncom=n;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   pcom=vector(1,n);      dirc[l1-l2] = 0;                    /* add zero */
   xicom=vector(1,n);      printf(" DIRC2 = %s \n",dirc);
   nrfunc=func;    }
   for (j=1;j<=n;j++) {    /* We add a separator at the end of dirc if not exists */
     pcom[j]=p[j];    l1 = strlen( dirc );                  /* length of directory */
     xicom[j]=xi[j];    if( dirc[l1-1] != DIRSEPARATOR ){
   }      dirc[l1] =  DIRSEPARATOR;
   ax=0.0;      dirc[l1+1] = 0; 
   xx=1.0;      printf(" DIRC3 = %s \n",dirc);
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    }
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    ss = strrchr( name, '.' );            /* find last / */
 #ifdef DEBUG    if (ss >0){
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      ss++;
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      strcpy(ext,ss);                     /* save extension */
 #endif      l1= strlen( name);
   for (j=1;j<=n;j++) {      l2= strlen(ss)+1;
     xi[j] *= xmin;      strncpy( finame, name, l1-l2);
     p[j] += xi[j];      finame[l1-l2]= 0;
   }    }
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);    return( 0 );                          /* we're done */
 }  }
   
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /******************************************/
             double (*func)(double []))  
 {  void replace_back_to_slash(char *s, char*t)
   void linmin(double p[], double xi[], int n, double *fret,  {
               double (*func)(double []));    int i;
   int i,ibig,j;    int lg=0;
   double del,t,*pt,*ptt,*xit;    i=0;
   double fp,fptt;    lg=strlen(t);
   double *xits;    for(i=0; i<= lg; i++) {
   pt=vector(1,n);      (s[i] = t[i]);
   ptt=vector(1,n);      if (t[i]== '\\') s[i]='/';
   xit=vector(1,n);    }
   xits=vector(1,n);  }
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  char *trimbb(char *out, char *in)
   for (*iter=1;;++(*iter)) {  { /* Trim multiple blanks in line */
     fp=(*fret);    char *s;
     ibig=0;    s=out;
     del=0.0;    while (*in != '\0'){
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);        in++;
     for (i=1;i<=n;i++)      }
       printf(" %d %.12f",i, p[i]);      *out++ = *in++;
     fprintf(ficlog," %d %.12f",i, p[i]);    }
     printf("\n");    *out='\0';
     fprintf(ficlog,"\n");    return s;
     for (i=1;i<=n;i++) {  }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  int nbocc(char *s, char occ)
 #ifdef DEBUG  {
       printf("fret=%lf \n",*fret);    int i,j=0;
       fprintf(ficlog,"fret=%lf \n",*fret);    int lg=20;
 #endif    i=0;
       printf("%d",i);fflush(stdout);    lg=strlen(s);
       fprintf(ficlog,"%d",i);fflush(ficlog);    for(i=0; i<= lg; i++) {
       linmin(p,xit,n,fret,func);    if  (s[i] == occ ) j++;
       if (fabs(fptt-(*fret)) > del) {    }
         del=fabs(fptt-(*fret));    return j;
         ibig=i;  }
       }  
 #ifdef DEBUG  void cutv(char *u,char *v, char*t, char occ)
       printf("%d %.12e",i,(*fret));  {
       fprintf(ficlog,"%d %.12e",i,(*fret));    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       for (j=1;j<=n;j++) {       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);       gives u="abcedf" and v="ghi2j" */
         printf(" x(%d)=%.12e",j,xit[j]);    int i,lg,j,p=0;
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);    i=0;
       }    for(j=0; j<=strlen(t)-1; j++) {
       for(j=1;j<=n;j++) {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
         printf(" p=%.12e",p[j]);    }
         fprintf(ficlog," p=%.12e",p[j]);  
       }    lg=strlen(t);
       printf("\n");    for(j=0; j<p; j++) {
       fprintf(ficlog,"\n");      (u[j] = t[j]);
 #endif    }
     }       u[p]='\0';
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG     for(j=0; j<= lg; j++) {
       int k[2],l;      if (j>=(p+1))(v[j-p-1] = t[j]);
       k[0]=1;    }
       k[1]=-1;  }
       printf("Max: %.12e",(*func)(p));  
       fprintf(ficlog,"Max: %.12e",(*func)(p));  /********************** nrerror ********************/
       for (j=1;j<=n;j++) {  
         printf(" %.12e",p[j]);  void nrerror(char error_text[])
         fprintf(ficlog," %.12e",p[j]);  {
       }    fprintf(stderr,"ERREUR ...\n");
       printf("\n");    fprintf(stderr,"%s\n",error_text);
       fprintf(ficlog,"\n");    exit(EXIT_FAILURE);
       for(l=0;l<=1;l++) {  }
         for (j=1;j<=n;j++) {  /*********************** vector *******************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  double *vector(int nl, int nh)
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  {
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    double *v;
         }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    if (!v) nrerror("allocation failure in vector");
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    return v-nl+NR_END;
       }  }
 #endif  
   /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
       free_vector(xit,1,n);  {
       free_vector(xits,1,n);    free((FREE_ARG)(v+nl-NR_END));
       free_vector(ptt,1,n);  }
       free_vector(pt,1,n);  
       return;  /************************ivector *******************************/
     }  int *ivector(long nl,long nh)
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  {
     for (j=1;j<=n;j++) {    int *v;
       ptt[j]=2.0*p[j]-pt[j];    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       xit[j]=p[j]-pt[j];    if (!v) nrerror("allocation failure in ivector");
       pt[j]=p[j];    return v-nl+NR_END;
     }  }
     fptt=(*func)(ptt);  
     if (fptt < fp) {  /******************free ivector **************************/
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  void free_ivector(int *v, long nl, long nh)
       if (t < 0.0) {  {
         linmin(p,xit,n,fret,func);    free((FREE_ARG)(v+nl-NR_END));
         for (j=1;j<=n;j++) {  }
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  /************************lvector *******************************/
         }  long *lvector(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);    long *v;
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         for(j=1;j<=n;j++){    if (!v) nrerror("allocation failure in ivector");
           printf(" %.12e",xit[j]);    return v-nl+NR_END;
           fprintf(ficlog," %.12e",xit[j]);  }
         }  
         printf("\n");  /******************free lvector **************************/
         fprintf(ficlog,"\n");  void free_lvector(long *v, long nl, long nh)
 #endif  {
       }    free((FREE_ARG)(v+nl-NR_END));
     }  }
   }  
 }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 /**** Prevalence limit ****************/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 {    int **m; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    
      matrix by transitions matrix until convergence is reached */    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   int i, ii,j,k;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double min, max, maxmin, maxmax,sumnew=0.;    m += NR_END; 
   double **matprod2();    m -= nrl; 
   double **out, cov[NCOVMAX], **pmij();    
   double **newm;    
   double agefin, delaymax=50 ; /* Max number of years to converge */    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   for (ii=1;ii<=nlstate+ndeath;ii++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     for (j=1;j<=nlstate+ndeath;j++){    m[nrl] += NR_END; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    m[nrl] -= ncl; 
     }    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
    cov[1]=1.;    
      /* return pointer to array of pointers to rows */ 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    return m; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  } 
     newm=savm;  
     /* Covariates have to be included here again */  /****************** free_imatrix *************************/
      cov[2]=agefin;  void free_imatrix(m,nrl,nrh,ncl,nch)
          int **m;
       for (k=1; k<=cptcovn;k++) {        long nch,ncl,nrh,nrl; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];       /* free an int matrix allocated by imatrix() */ 
         /*      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((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    free((FREE_ARG) (m+nrl-NR_END)); 
       for (k=1; k<=cptcovprod;k++)  } 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   /******************* matrix *******************************/
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  double **matrix(long nrl, long nrh, long ncl, long nch)
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  {
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    double **m;
   
     savm=oldm;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     oldm=newm;    if (!m) nrerror("allocation failure 1 in matrix()");
     maxmax=0.;    m += NR_END;
     for(j=1;j<=nlstate;j++){    m -= nrl;
       min=1.;  
       max=0.;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for(i=1; i<=nlstate; i++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         sumnew=0;    m[nrl] += NR_END;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    m[nrl] -= ncl;
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         min=FMIN(min,prlim[i][j]);    return m;
       }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       maxmin=max-min;     */
       maxmax=FMAX(maxmax,maxmin);  }
     }  
     if(maxmax < ftolpl){  /*************************free matrix ************************/
       return prlim;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     }  {
   }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 }    free((FREE_ARG)(m+nrl-NR_END));
   }
 /*************** transition probabilities ***************/  
   /******************* ma3x *******************************/
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 {  {
   double s1, s2;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   /*double t34;*/    double ***m;
   int i,j,j1, nc, ii, jj;  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for(i=1; i<= nlstate; i++){    if (!m) nrerror("allocation failure 1 in matrix()");
     for(j=1; j<i;j++){    m += NR_END;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    m -= nrl;
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       }    m[nrl] += NR_END;
       ps[i][j]=s2;    m[nrl] -= ncl;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    m[nrl][ncl] += NR_END;
       }    m[nrl][ncl] -= nll;
       ps[i][j]=s2;    for (j=ncl+1; j<=nch; j++) 
     }      m[nrl][j]=m[nrl][j-1]+nlay;
   }    
     /*ps[3][2]=1;*/    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for(i=1; i<= nlstate; i++){      for (j=ncl+1; j<=nch; j++) 
      s1=0;        m[i][j]=m[i][j-1]+nlay;
     for(j=1; j<i; j++)    }
       s1+=exp(ps[i][j]);    return m; 
     for(j=i+1; j<=nlstate+ndeath; j++)    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       s1+=exp(ps[i][j]);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     ps[i][i]=1./(s1+1.);    */
     for(j=1; j<i; j++)  }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  /*************************free ma3x ************************/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  {
   } /* end i */    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    free((FREE_ARG)(m+nrl-NR_END));
     for(jj=1; jj<= nlstate+ndeath; jj++){  }
       ps[ii][jj]=0;  
       ps[ii][ii]=1;  /*************** function subdirf ***********/
     }  char *subdirf(char fileres[])
   }  {
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    strcat(tmpout,"/"); /* Add to the right */
     for(jj=1; jj<= nlstate+ndeath; jj++){    strcat(tmpout,fileres);
      printf("%lf ",ps[ii][jj]);    return tmpout;
    }  }
     printf("\n ");  
     }  /*************** function subdirf2 ***********/
     printf("\n ");printf("%lf ",cov[2]);*/  char *subdirf2(char fileres[], char *preop)
 /*  {
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    
   goto end;*/    /* Caution optionfilefiname is hidden */
     return ps;    strcpy(tmpout,optionfilefiname);
 }    strcat(tmpout,"/");
     strcat(tmpout,preop);
 /**************** Product of 2 matrices ******************/    strcat(tmpout,fileres);
     return tmpout;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  }
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /*************** function subdirf3 ***********/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  char *subdirf3(char fileres[], char *preop, char *preop2)
   /* in, b, out are matrice of pointers which should have been initialized  {
      before: only the contents of out is modified. The function returns    
      a pointer to pointers identical to out */    /* Caution optionfilefiname is hidden */
   long i, j, k;    strcpy(tmpout,optionfilefiname);
   for(i=nrl; i<= nrh; i++)    strcat(tmpout,"/");
     for(k=ncolol; k<=ncoloh; k++)    strcat(tmpout,preop);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    strcat(tmpout,preop2);
         out[i][k] +=in[i][j]*b[j][k];    strcat(tmpout,fileres);
     return tmpout;
   return out;  }
 }  
   /***************** f1dim *************************/
   extern int ncom; 
 /************* Higher Matrix Product ***************/  extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )   
 {  double f1dim(double x) 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  { 
      duration (i.e. until    int j; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    double f;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    double *xt; 
      (typically every 2 years instead of every month which is too big).   
      Model is determined by parameters x and covariates have to be    xt=vector(1,ncom); 
      included manually here.    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
      */    free_vector(xt,1,ncom); 
     return f; 
   int i, j, d, h, k;  } 
   double **out, cov[NCOVMAX];  
   double **newm;  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   /* Hstepm could be zero and should return the unit matrix */  { 
   for (i=1;i<=nlstate+ndeath;i++)    int iter; 
     for (j=1;j<=nlstate+ndeath;j++){    double a,b,d,etemp;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    double fu,fv,fw,fx;
       po[i][j][0]=(i==j ? 1.0 : 0.0);    double ftemp;
     }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double e=0.0; 
   for(h=1; h <=nhstepm; h++){   
     for(d=1; d <=hstepm; d++){    a=(ax < cx ? ax : cx); 
       newm=savm;    b=(ax > cx ? ax : cx); 
       /* Covariates have to be included here again */    x=w=v=bx; 
       cov[1]=1.;    fw=fv=fx=(*f)(x); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    for (iter=1;iter<=ITMAX;iter++) { 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      xm=0.5*(a+b); 
       for (k=1; k<=cptcovage;k++)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       for (k=1; k<=cptcovprod;k++)      printf(".");fflush(stdout);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  #endif
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       savm=oldm;        *xmin=x; 
       oldm=newm;        return fx; 
     }      } 
     for(i=1; i<=nlstate+ndeath; i++)      ftemp=fu;
       for(j=1;j<=nlstate+ndeath;j++) {      if (fabs(e) > tol1) { 
         po[i][j][h]=newm[i][j];        r=(x-w)*(fx-fv); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        q=(x-v)*(fx-fw); 
          */        p=(x-v)*q-(x-w)*r; 
       }        q=2.0*(q-r); 
   } /* end h */        if (q > 0.0) p = -p; 
   return po;        q=fabs(q); 
 }        etemp=e; 
         e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 /*************** log-likelihood *************/          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 double func( double *x)        else { 
 {          d=p/q; 
   int i, ii, j, k, mi, d, kk;          u=x+d; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];          if (u-a < tol2 || b-u < tol2) 
   double **out;            d=SIGN(tol1,xm-x); 
   double sw; /* Sum of weights */        } 
   double lli; /* Individual log likelihood */      } else { 
   long ipmx;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   /*extern weight */      } 
   /* We are differentiating ll according to initial status */      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      fu=(*f)(u); 
   /*for(i=1;i<imx;i++)      if (fu <= fx) { 
     printf(" %d\n",s[4][i]);        if (u >= x) a=x; else b=x; 
   */        SHFT(v,w,x,u) 
   cov[1]=1.;          SHFT(fv,fw,fx,fu) 
           } else { 
   for(k=1; k<=nlstate; k++) ll[k]=0.;            if (u < x) a=u; else b=u; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){            if (fu <= fw || w == x) { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];              v=w; 
     for(mi=1; mi<= wav[i]-1; mi++){              w=u; 
       for (ii=1;ii<=nlstate+ndeath;ii++)              fv=fw; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);              fw=fu; 
       for(d=0; d<dh[mi][i]; d++){            } else if (fu <= fv || v == x || v == w) { 
         newm=savm;              v=u; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;              fv=fu; 
         for (kk=1; kk<=cptcovage;kk++) {            } 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          } 
         }    } 
            nrerror("Too many iterations in brent"); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    *xmin=x; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    return fx; 
         savm=oldm;  } 
         oldm=newm;  
          /****************** mnbrak ***********************/
          
       } /* end mult */  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                    double (*func)(double)) 
       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]]);*/    double ulim,u,r,q, dum;
       ipmx +=1;    double fu; 
       sw += weight[i];   
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    *fa=(*func)(*ax); 
     } /* end of wave */    *fb=(*func)(*bx); 
   } /* end of individual */    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        SHFT(dum,*fb,*fa,dum) 
   /* 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 */    *cx=(*bx)+GOLD*(*bx-*ax); 
   return -l;    *fc=(*func)(*cx); 
 }    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 /*********** Maximum Likelihood Estimation ***************/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 {      if ((*bx-u)*(u-*cx) > 0.0) { 
   int i,j, iter;        fu=(*func)(u); 
   double **xi,*delti;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double fret;        fu=(*func)(u); 
   xi=matrix(1,npar,1,npar);        if (fu < *fc) { 
   for (i=1;i<=npar;i++)          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for (j=1;j<=npar;j++)            SHFT(*fb,*fc,fu,(*func)(u)) 
       xi[i][j]=(i==j ? 1.0 : 0.0);            } 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   powell(p,xi,npar,ftol,&iter,&fret,func);        u=ulim; 
         fu=(*func)(u); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      } else { 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        u=(*cx)+GOLD*(*cx-*bx); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        fu=(*func)(u); 
       } 
 }      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
 /**** Computes Hessian and covariance matrix ***/        } 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  } 
 {  
   double  **a,**y,*x,pd;  /*************** linmin ************************/
   double **hess;  
   int i, j,jk;  int ncom; 
   int *indx;  double *pcom,*xicom;
   double (*nrfunc)(double []); 
   double hessii(double p[], double delta, int theta, double delti[]);   
   double hessij(double p[], double delti[], int i, int j);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   void lubksb(double **a, int npar, int *indx, double b[]) ;  { 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
   hess=matrix(1,npar,1,npar);    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   printf("\nCalculation of the hessian matrix. Wait...\n");                double *fc, double (*func)(double)); 
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    int j; 
   for (i=1;i<=npar;i++){    double xx,xmin,bx,ax; 
     printf("%d",i);fflush(stdout);    double fx,fb,fa;
     fprintf(ficlog,"%d",i);fflush(ficlog);   
     hess[i][i]=hessii(p,ftolhess,i,delti);    ncom=n; 
     /*printf(" %f ",p[i]);*/    pcom=vector(1,n); 
     /*printf(" %lf ",hess[i][i]);*/    xicom=vector(1,n); 
   }    nrfunc=func; 
      for (j=1;j<=n;j++) { 
   for (i=1;i<=npar;i++) {      pcom[j]=p[j]; 
     for (j=1;j<=npar;j++)  {      xicom[j]=xi[j]; 
       if (j>i) {    } 
         printf(".%d%d",i,j);fflush(stdout);    ax=0.0; 
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    xx=1.0; 
         hess[i][j]=hessij(p,delti,i,j);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         hess[j][i]=hess[i][j];        *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         /*printf(" %lf ",hess[i][j]);*/  #ifdef DEBUG
       }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   }  #endif
   printf("\n");    for (j=1;j<=n;j++) { 
   fprintf(ficlog,"\n");      xi[j] *= xmin; 
       p[j] += xi[j]; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    } 
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    free_vector(xicom,1,n); 
      free_vector(pcom,1,n); 
   a=matrix(1,npar,1,npar);  } 
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);  char *asc_diff_time(long time_sec, char ascdiff[])
   indx=ivector(1,npar);  {
   for (i=1;i<=npar;i++)    long sec_left, days, hours, minutes;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    days = (time_sec) / (60*60*24);
   ludcmp(a,npar,indx,&pd);    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
   for (j=1;j<=npar;j++) {    sec_left = (sec_left) %(60*60);
     for (i=1;i<=npar;i++) x[i]=0;    minutes = (sec_left) /60;
     x[j]=1;    sec_left = (sec_left) % (60);
     lubksb(a,npar,indx,x);    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     for (i=1;i<=npar;i++){    return ascdiff;
       matcov[i][j]=x[i];  }
     }  
   }  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   printf("\n#Hessian matrix#\n");              double (*func)(double [])) 
   fprintf(ficlog,"\n#Hessian matrix#\n");  { 
   for (i=1;i<=npar;i++) {    void linmin(double p[], double xi[], int n, double *fret, 
     for (j=1;j<=npar;j++) {                double (*func)(double [])); 
       printf("%.3e ",hess[i][j]);    int i,ibig,j; 
       fprintf(ficlog,"%.3e ",hess[i][j]);    double del,t,*pt,*ptt,*xit;
     }    double fp,fptt;
     printf("\n");    double *xits;
     fprintf(ficlog,"\n");    int niterf, itmp;
   }  
     pt=vector(1,n); 
   /* Recompute Inverse */    ptt=vector(1,n); 
   for (i=1;i<=npar;i++)    xit=vector(1,n); 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    xits=vector(1,n); 
   ludcmp(a,npar,indx,&pd);    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
   /*  printf("\n#Hessian matrix recomputed#\n");    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
   for (j=1;j<=npar;j++) {      ibig=0; 
     for (i=1;i<=npar;i++) x[i]=0;      del=0.0; 
     x[j]=1;      last_time=curr_time;
     lubksb(a,npar,indx,x);      (void) gettimeofday(&curr_time,&tzp);
     for (i=1;i<=npar;i++){      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);
       y[i][j]=x[i];      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);
       printf("%.3e ",y[i][j]);  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
       fprintf(ficlog,"%.3e ",y[i][j]);     for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
     printf("\n");        fprintf(ficlog," %d %.12lf",i, p[i]);
     fprintf(ficlog,"\n");        fprintf(ficrespow," %.12lf", p[i]);
   }      }
   */      printf("\n");
       fprintf(ficlog,"\n");
   free_matrix(a,1,npar,1,npar);      fprintf(ficrespow,"\n");fflush(ficrespow);
   free_matrix(y,1,npar,1,npar);      if(*iter <=3){
   free_vector(x,1,npar);        tm = *localtime(&curr_time.tv_sec);
   free_ivector(indx,1,npar);        strcpy(strcurr,asctime(&tm));
   free_matrix(hess,1,npar,1,npar);  /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time; 
         itmp = strlen(strcurr);
 }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
 /*************** hessian matrix ****************/        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 double hessii( double x[], double delta, int theta, double delti[])        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 {        for(niterf=10;niterf<=30;niterf+=10){
   int i;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   int l=1, lmax=20;          tmf = *localtime(&forecast_time.tv_sec);
   double k1,k2;  /*      asctime_r(&tmf,strfor); */
   double p2[NPARMAX+1];          strcpy(strfor,asctime(&tmf));
   double res;          itmp = strlen(strfor);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          if(strfor[itmp-1]=='\n')
   double fx;          strfor[itmp-1]='\0';
   int k=0,kmax=10;          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);
   double l1;          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);
         }
   fx=func(x);      }
   for (i=1;i<=npar;i++) p2[i]=x[i];      for (i=1;i<=n;i++) { 
   for(l=0 ; l <=lmax; l++){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     l1=pow(10,l);        fptt=(*fret); 
     delts=delt;  #ifdef DEBUG
     for(k=1 ; k <kmax; k=k+1){        printf("fret=%lf \n",*fret);
       delt = delta*(l1*k);        fprintf(ficlog,"fret=%lf \n",*fret);
       p2[theta]=x[theta] +delt;  #endif
       k1=func(p2)-fx;        printf("%d",i);fflush(stdout);
       p2[theta]=x[theta]-delt;        fprintf(ficlog,"%d",i);fflush(ficlog);
       k2=func(p2)-fx;        linmin(p,xit,n,fret,func); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */        if (fabs(fptt-(*fret)) > del) { 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          del=fabs(fptt-(*fret)); 
                ibig=i; 
 #ifdef DEBUG        } 
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  #ifdef DEBUG
       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);        printf("%d %.12e",i,(*fret));
 #endif        fprintf(ficlog,"%d %.12e",i,(*fret));
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        for (j=1;j<=n;j++) {
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         k=kmax;          printf(" x(%d)=%.12e",j,xit[j]);
       }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        }
         k=kmax; l=lmax*10.;        for(j=1;j<=n;j++) {
       }          printf(" p=%.12e",p[j]);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          fprintf(ficlog," p=%.12e",p[j]);
         delts=delt;        }
       }        printf("\n");
     }        fprintf(ficlog,"\n");
   }  #endif
   delti[theta]=delts;      } 
   return res;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
    #ifdef DEBUG
 }        int k[2],l;
         k[0]=1;
 double hessij( double x[], double delti[], int thetai,int thetaj)        k[1]=-1;
 {        printf("Max: %.12e",(*func)(p));
   int i;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   int l=1, l1, lmax=20;        for (j=1;j<=n;j++) {
   double k1,k2,k3,k4,res,fx;          printf(" %.12e",p[j]);
   double p2[NPARMAX+1];          fprintf(ficlog," %.12e",p[j]);
   int k;        }
         printf("\n");
   fx=func(x);        fprintf(ficlog,"\n");
   for (k=1; k<=2; k++) {        for(l=0;l<=1;l++) {
     for (i=1;i<=npar;i++) p2[i]=x[i];          for (j=1;j<=n;j++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     k1=func(p2)-fx;            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[thetai]=x[thetai]+delti[thetai]/k;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     k2=func(p2)-fx;        }
    #endif
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;        free_vector(xit,1,n); 
          free_vector(xits,1,n); 
     p2[thetai]=x[thetai]-delti[thetai]/k;        free_vector(ptt,1,n); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        free_vector(pt,1,n); 
     k4=func(p2)-fx;        return; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      } 
 #ifdef DEBUG      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      for (j=1;j<=n;j++) { 
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        ptt[j]=2.0*p[j]-pt[j]; 
 #endif        xit[j]=p[j]-pt[j]; 
   }        pt[j]=p[j]; 
   return res;      } 
 }      fptt=(*func)(ptt); 
       if (fptt < fp) { 
 /************** Inverse of matrix **************/        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 void ludcmp(double **a, int n, int *indx, double *d)        if (t < 0.0) { 
 {          linmin(p,xit,n,fret,func); 
   int i,imax,j,k;          for (j=1;j<=n;j++) { 
   double big,dum,sum,temp;            xi[j][ibig]=xi[j][n]; 
   double *vv;            xi[j][n]=xit[j]; 
            }
   vv=vector(1,n);  #ifdef DEBUG
   *d=1.0;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (i=1;i<=n;i++) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     big=0.0;          for(j=1;j<=n;j++){
     for (j=1;j<=n;j++)            printf(" %.12e",xit[j]);
       if ((temp=fabs(a[i][j])) > big) big=temp;            fprintf(ficlog," %.12e",xit[j]);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          }
     vv[i]=1.0/big;          printf("\n");
   }          fprintf(ficlog,"\n");
   for (j=1;j<=n;j++) {  #endif
     for (i=1;i<j;i++) {        }
       sum=a[i][j];      } 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    } 
       a[i][j]=sum;  } 
     }  
     big=0.0;  /**** Prevalence limit (stable or period prevalence)  ****************/
     for (i=j;i<=n;i++) {  
       sum=a[i][j];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       for (k=1;k<j;k++)  {
         sum -= a[i][k]*a[k][j];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       a[i][j]=sum;       matrix by transitions matrix until convergence is reached */
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;    int i, ii,j,k;
         imax=i;    double min, max, maxmin, maxmax,sumnew=0.;
       }    double **matprod2();
     }    double **out, cov[NCOVMAX+1], **pmij();
     if (j != imax) {    double **newm;
       for (k=1;k<=n;k++) {    double agefin, delaymax=50 ; /* Max number of years to converge */
         dum=a[imax][k];  
         a[imax][k]=a[j][k];    for (ii=1;ii<=nlstate+ndeath;ii++)
         a[j][k]=dum;      for (j=1;j<=nlstate+ndeath;j++){
       }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       *d = -(*d);      }
       vv[imax]=vv[j];  
     }     cov[1]=1.;
     indx[j]=imax;   
     if (a[j][j] == 0.0) a[j][j]=TINY;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     if (j != n) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       dum=1.0/(a[j][j]);      newm=savm;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      /* Covariates have to be included here again */
     }       cov[2]=agefin;
   }    
   free_vector(vv,1,n);  /* Doesn't work */        for (k=1; k<=cptcovn;k++) {
 ;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 }          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         }
 void lubksb(double **a, int n, int *indx, double b[])        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 {        for (k=1; k<=cptcovprod;k++)
   int i,ii=0,ip,j;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double sum;  
          /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   for (i=1;i<=n;i++) {        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     ip=indx[i];        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     sum=b[ip];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     b[ip]=b[i];  
     if (ii)      savm=oldm;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      oldm=newm;
     else if (sum) ii=i;      maxmax=0.;
     b[i]=sum;      for(j=1;j<=nlstate;j++){
   }        min=1.;
   for (i=n;i>=1;i--) {        max=0.;
     sum=b[i];        for(i=1; i<=nlstate; i++) {
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          sumnew=0;
     b[i]=sum/a[i][i];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   }          prlim[i][j]= newm[i][j]/(1-sumnew);
 }          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
 /************ Frequencies ********************/        }
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        maxmin=max-min;
 {  /* Some frequencies */        maxmax=FMAX(maxmax,maxmin);
        }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      if(maxmax < ftolpl){
   int first;        return prlim;
   double ***freq; /* Frequencies */      }
   double *pp;    }
   double pos, k2, dateintsum=0,k2cpt=0;  }
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  /*************** transition probabilities ***************/ 
    
   pp=vector(1,nlstate);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
   strcpy(fileresp,"p");    double s1, s2;
   strcat(fileresp,fileres);    /*double t34;*/
   if((ficresp=fopen(fileresp,"w"))==NULL) {    int i,j,j1, nc, ii, jj;
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      for(i=1; i<= nlstate; i++){
     exit(0);        for(j=1; j<i;j++){
   }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            /*s2 += param[i][j][nc]*cov[nc];*/
   j1=0;            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); */
   j=cptcoveff;          }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          ps[i][j]=s2;
   /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   first=1;        }
         for(j=i+1; j<=nlstate+ndeath;j++){
   for(k1=1; k1<=j;k1++){          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for(i1=1; i1<=ncodemax[k1];i1++){            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       j1++;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          }
         scanf("%d", i);*/          ps[i][j]=s2;
       for (i=-1; i<=nlstate+ndeath; i++)          }
         for (jk=-1; jk<=nlstate+ndeath; jk++)        }
           for(m=agemin; m <= agemax+3; m++)      /*ps[3][2]=1;*/
             freq[i][jk][m]=0;      
            for(i=1; i<= nlstate; i++){
       dateintsum=0;        s1=0;
       k2cpt=0;        for(j=1; j<i; j++){
       for (i=1; i<=imx; i++) {          s1+=exp(ps[i][j]);
         bool=1;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         if  (cptcovn>0) {        }
           for (z1=1; z1<=cptcoveff; z1++)        for(j=i+1; j<=nlstate+ndeath; j++){
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          s1+=exp(ps[i][j]);
               bool=0;          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }        }
         if (bool==1) {        ps[i][i]=1./(s1+1.);
           for(m=firstpass; m<=lastpass; m++){        for(j=1; j<i; j++)
             k2=anint[m][i]+(mint[m][i]/12.);          ps[i][j]= exp(ps[i][j])*ps[i][i];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(j=i+1; j<=nlstate+ndeath; j++)
               if(agev[m][i]==0) agev[m][i]=agemax+1;          ps[i][j]= exp(ps[i][j])*ps[i][i];
               if(agev[m][i]==1) agev[m][i]=agemax+2;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
               if (m<lastpass) {      } /* end i */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
               }        for(jj=1; jj<= nlstate+ndeath; jj++){
                        ps[ii][jj]=0;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          ps[ii][ii]=1;
                 dateintsum=dateintsum+k2;        }
                 k2cpt++;      }
               }      
             }  
           }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
         }  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       }  /*         printf("ddd %lf ",ps[ii][jj]); */
          /*       } */
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  /*       printf("\n "); */
   /*        } */
       if  (cptcovn>0) {  /*        printf("\n ");printf("%lf ",cov[2]); */
         fprintf(ficresp, "\n#********** Variable ");         /*
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         fprintf(ficresp, "**********\n#");        goto end;*/
       }      return ps;
       for(i=1; i<=nlstate;i++)  }
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
       fprintf(ficresp, "\n");  /**************** Product of 2 matrices ******************/
        
       for(i=(int)agemin; i <= (int)agemax+3; i++){  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         if(i==(int)agemax+3){  {
           fprintf(ficlog,"Total");    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         }else{       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
           if(first==1){    /* in, b, out are matrice of pointers which should have been initialized 
             first=0;       before: only the contents of out is modified. The function returns
             printf("See log file for details...\n");       a pointer to pointers identical to out */
           }    long i, j, k;
           fprintf(ficlog,"Age %d", i);    for(i=nrl; i<= nrh; i++)
         }      for(k=ncolol; k<=ncoloh; k++)
         for(jk=1; jk <=nlstate ; jk++){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          out[i][k] +=in[i][j]*b[j][k];
             pp[jk] += freq[jk][m][i];  
         }    return out;
         for(jk=1; jk <=nlstate ; jk++){  }
           for(m=-1, pos=0; m <=0 ; m++)  
             pos += freq[jk][m][i];  
           if(pp[jk]>=1.e-10){  /************* Higher Matrix Product ***************/
             if(first==1){  
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
             }  {
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    /* Computes the transition matrix starting at age 'age' over 
           }else{       'nhstepm*hstepm*stepm' months (i.e. until
             if(first==1)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       nhstepm*hstepm matrices. 
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       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).
        Model is determined by parameters x and covariates have to be 
         for(jk=1; jk <=nlstate ; jk++){       included manually here. 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];       */
         }  
     int i, j, d, h, k;
         for(jk=1,pos=0; jk <=nlstate ; jk++)    double **out, cov[NCOVMAX+1];
           pos += pp[jk];    double **newm;
         for(jk=1; jk <=nlstate ; jk++){  
           if(pos>=1.e-5){    /* Hstepm could be zero and should return the unit matrix */
             if(first==1)    for (i=1;i<=nlstate+ndeath;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);        oldm[i][j]=(i==j ? 1.0 : 0.0);
           }else{        po[i][j][0]=(i==j ? 1.0 : 0.0);
             if(first==1)      }
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for(h=1; h <=nhstepm; h++){
           }      for(d=1; d <=hstepm; d++){
           if( i <= (int) agemax){        newm=savm;
             if(pos>=1.e-5){        /* Covariates have to be included here again */
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        cov[1]=1.;
               probs[i][jk][j1]= pp[jk]/pos;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
               /*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 (k=1; k<=cptcovn;k++) 
             }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
             else        for (k=1; k<=cptcovage;k++)
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           }        for (k=1; k<=cptcovprod;k++)
         }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
          
         for(jk=-1; jk <=nlstate+ndeath; jk++)  
           for(m=-1; m <=nlstate+ndeath; m++)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
             if(freq[jk][m][i] !=0 ) {        /*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(" %d%d=%.0f",jk,m,freq[jk][m][i]);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);        savm=oldm;
             }        oldm=newm;
         if(i <= (int) agemax)      }
           fprintf(ficresp,"\n");      for(i=1; i<=nlstate+ndeath; i++)
         if(first==1)        for(j=1;j<=nlstate+ndeath;j++) {
           printf("Others in log...\n");          po[i][j][h]=newm[i][j];
         fprintf(ficlog,"\n");          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       }        }
     }      /*printf("h=%d ",h);*/
   }    } /* end h */
   dateintmean=dateintsum/k2cpt;  /*     printf("\n H=%d \n",h); */
      return po;
   fclose(ficresp);  }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  
    /*************** log-likelihood *************/
   /* End of Freq */  double func( double *x)
 }  {
     int i, ii, j, k, mi, d, kk;
 /************ Prevalence ********************/    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
 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)    double **out;
 {  /* Some frequencies */    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int s1, s2;
   double ***freq; /* Frequencies */    double bbh, survp;
   double *pp;    long ipmx;
   double pos, k2;    /*extern weight */
     /* We are differentiating ll according to initial status */
   pp=vector(1,nlstate);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    */
   j1=0;    cov[1]=1.;
    
   j=cptcoveff;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
      if(mle==1){
   for(k1=1; k1<=j;k1++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i1=1; i1<=ncodemax[k1];i1++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       j1++;        for(mi=1; mi<= wav[i]-1; mi++){
                for (ii=1;ii<=nlstate+ndeath;ii++)
       for (i=-1; i<=nlstate+ndeath; i++)              for (j=1;j<=nlstate+ndeath;j++){
         for (jk=-1; jk<=nlstate+ndeath; jk++)                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=agemin; m <= agemax+3; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             freq[i][jk][m]=0;            }
                for(d=0; d<dh[mi][i]; d++){
       for (i=1; i<=imx; i++) {            newm=savm;
         bool=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if  (cptcovn>0) {            for (kk=1; kk<=cptcovage;kk++) {
           for (z1=1; z1<=cptcoveff; z1++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            }
               bool=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (bool==1) {            savm=oldm;
           for(m=firstpass; m<=lastpass; m++){            oldm=newm;
             k2=anint[m][i]+(mint[m][i]/12.);          } /* end mult */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        
               if(agev[m][i]==0) agev[m][i]=agemax+1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
               if(agev[m][i]==1) agev[m][i]=agemax+2;          /* But now since version 0.9 we anticipate for bias at large stepm.
               if (m<lastpass) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
                 if (calagedate>0)           * (in months) between two waves is not a multiple of stepm, we rounded to 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];           * the nearest (and in case of equal distance, to the lowest) interval but now
                 else           * we keep into memory the bias bh[mi][i] and also the previous matrix product
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];           * probability in order to take into account the bias as a fraction of the way
               }           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
             }           * -stepm/2 to stepm/2 .
           }           * For 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(i=(int)agemin; i <= (int)agemax+3; i++){          s1=s[mw[mi][i]][i];
         for(jk=1; jk <=nlstate ; jk++){          s2=s[mw[mi+1][i]][i];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          bbh=(double)bh[mi][i]/(double)stepm; 
             pp[jk] += freq[jk][m][i];          /* bias bh is positive if real duration
         }           * is higher than the multiple of stepm and negative otherwise.
         for(jk=1; jk <=nlstate ; jk++){           */
           for(m=-1, pos=0; m <=0 ; m++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
             pos += freq[jk][m][i];          if( s2 > nlstate){ 
         }            /* i.e. if s2 is a death state and if the date of death is known 
                       then the contribution to the likelihood is the probability to 
         for(jk=1; jk <=nlstate ; jk++){               die between last step unit time and current  step unit time, 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)               which is also equal to probability to die before dh 
             pp[jk] += freq[jk][m][i];               minus probability to die before dh-stepm . 
         }               In version up to 0.92 likelihood was computed
                  as if date of death was unknown. Death was treated as any other
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          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
         for(jk=1; jk <=nlstate ; jk++){              to consider that at each interview the state was recorded
           if( i <= (int) agemax){          (healthy, disable or death) and IMaCh was corrected; but when we
             if(pos>=1.e-5){          introduced the exact date of death then we should have modified
               probs[i][jk][j1]= pp[jk]/pos;          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
         }/* end jk */          and month of death but the probability to survive from last
       }/* end i */          interview up to one month before death multiplied by the
     } /* end i1 */          probability to die within a month. Thanks to Chris
   } /* end k1 */          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
            which slows down the processing. The difference can be up to 10%
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          lower mortality.
   free_vector(pp,1,nlstate);            */
              lli=log(out[s1][s2] - savm[s1][s2]);
 }  /* End of Freq */  
   
 /************* Waves Concatenation ***************/          } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 {            /*survp += out[s1][j]; */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            lli= log(survp);
      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] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          else if  (s2==-4) { 
      and mw[mi+1][i]. dh depends on stepm.            for (j=3,survp=0. ; j<=nlstate; j++)  
      */              survp += (1.+bbh)*out[s1][j]- bbh*savm[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==-5) { 
   int first;            for (j=1,survp=0. ; j<=2; 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{
   jmean=0.;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for(i=1; i<=imx; i++){            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     mi=0;          } 
     m=firstpass;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     while(s[m][i] <= nlstate){          /*if(lli ==000.0)*/
       if(s[m][i]>=1)          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         mw[++mi][i]=m;          ipmx +=1;
       if(m >=lastpass)          sw += weight[i];
         break;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       else        } /* end of wave */
         m++;      } /* end of individual */
     }/* end while */    }  else if(mle==2){
     if (s[m][i] > nlstate){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       mi++;     /* Death is another wave */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       /* if(mi==0)  never been interviewed correctly before death */        for(mi=1; mi<= wav[i]-1; mi++){
          /* Only death is a correct wave */          for (ii=1;ii<=nlstate+ndeath;ii++)
       mw[mi][i]=m;            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
     wav[i]=mi;            }
     if(mi==0){          for(d=0; d<=dh[mi][i]; d++){
       if(first==0){            newm=savm;
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         first=1;            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if(first==1){            }
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     } /* end mi==0 */            savm=oldm;
   }            oldm=newm;
           } /* end mult */
   for(i=1; i<=imx; i++){        
     for(mi=1; mi<wav[i];mi++){          s1=s[mw[mi][i]][i];
       if (stepm <=0)          s2=s[mw[mi+1][i]][i];
         dh[mi][i]=1;          bbh=(double)bh[mi][i]/(double)stepm; 
       else{          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 (s[mw[mi+1][i]][i] > nlstate) {          ipmx +=1;
           if (agedc[i] < 2*AGESUP) {          sw += weight[i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if(j==0) j=1;  /* Survives at least one month after exam */        } /* end of wave */
           k=k+1;      } /* end of individual */
           if (j >= jmax) jmax=j;    }  else if(mle==3){  /* exponential inter-extrapolation */
           if (j <= jmin) jmin=j;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           sum=sum+j;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        for(mi=1; mi<= wav[i]-1; mi++){
           }          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
         else{              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           k=k+1;            }
           if (j >= jmax) jmax=j;          for(d=0; d<dh[mi][i]; d++){
           else if (j <= jmin)jmin=j;            newm=savm;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           sum=sum+j;            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         jk= j/stepm;            }
         jl= j -jk*stepm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         ju= j -(jk+1)*stepm;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if(jl <= -ju)            savm=oldm;
           dh[mi][i]=jk;            oldm=newm;
         else          } /* end mult */
           dh[mi][i]=jk+1;        
         if(dh[mi][i]==0)          s1=s[mw[mi][i]][i];
           dh[mi][i]=1; /* At least one step */          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 */
   }          ipmx +=1;
   jmean=sum/k;          sw += weight[i];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        } /* end of wave */
  }      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
 /*********** Tricode ****************************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 void tricode(int *Tvar, int **nbcode, int imx)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {        for(mi=1; mi<= wav[i]-1; mi++){
   int Ndum[20],ij=1, k, j, i;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int cptcode=0;            for (j=1;j<=nlstate+ndeath;j++){
   cptcoveff=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (k=0; k<19; k++) Ndum[k]=0;            }
   for (k=1; k<=7; k++) ncodemax[k]=0;          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for (i=1; i<=imx; i++) {            for (kk=1; kk<=cptcovage;kk++) {
       ij=(int)(covar[Tvar[j]][i]);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       Ndum[ij]++;            }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          
       if (ij > cptcode) cptcode=ij;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for (i=0; i<=cptcode; i++) {            oldm=newm;
       if(Ndum[i]!=0) ncodemax[j]++;          } /* end mult */
     }        
     ij=1;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
     for (i=1; i<=ncodemax[j]; i++) {            lli=log(out[s1][s2] - savm[s1][s2]);
       for (k=0; k<=19; k++) {          }else{
         if (Ndum[k] != 0) {            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           nbcode[Tvar[j]][ij]=k;          }
                    ipmx +=1;
           ij++;          sw += weight[i];
         }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if (ij > ncodemax[j]) break;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       }          } /* end of wave */
     }      } /* end of individual */
   }      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       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(mi=1; mi<= wav[i]-1; mi++){
  for (i=1; i<=ncovmodel-2; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
    ij=Tvar[i];            for (j=1;j<=nlstate+ndeath;j++){
    Ndum[ij]++;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
  ij=1;          for(d=0; d<dh[mi][i]; d++){
  for (i=1; i<=10; i++) {            newm=savm;
    if((Ndum[i]!=0) && (i<=ncovcol)){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      Tvaraff[ij]=i;            for (kk=1; kk<=cptcovage;kk++) {
      ij++;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
    }            }
  }          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  cptcoveff=ij-1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 /*********** Health Expectancies ****************/          } /* end mult */
         
 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 )          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   /* Health expectancies */          ipmx +=1;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          sw += weight[i];
   double age, agelim, hf;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double ***p3mat,***varhe;          /*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]);*/
   double **dnewm,**doldm;        } /* end of wave */
   double *xp;      } /* end of individual */
   double **gp, **gm;    } /* End of if */
   double ***gradg, ***trgradg;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   int theta;    /* 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 */
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    return -l;
   xp=vector(1,npar);  }
   dnewm=matrix(1,nlstate*2,1,npar);  
   doldm=matrix(1,nlstate*2,1,nlstate*2);  /*************** log-likelihood *************/
    double funcone( double *x)
   fprintf(ficreseij,"# Health expectancies\n");  {
   fprintf(ficreseij,"# Age");    /* Same as likeli but slower because of a lot of printf and if */
   for(i=1; i<=nlstate;i++)    int i, ii, j, k, mi, d, kk;
     for(j=1; j<=nlstate;j++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    double **out;
   fprintf(ficreseij,"\n");    double lli; /* Individual log likelihood */
     double llt;
   if(estepm < stepm){    int s1, s2;
     printf ("Problem %d lower than %d\n",estepm, stepm);    double bbh, survp;
   }    /*extern weight */
   else  hstepm=estepm;      /* We are differentiating ll according to initial status */
   /* We compute the life expectancy from trapezoids spaced every estepm months    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
    * This is mainly to measure the difference between two models: for example    /*for(i=1;i<imx;i++) 
    * if stepm=24 months pijx are given only every 2 years and by summing them      printf(" %d\n",s[4][i]);
    * we are calculating an estimate of the Life Expectancy assuming a linear    */
    * progression inbetween and thus overestimating or underestimating according    cov[1]=1.;
    * to the curvature of the survival function. If, for the same date, we  
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    for(k=1; k<=nlstate; k++) ll[k]=0.;
    * to compare the new estimate of Life expectancy with the same linear  
    * hypothesis. A more precise result, taking into account a more precise    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    * curvature will be obtained if estepm is as small as stepm. */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
   /* For example we decided to compute the life expectancy with the smallest unit */        for (ii=1;ii<=nlstate+ndeath;ii++)
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          for (j=1;j<=nlstate+ndeath;j++){
      nhstepm is the number of hstepm from age to agelim            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      nstepm is the number of stepm from age to agelin.            savm[ii][j]=(ii==j ? 1.0 : 0.0);
      Look at hpijx to understand the reason of that which relies in memory size          }
      and note for a fixed period like estepm months */        for(d=0; d<dh[mi][i]; d++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          newm=savm;
      survival function given by stepm (the optimization length). Unfortunately it          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      means that if the survival funtion is printed only each two years of age and if          for (kk=1; kk<=cptcovage;kk++) {
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      results. So we changed our mind and took the option of the best precision.          }
   */          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
   agelim=AGESUP;          oldm=newm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        } /* end mult */
     /* nhstepm age range expressed in number of stepm */        
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        s1=s[mw[mi][i]][i];
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        s2=s[mw[mi+1][i]][i];
     /* if (stepm >= YEARM) hstepm=1;*/        bbh=(double)bh[mi][i]/(double)stepm; 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        /* bias is positive if real duration
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         * is higher than the multiple of stepm and negative otherwise.
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);         */
     gp=matrix(0,nhstepm,1,nlstate*2);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     gm=matrix(0,nhstepm,1,nlstate*2);          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if  (s2==-2) {
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          for (j=1,survp=0. ; j<=nlstate; j++) 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            lli= log(survp);
          }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        } 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 */
     /* Computing Variances of health expectancies */        } 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 */
      for(theta=1; theta <=npar; theta++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       for(i=1; i<=npar; i++){          lli=log(out[s1][s2]); /* Original formula */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       }          lli=log(out[s1][s2]); /* Original formula */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          } /* End of if */
          ipmx +=1;
       cptj=0;        sw += weight[i];
       for(j=1; j<= nlstate; j++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(i=1; i<=nlstate; i++){        /*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]); */
           cptj=cptj+1;        if(globpr){
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;   %11.6f %11.6f %11.6f ", \
           }                  num[i],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,llt=0.,l=0.; k<=nlstate; k++){
                  llt +=ll[k]*gipmx/gsw;
                  fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       for(i=1; i<=npar; i++)          }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          fprintf(ficresilk," %10.6f\n", -llt);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
            } /* end of wave */
       cptj=0;    } /* end of individual */
       for(j=1; j<= nlstate; j++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         for(i=1;i<=nlstate;i++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           cptj=cptj+1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    if(globpr==0){ /* First time we count the contributions and weights */
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      gipmx=ipmx;
           }      gsw=sw;
         }    }
       }    return -l;
       for(j=1; j<= nlstate*2; j++)  }
         for(h=0; h<=nhstepm-1; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }  /*************** function likelione ***********/
      }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
      {
 /* End theta */    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);       to check the exact contribution to the likelihood.
        Plotting could be done.
      for(h=0; h<=nhstepm-1; h++)     */
       for(j=1; j<=nlstate*2;j++)    int k;
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];    if(*globpri !=0){ /* Just counts and sums, no printings */
            strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
      for(i=1;i<=nlstate*2;i++)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for(j=1;j<=nlstate*2;j++)        printf("Problem with resultfile: %s\n", fileresilk);
         varhe[i][j][(int)age] =0.;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
      printf("%d|",(int)age);fflush(stdout);      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
      for(h=0;h<=nhstepm-1;h++){      /*  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=0;k<=nhstepm-1;k++){      for(k=1; k<=nlstate; k++) 
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         for(i=1;i<=nlstate*2;i++)    }
           for(j=1;j<=nlstate*2;j++)  
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    *fretone=(*funcone)(p);
       }    if(*globpri !=0){
     }      fclose(ficresilk);
     /* Computing expectancies */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     for(i=1; i<=nlstate;i++)      fflush(fichtm); 
       for(j=1; j<=nlstate;j++)    } 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    return;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  }
            
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/  
   /*********** Maximum Likelihood Estimation ***************/
         }  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     fprintf(ficreseij,"%3.0f",age );  {
     cptj=0;    int i,j, iter;
     for(i=1; i<=nlstate;i++)    double **xi;
       for(j=1; j<=nlstate;j++){    double fret;
         cptj++;    double fretone; /* Only one call to likelihood */
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    /*  char filerespow[FILENAMELENGTH];*/
       }    xi=matrix(1,npar,1,npar);
     fprintf(ficreseij,"\n");    for (i=1;i<=npar;i++)
          for (j=1;j<=npar;j++)
     free_matrix(gm,0,nhstepm,1,nlstate*2);        xi[i][j]=(i==j ? 1.0 : 0.0);
     free_matrix(gp,0,nhstepm,1,nlstate*2);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    strcpy(filerespow,"pow"); 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    strcat(filerespow,fileres);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", filerespow);
   printf("\n");      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   fprintf(ficlog,"\n");    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
   free_vector(xp,1,npar);    for (i=1;i<=nlstate;i++)
   free_matrix(dnewm,1,nlstate*2,1,npar);      for(j=1;j<=nlstate+ndeath;j++)
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    fprintf(ficrespow,"\n");
 }  
     powell(p,xi,npar,ftol,&iter,&fret,func);
 /************ Variance ******************/  
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased)    free_matrix(xi,1,npar,1,npar);
 {    fclose(ficrespow);
   /* Variance of health expectancies */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   /* double **newm;*/    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **dnewm,**doldm;  
   double **dnewmp,**doldmp;  }
   int i, j, nhstepm, hstepm, h, nstepm ;  
   int k, cptcode;  /**** Computes Hessian and covariance matrix ***/
   double *xp;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double **gp, **gm;  /* for var eij */  {
   double ***gradg, ***trgradg; /*for var eij */    double  **a,**y,*x,pd;
   double **gradgp, **trgradgp; /* for var p point j */    double **hess;
   double *gpp, *gmp; /* for var p point j */    int i, j,jk;
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */    int *indx;
   double ***p3mat;  
   double age,agelim, hf;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   int theta;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   char digit[4];    void lubksb(double **a, int npar, int *indx, double b[]) ;
   char digitp[16];    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
   char fileresprobmorprev[FILENAMELENGTH];    hess=matrix(1,npar,1,npar);
   
   if(popbased==1)    printf("\nCalculation of the hessian matrix. Wait...\n");
     strcpy(digitp,"-populbased-");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   else    for (i=1;i<=npar;i++){
     strcpy(digitp,"-stablbased-");      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
   strcpy(fileresprobmorprev,"prmorprev");     
   sprintf(digit,"%-d",ij);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/      
   strcat(fileresprobmorprev,digit); /* Tvar to be done */      /*  printf(" %f ",p[i]);
   strcat(fileresprobmorprev,digitp); /* Popbased or not */          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   strcat(fileresprobmorprev,fileres);    }
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {    
     printf("Problem with resultfile: %s\n", fileresprobmorprev);    for (i=1;i<=npar;i++) {
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);      for (j=1;j<=npar;j++)  {
   }        if (j>i) { 
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          printf(".%d%d",i,j);fflush(stdout);
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");          hess[i][j]=hessij(p,delti,i,j,func,npar);
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);          
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){          hess[j][i]=hess[i][j];    
     fprintf(ficresprobmorprev," p.%-d SE",j);          /*printf(" %lf ",hess[i][j]);*/
     for(i=1; i<=nlstate;i++)        }
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);      }
   }      }
   fprintf(ficresprobmorprev,"\n");    printf("\n");
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    fprintf(ficlog,"\n");
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);  
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     exit(0);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   }    
   else{    a=matrix(1,npar,1,npar);
     fprintf(ficgp,"\n# Routine varevsij");    y=matrix(1,npar,1,npar);
   }    x=vector(1,npar);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    indx=ivector(1,npar);
     printf("Problem with html file: %s\n", optionfilehtm);    for (i=1;i<=npar;i++)
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     exit(0);    ludcmp(a,npar,indx,&pd);
   }  
   else{    for (j=1;j<=npar;j++) {
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");      for (i=1;i<=npar;i++) x[i]=0;
   }      x[j]=1;
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   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");        matcov[i][j]=x[i];
   fprintf(ficresvij,"# Age");      }
   for(i=1; i<=nlstate;i++)    }
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    printf("\n#Hessian matrix#\n");
   fprintf(ficresvij,"\n");    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
   xp=vector(1,npar);      for (j=1;j<=npar;j++) { 
   dnewm=matrix(1,nlstate,1,npar);        printf("%.3e ",hess[i][j]);
   doldm=matrix(1,nlstate,1,nlstate);        fprintf(ficlog,"%.3e ",hess[i][j]);
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);      }
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      printf("\n");
       fprintf(ficlog,"\n");
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);    }
   gpp=vector(nlstate+1,nlstate+ndeath);  
   gmp=vector(nlstate+1,nlstate+ndeath);    /* Recompute Inverse */
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   if(estepm < stepm){    ludcmp(a,npar,indx,&pd);
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }    /*  printf("\n#Hessian matrix recomputed#\n");
   else  hstepm=estepm;    
   /* For example we decided to compute the life expectancy with the smallest unit */    for (j=1;j<=npar;j++) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (i=1;i<=npar;i++) x[i]=0;
      nhstepm is the number of hstepm from age to agelim      x[j]=1;
      nstepm is the number of stepm from age to agelin.      lubksb(a,npar,indx,x);
      Look at hpijx to understand the reason of that which relies in memory size      for (i=1;i<=npar;i++){ 
      and note for a fixed period like k years */        y[i][j]=x[i];
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        printf("%.3e ",y[i][j]);
      survival function given by stepm (the optimization length). Unfortunately it        fprintf(ficlog,"%.3e ",y[i][j]);
      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      printf("\n");
      results. So we changed our mind and took the option of the best precision.      fprintf(ficlog,"\n");
   */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    */
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    free_matrix(a,1,npar,1,npar);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_matrix(y,1,npar,1,npar);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    free_vector(x,1,npar);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_ivector(indx,1,npar);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    free_matrix(hess,1,npar,1,npar);
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);  
   }
   
     for(theta=1; theta <=npar; theta++){  /*************** hessian matrix ****************/
       for(i=1; i<=npar; i++){ /* Computes gradient */  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    int i;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int l=1, lmax=20;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double k1,k2;
     double p2[MAXPARM+1]; /* identical to x */
       if (popbased==1) {    double res;
         for(i=1; i<=nlstate;i++)    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           prlim[i][i]=probs[(int)age][i][ij];    double fx;
       }    int k=0,kmax=10;
      double l1;
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    fx=func(x);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    for (i=1;i<=npar;i++) p2[i]=x[i];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    for(l=0 ; l <=lmax; l++){
         }      l1=pow(10,l);
       }      delts=delt;
       /* This for computing forces of mortality (h=1)as a weighted average */      for(k=1 ; k <kmax; k=k+1){
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){        delt = delta*(l1*k);
         for(i=1; i<= nlstate; i++)        p2[theta]=x[theta] +delt;
           gpp[j] += prlim[i][i]*p3mat[i][j][1];        k1=func(p2)-fx;
       }            p2[theta]=x[theta]-delt;
       /* end force of mortality */        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
       for(i=1; i<=npar; i++) /* Computes gradient */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    #ifdef DEBUGHESS
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
          fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       if (popbased==1) {  #endif
         for(i=1; i<=nlstate;i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           prlim[i][i]=probs[(int)age][i][ij];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       }          k=kmax;
         }
       for(j=1; j<= nlstate; j++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         for(h=0; h<=nhstepm; h++){          k=kmax; l=lmax*10.;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         }          delts=delt;
       }        }
       /* This for computing force of mortality (h=1)as a weighted average */      }
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    }
         for(i=1; i<= nlstate; i++)    delti[theta]=delts;
           gmp[j] += prlim[i][i]*p3mat[i][j][1];    return res; 
       }        
       /* end force of mortality */  }
   
       for(j=1; j<= nlstate; j++) /* vareij */  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
         for(h=0; h<=nhstepm; h++){  {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    int i;
         }    int l=1, l1, lmax=20;
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */    double k1,k2,k3,k4,res,fx;
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];    double p2[MAXPARM+1];
       }    int k;
   
     } /* End theta */    fx=func(x);
     for (k=1; k<=2; k++) {
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
     for(h=0; h<=nhstepm; h++) /* veij */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       for(j=1; j<=nlstate;j++)      k1=func(p2)-fx;
         for(theta=1; theta <=npar; theta++)    
           trgradg[h][j][theta]=gradg[h][theta][j];      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */      k2=func(p2)-fx;
       for(theta=1; theta <=npar; theta++)    
         trgradgp[j][theta]=gradgp[theta][j];      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      k3=func(p2)-fx;
     for(i=1;i<=nlstate;i++)    
       for(j=1;j<=nlstate;j++)      p2[thetai]=x[thetai]-delti[thetai]/k;
         vareij[i][j][(int)age] =0.;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
     for(h=0;h<=nhstepm;h++){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       for(k=0;k<=nhstepm;k++){  #ifdef DEBUG
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      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);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      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);
         for(i=1;i<=nlstate;i++)  #endif
           for(j=1;j<=nlstate;j++)    }
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    return res;
       }  }
     }  
   /************** Inverse of matrix **************/
     /* pptj */  void ludcmp(double **a, int n, int *indx, double *d) 
     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);    int i,imax,j,k; 
     for(j=nlstate+1;j<=nlstate+ndeath;j++)    double big,dum,sum,temp; 
       for(i=nlstate+1;i<=nlstate+ndeath;i++)    double *vv; 
         varppt[j][i]=doldmp[j][i];   
     /* end ppptj */    vv=vector(1,n); 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);      *d=1.0; 
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    for (i=1;i<=n;i++) { 
        big=0.0; 
     if (popbased==1) {      for (j=1;j<=n;j++) 
       for(i=1; i<=nlstate;i++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
         prlim[i][i]=probs[(int)age][i][ij];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     }      vv[i]=1.0/big; 
        } 
     /* This for computing force of mortality (h=1)as a weighted average */    for (j=1;j<=n;j++) { 
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){      for (i=1;i<j;i++) { 
       for(i=1; i<= nlstate; i++)        sum=a[i][j]; 
         gmp[j] += prlim[i][i]*p3mat[i][j][1];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     }            a[i][j]=sum; 
     /* end force of mortality */      } 
       big=0.0; 
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);      for (i=j;i<=n;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<j;k++) 
       for(i=1; i<=nlstate;i++){          sum -= a[i][k]*a[k][j]; 
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);        a[i][j]=sum; 
       }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     }          big=dum; 
     fprintf(ficresprobmorprev,"\n");          imax=i; 
         } 
     fprintf(ficresvij,"%.0f ",age );      } 
     for(i=1; i<=nlstate;i++)      if (j != imax) { 
       for(j=1; j<=nlstate;j++){        for (k=1;k<=n;k++) { 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          dum=a[imax][k]; 
       }          a[imax][k]=a[j][k]; 
     fprintf(ficresvij,"\n");          a[j][k]=dum; 
     free_matrix(gp,0,nhstepm,1,nlstate);        } 
     free_matrix(gm,0,nhstepm,1,nlstate);        *d = -(*d); 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        vv[imax]=vv[j]; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      } 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      indx[j]=imax; 
   } /* End age */      if (a[j][j] == 0.0) a[j][j]=TINY; 
   free_vector(gpp,nlstate+1,nlstate+ndeath);      if (j != n) { 
   free_vector(gmp,nlstate+1,nlstate+ndeath);        dum=1.0/(a[j][j]); 
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   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");    } 
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    free_vector(vv,1,n);  /* Doesn't work */
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");  ;
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);  } 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);  
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);  void lubksb(double **a, int n, int *indx, double b[]) 
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);  { 
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);    int i,ii=0,ip,j; 
   /*  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);    double sum; 
 */   
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
   free_vector(xp,1,npar);      sum=b[ip]; 
   free_matrix(doldm,1,nlstate,1,nlstate);      b[ip]=b[i]; 
   free_matrix(dnewm,1,nlstate,1,npar);      if (ii) 
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);      else if (sum) ii=i; 
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      b[i]=sum; 
   fclose(ficresprobmorprev);    } 
   fclose(ficgp);    for (i=n;i>=1;i--) { 
   fclose(fichtm);      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 }      b[i]=sum/a[i][i]; 
     } 
 /************ Variance of prevlim ******************/  } 
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  
 {  void pstamp(FILE *fichier)
   /* Variance of prevalence limit */  {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   double **newm;  }
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm;  /************ Frequencies ********************/
   int k, cptcode;  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   double *xp;  {  /* Some frequencies */
   double *gp, *gm;    
   double **gradg, **trgradg;    int i, m, jk, k1,i1, j1, bool, z1,j;
   double age,agelim;    int first;
   int theta;    double ***freq; /* Frequencies */
        double *pp, **prop;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   fprintf(ficresvpl,"# Age");    char fileresp[FILENAMELENGTH];
   for(i=1; i<=nlstate;i++)    
       fprintf(ficresvpl," %1d-%1d",i,i);    pp=vector(1,nlstate);
   fprintf(ficresvpl,"\n");    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
   xp=vector(1,npar);    strcat(fileresp,fileres);
   dnewm=matrix(1,nlstate,1,npar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   doldm=matrix(1,nlstate,1,nlstate);      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   hstepm=1*YEARM; /* Every year of age */      exit(0);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    }
   agelim = AGESUP;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    j1=0;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    
     if (stepm >= YEARM) hstepm=1;    j=cptcoveff;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);    first=1;
     gm=vector(1,nlstate);  
     for(k1=1; k1<=j;k1++){
     for(theta=1; theta <=npar; theta++){      for(i1=1; i1<=ncodemax[k1];i1++){
       for(i=1; i<=npar; i++){ /* Computes gradient */        j1++;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       }          scanf("%d", i);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (i=-5; i<=nlstate+ndeath; i++)  
       for(i=1;i<=nlstate;i++)          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         gp[i] = prlim[i][i];            for(m=iagemin; m <= iagemax+3; m++)
                  freq[i][jk][m]=0;
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1; i<=nlstate; i++)  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(m=iagemin; m <= iagemax+3; m++)
       for(i=1;i<=nlstate;i++)          prop[i][m]=0;
         gm[i] = prlim[i][i];        
         dateintsum=0;
       for(i=1;i<=nlstate;i++)        k2cpt=0;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        for (i=1; i<=imx; i++) {
     } /* End theta */          bool=1;
           if  (cptcovn>0) {
     trgradg =matrix(1,nlstate,1,npar);            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for(j=1; j<=nlstate;j++)                bool=0;
       for(theta=1; theta <=npar; theta++)          }
         trgradg[j][theta]=gradg[theta][j];          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
     for(i=1;i<=nlstate;i++)              k2=anint[m][i]+(mint[m][i]/12.);
       varpl[i][(int)age] =0.;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     for(i=1;i<=nlstate;i++)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     fprintf(ficresvpl,"%.0f ",age );                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     for(i=1; i<=nlstate;i++)                }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));                
     fprintf(ficresvpl,"\n");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     free_vector(gp,1,nlstate);                  dateintsum=dateintsum+k2;
     free_vector(gm,1,nlstate);                  k2cpt++;
     free_matrix(gradg,1,npar,1,nlstate);                }
     free_matrix(trgradg,1,nlstate,1,npar);                /*}*/
   } /* End age */            }
           }
   free_vector(xp,1,npar);        }
   free_matrix(doldm,1,nlstate,1,npar);         
   free_matrix(dnewm,1,nlstate,1,nlstate);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         pstamp(ficresp);
 }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
 /************ Variance of one-step probabilities  ******************/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          fprintf(ficresp, "**********\n#");
 {        }
   int i, j=0,  i1, k1, l1, t, tj;        for(i=1; i<=nlstate;i++) 
   int k2, l2, j1,  z1;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   int k=0,l, cptcode;        fprintf(ficresp, "\n");
   int first=1, first1;        
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;        for(i=iagemin; i <= iagemax+3; i++){
   double **dnewm,**doldm;          if(i==iagemax+3){
   double *xp;            fprintf(ficlog,"Total");
   double *gp, *gm;          }else{
   double **gradg, **trgradg;            if(first==1){
   double **mu;              first=0;
   double age,agelim, cov[NCOVMAX];              printf("See log file for details...\n");
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */            }
   int theta;            fprintf(ficlog,"Age %d", i);
   char fileresprob[FILENAMELENGTH];          }
   char fileresprobcov[FILENAMELENGTH];          for(jk=1; jk <=nlstate ; jk++){
   char fileresprobcor[FILENAMELENGTH];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
   double ***varpij;          }
           for(jk=1; jk <=nlstate ; jk++){
   strcpy(fileresprob,"prob");            for(m=-1, pos=0; m <=0 ; m++)
   strcat(fileresprob,fileres);              pos += freq[jk][m][i];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            if(pp[jk]>=1.e-10){
     printf("Problem with resultfile: %s\n", fileresprob);              if(first==1){
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }              }
   strcpy(fileresprobcov,"probcov");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   strcat(fileresprobcov,fileres);            }else{
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {              if(first==1)
     printf("Problem with resultfile: %s\n", fileresprobcov);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   }            }
   strcpy(fileresprobcor,"probcor");          }
   strcat(fileresprobcor,fileres);  
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {          for(jk=1; jk <=nlstate ; jk++){
     printf("Problem with resultfile: %s\n", fileresprobcor);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);              pp[jk] += freq[jk][m][i];
   }          }       
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);            pos += pp[jk];
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);            posprop += prop[jk][i];
   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);            if(pos>=1.e-5){
                if(first==1)
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   fprintf(ficresprob,"# Age");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");            }else{
   fprintf(ficresprobcov,"# Age");              if(first==1)
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficresprobcov,"# Age");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
             if( i <= iagemax){
   for(i=1; i<=nlstate;i++)              if(pos>=1.e-5){
     for(j=1; j<=(nlstate+ndeath);j++){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);                /*probs[i][jk][j1]= pp[jk]/pos;*/
       fprintf(ficresprobcov," p%1d-%1d ",i,j);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       fprintf(ficresprobcor," p%1d-%1d ",i,j);              }
     }                else
   fprintf(ficresprob,"\n");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   fprintf(ficresprobcov,"\n");            }
   fprintf(ficresprobcor,"\n");          }
   xp=vector(1,npar);          
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          for(jk=-1; jk <=nlstate+ndeath; jk++)
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));            for(m=-1; m <=nlstate+ndeath; m++)
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);              if(freq[jk][m][i] !=0 ) {
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);              if(first==1)
   first=1;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);              }
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);          if(i <= iagemax)
     exit(0);            fprintf(ficresp,"\n");
   }          if(first==1)
   else{            printf("Others in log...\n");
     fprintf(ficgp,"\n# Routine varprob");          fprintf(ficlog,"\n");
   }        }
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {      }
     printf("Problem with html file: %s\n", optionfilehtm);    }
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    dateintmean=dateintsum/k2cpt; 
     exit(0);   
   }    fclose(ficresp);
   else{    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    free_vector(pp,1,nlstate);
     fprintf(fichtm,"\n");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
     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");  
     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");  /************ Prevalence ********************/
   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)
   }  {  
     /* 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).
   cov[1]=1;       We still use firstpass and lastpass as another selection.
   tj=cptcoveff;    */
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}   
   j1=0;    int i, m, jk, k1, i1, j1, bool, z1,j;
   for(t=1; t<=tj;t++){    double ***freq; /* Frequencies */
     for(i1=1; i1<=ncodemax[t];i1++){    double *pp, **prop;
       j1++;    double pos,posprop; 
          double  y2; /* in fractional years */
       if  (cptcovn>0) {    int iagemin, iagemax;
         fprintf(ficresprob, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    iagemin= (int) agemin;
         fprintf(ficresprob, "**********\n#");    iagemax= (int) agemax;
         fprintf(ficresprobcov, "\n#********** Variable ");    /*pp=vector(1,nlstate);*/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         fprintf(ficresprobcov, "**********\n#");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
            j1=0;
         fprintf(ficgp, "\n#********** Variable ");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    j=cptcoveff;
         fprintf(ficgp, "**********\n#");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
            
            for(k1=1; k1<=j;k1++){
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");      for(i1=1; i1<=ncodemax[k1];i1++){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        j1++;
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");        
                for (i=1; i<=nlstate; i++)  
         fprintf(ficresprobcor, "\n#********** Variable ");              for(m=iagemin; m <= iagemax+3; m++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            prop[i][m]=0.0;
         fprintf(ficgp, "**********\n#");           
       }        for (i=1; i<=imx; i++) { /* Each individual */
                bool=1;
       for (age=bage; age<=fage; age ++){          if  (cptcovn>0) {
         cov[2]=age;            for (z1=1; z1<=cptcoveff; z1++) 
         for (k=1; k<=cptcovn;k++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];                bool=0;
         }          } 
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          if (bool==1) { 
         for (k=1; k<=cptcovprod;k++)            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                      if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         gp=vector(1,(nlstate)*(nlstate+ndeath));                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); 
         gm=vector(1,(nlstate)*(nlstate+ndeath));                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                      /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
         for(theta=1; theta <=npar; theta++){                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
           for(i=1; i<=npar; i++)                  prop[s[m][i]][iagemax+3] += weight[i]; 
             xp[i] = x[i] + (i==theta ?delti[theta]:0);                } 
                        }
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            } /* end selection of waves */
                    }
           k=0;        }
           for(i=1; i<= (nlstate); i++){        for(i=iagemin; i <= iagemax+3; i++){  
             for(j=1; j<=(nlstate+ndeath);j++){          
               k=k+1;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
               gp[k]=pmmij[i][j];            posprop += prop[jk][i]; 
             }          } 
           }  
                    for(jk=1; jk <=nlstate ; jk++){     
           for(i=1; i<=npar; i++)            if( i <=  iagemax){ 
             xp[i] = x[i] - (i==theta ?delti[theta]:0);              if(posprop>=1.e-5){ 
                    probs[i][jk][j1]= prop[jk][i]/posprop;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);              } else
           k=0;                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
           for(i=1; i<=(nlstate); i++){            } 
             for(j=1; j<=(nlstate+ndeath);j++){          }/* end jk */ 
               k=k+1;        }/* end i */ 
               gm[k]=pmmij[i][j];      } /* end i1 */
             }    } /* end k1 */
           }    
          /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    /*free_vector(pp,1,nlstate);*/
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         }  }  /* End of prevalence */
   
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)  /************* Waves Concatenation ***************/
           for(theta=1; theta <=npar; theta++)  
             trgradg[j][theta]=gradg[theta][j];  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)
          {
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);       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
         pmij(pmmij,cov,ncovmodel,x,nlstate);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
               and mw[mi+1][i]. dh depends on stepm.
         k=0;       */
         for(i=1; i<=(nlstate); i++){  
           for(j=1; j<=(nlstate+ndeath);j++){    int i, mi, m;
             k=k+1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
             mu[k][(int) age]=pmmij[i][j];       double sum=0., jmean=0.;*/
           }    int first;
         }    int j, k=0,jk, ju, jl;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    double sum=0.;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    first=0;
             varpij[i][j][(int)age] = doldm[i][j];    jmin=1e+5;
     jmax=-1;
         /*printf("\n%d ",(int)age);    jmean=0.;
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    for(i=1; i<=imx; i++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      mi=0;
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      m=firstpass;
      }*/      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         fprintf(ficresprob,"\n%d ",(int)age);          mw[++mi][i]=m;
         fprintf(ficresprobcov,"\n%d ",(int)age);        if(m >=lastpass)
         fprintf(ficresprobcor,"\n%d ",(int)age);          break;
         else
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)          m++;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));      }/* end while */
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){      if (s[m][i] > nlstate){
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);        mi++;     /* Death is another wave */
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);        /* if(mi==0)  never been interviewed correctly before death */
         }           /* Only death is a correct wave */
         i=0;        mw[mi][i]=m;
         for (k=1; k<=(nlstate);k++){      }
           for (l=1; l<=(nlstate+ndeath);l++){  
             i=i++;      wav[i]=mi;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);      if(mi==0){
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);        nbwarn++;
             for (j=1; j<=i;j++){        if(first==0){
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));          first=1;
             }        }
           }        if(first==1){
         }/* end of loop for state */          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       } /* end of loop for age */        }
       } /* end mi==0 */
       /* Confidence intervalle of pij  */    } /* End individuals */
       /*  
       fprintf(ficgp,"\nset noparametric;unset label");    for(i=1; i<=imx; i++){
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");      for(mi=1; mi<wav[i];mi++){
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        if (stepm <=0)
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);          dh[mi][i]=1;
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);        else{
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);            if (agedc[i] < 2*AGESUP) {
       */              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/              else if(j<0){
       first1=1;                nberr++;
       for (k2=1; k2<=(nlstate);k2++){                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 (l2=1; l2<=(nlstate+ndeath);l2++){                j=1; /* Temporary Dangerous patch */
           if(l2==k2) continue;                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);
           j=(k2-1)*(nlstate+ndeath)+l2;                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]);
           for (k1=1; k1<=(nlstate);k1++){                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
             for (l1=1; l1<=(nlstate+ndeath);l1++){              }
               if(l1==k1) continue;              k=k+1;
               i=(k1-1)*(nlstate+ndeath)+l1;              if (j >= jmax){
               if(i<=j) continue;                jmax=j;
               for (age=bage; age<=fage; age ++){                ijmax=i;
                 if ((int)age %5==0){              }
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;              if (j <= jmin){
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;                jmin=j;
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;                ijmin=i;
                   mu1=mu[i][(int) age]/stepm*YEARM ;              }
                   mu2=mu[j][(int) age]/stepm*YEARM;              sum=sum+j;
                   c12=cv12/sqrt(v1*v2);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                   /* Computing eigen value of matrix of covariance */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,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.;          }
                   /* Eigen vectors */          else{
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
                   /*v21=sqrt(1.-v11*v11); *//* error */  /*        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]); */
                   v21=(lc1-v1)/cv12*v11;  
                   v12=-v21;            k=k+1;
                   v22=v11;            if (j >= jmax) {
                   tnalp=v21/v11;              jmax=j;
                   if(first1==1){              ijmax=i;
                     first1=0;            }
                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);            else if (j <= jmin){
                   }              jmin=j;
                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);              ijmin=i;
                   /*printf(fignu*/            }
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                   if(first==1){            if(j<0){
                     first=0;              nberr++;
                     fprintf(ficgp,"\nset parametric;unset label");              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");            }
                     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);            sum=sum+j;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);          }
                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);          jk= j/stepm;
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);          jl= j -jk*stepm;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);          ju= j -(jk+1)*stepm;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\            if(jl==0){
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\              dh[mi][i]=jk;
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));              bh[mi][i]=0;
                   }else{            }else{ /* We want a negative bias in order to only have interpolation ie
                     first=0;                    * at the price of an extra matrix product in likelihood */
                     fprintf(fichtm," %d (%.3f),",(int) age, c12);              dh[mi][i]=jk+1;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);              bh[mi][i]=ju;
                     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",\          }else{
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\            if(jl <= -ju){
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));              dh[mi][i]=jk;
                   }/* if first */              bh[mi][i]=jl;       /* bias is positive if real duration
                 } /* age mod 5 */                                   * is higher than the multiple of stepm and negative otherwise.
               } /* end loop age */                                   */
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);            }
               first=1;            else{
             } /*l12 */              dh[mi][i]=jk+1;
           } /* k12 */              bh[mi][i]=ju;
         } /*l1 */            }
       }/* k1 */            if(dh[mi][i]==0){
     } /* loop covariates */              dh[mi][i]=1; /* At least one step */
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);              bh[mi][i]=ju; /* At least one step */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));              /*  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);*/
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));            }
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);          } /* end if mle */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      } /* end wave */
   }    }
   free_vector(xp,1,npar);    jmean=sum/k;
   fclose(ficresprob);    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);
   fclose(ficresprobcov);    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);
   fclose(ficresprobcor);   }
   fclose(ficgp);  
   fclose(fichtm);  /*********** Tricode ****************************/
 }  void tricode(int *Tvar, int **nbcode, int imx)
   {
     
 /******************* Printing html file ***********/    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  
                   int lastpass, int stepm, int weightopt, char model[],\    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    int cptcode=0;
                   int popforecast, int estepm ,\    cptcoveff=0; 
                   double jprev1, double mprev1,double anprev1, \   
                   double jprev2, double mprev2,double anprev2){    for (k=0; k<maxncov; k++) Ndum[k]=0;
   int jj1, k1, i1, cpt;    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   /*char optionfilehtm[FILENAMELENGTH];*/  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
     printf("Problem with %s \n",optionfilehtm), exit(0);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);                                 modality*/ 
   }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
         Ndum[ij]++; /*counts the occurence of this modality */
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n        if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate  (should be 0 or 1 now) 
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n                                         Tvar[j]. If V=sex and male is 0 and 
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n                                         female is 1, then  cptcode=1.*/
  - Life expectancies by age and initial health status (estepm=%2d months):      }
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
         if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");                                         th covariate. In fact
                                          ncodemax[j]=2
  m=cptcoveff;                                         (dichotom. variables only) but
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                                         it can be more */
       } /* Ndum[-1] number of undefined modalities */
  jj1=0;  
  for(k1=1; k1<=m;k1++){      ij=1; 
    for(i1=1; i1<=ncodemax[k1];i1++){      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
      jj1++;        for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
      if (cptcovn > 0) {          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
        for (cpt=1; cpt<=cptcoveff;cpt++)                                       k is a modality. If we have model=V1+V1*sex 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            ij++;
      }          }
      /* Pij */          if (ij > ncodemax[j]) break; 
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>        }  
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          } 
      /* Quasi-incidences */    }  
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>  
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);   for (k=0; k< maxncov; k++) Ndum[k]=0;
        /* Stable prevalence in each health state */  
        for(cpt=1; cpt<nlstate;cpt++){   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
        }     Ndum[ij]++;
      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);   ij=1;
      }   for (i=1; i<= maxncov; i++) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and     if((Ndum[i]!=0) && (i<=ncovcol)){
 health expectancies in states (1) and (2): e%s%d.png<br>       Tvaraff[ij]=i; /*For printing */
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);       ij++;
    } /* end i1 */     }
  }/* End k1 */   }
  fprintf(fichtm,"</ul>");   ij--;
    cptcoveff=ij; /*Number of simple covariates*/
   }
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n  
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  /*********** Health Expectancies ****************/
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n  
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n  
  - 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    /* Health expectancies, no variances */
  - 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);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     int nhstepma, nstepma; /* Decreasing with age */
  if(popforecast==1) fprintf(fichtm,"\n    double age, agelim, hf;
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    double ***p3mat;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    double eip;
         <br>",fileres,fileres,fileres,fileres);  
  else    pstamp(ficreseij);
    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(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++){
  m=cptcoveff;      for(j=1; j<=nlstate;j++){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        fprintf(ficreseij," e%1d%1d ",i,j);
       }
  jj1=0;      fprintf(ficreseij," e%1d. ",i);
  for(k1=1; k1<=m;k1++){    }
    for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficreseij,"\n");
      jj1++;  
      if (cptcovn > 0) {    
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    if(estepm < stepm){
        for (cpt=1; cpt<=cptcoveff;cpt++)      printf ("Problem %d lower than %d\n",estepm, stepm);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    else  hstepm=estepm;   
      }    /* We compute the life expectancy from trapezoids spaced every estepm months
      for(cpt=1; cpt<=nlstate;cpt++) {     * This is mainly to measure the difference between two models: for example
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident     * if stepm=24 months pijx are given only every 2 years and by summing them
 interval) in state (%d): v%s%d%d.png <br>     * we are calculating an estimate of the Life Expectancy assuming a linear 
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);       * progression in between and thus overestimating or underestimating according
      }     * to the curvature of the survival function. If, for the same date, we 
    } /* end i1 */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
  }/* End k1 */     * to compare the new estimate of Life expectancy with the same linear 
  fprintf(fichtm,"</ul>");     * hypothesis. A more precise result, taking into account a more precise
 fclose(fichtm);     * curvature will be obtained if estepm is as small as stepm. */
 }  
     /* For example we decided to compute the life expectancy with the smallest unit */
 /******************* Gnuplot file **************/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;       Look at hpijx to understand the reason of that which relies in memory size
   int ng;       and note for a fixed period like estepm months */
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     printf("Problem with file %s",optionfilegnuplot);       survival function given by stepm (the optimization length). Unfortunately it
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);       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 
        results. So we changed our mind and took the option of the best precision.
 #ifdef windows    */
     fprintf(ficgp,"cd \"%s\" \n",pathc);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 #endif  
 m=pow(2,cptcoveff);    agelim=AGESUP;
      /* If stepm=6 months */
  /* 1eme*/      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   for (cpt=1; cpt<= nlstate ; cpt ++) {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
    for (k1=1; k1<= m ; k1 ++) {      
   /* nhstepm age range expressed in number of stepm */
 #ifdef windows    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    /* if (stepm >= YEARM) hstepm=1;*/
 #endif    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 #ifdef unix    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    for (age=bage; age<=fage; age ++){ 
 #endif      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* 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\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     for (i=1; i<= nlstate ; i ++) {         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      
   else fprintf(ficgp," \%%*lf (\%%*lf)");      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 }      
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for (i=1; i<= nlstate ; i ++) {      
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      printf("%d|",(int)age);fflush(stdout);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 }        
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      /* Computing expectancies */
 #ifdef unix      for(i=1; i<=nlstate;i++)
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");        for(j=1; j<=nlstate;j++)
 #endif          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
    }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   }            
   /*2 eme*/            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
   for (k1=1; k1<= m ; k1 ++) {          }
     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);      fprintf(ficreseij,"%3.0f",age );
          for(i=1; i<=nlstate;i++){
     for (i=1; i<= nlstate+1 ; i ++) {        eip=0;
       k=2*i;        for(j=1; j<=nlstate;j++){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          eip +=eij[i][j][(int)age];
       for (j=1; j<= nlstate+1 ; j ++) {          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficreseij,"%9.4f", eip );
 }        }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      fprintf(ficreseij,"\n");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    }
       for (j=1; j<= nlstate+1 ; j ++) {    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    printf("\n");
         else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficlog,"\n");
 }      
       fprintf(ficgp,"\" t\"\" w l 0,");  }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  {
 }      /* Covariances of health expectancies eij and of total life expectancies according
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");     to initial status i, ei. .
       else fprintf(ficgp,"\" t\"\" w l 0,");    */
     }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   }    int nhstepma, nstepma; /* Decreasing with age */
      double age, agelim, hf;
   /*3eme*/    double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
   for (k1=1; k1<= m ; k1 ++) {    double *xp, *xm;
     for (cpt=1; cpt<= nlstate ; cpt ++) {    double **gp, **gm;
       k=2+nlstate*(2*cpt-2);    double ***gradg, ***trgradg;
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    int theta;
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    double eip, vip;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    xp=vector(1,npar);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    xm=vector(1,npar);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
 */    
       for (i=1; i< nlstate ; i ++) {    pstamp(ficresstdeij);
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
       }    for(i=1; i<=nlstate;i++){
     }      for(j=1; j<=nlstate;j++)
   }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
        fprintf(ficresstdeij," e%1d. ",i);
   /* CV preval stat */    }
     for (k1=1; k1<= m ; k1 ++) {    fprintf(ficresstdeij,"\n");
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;    pstamp(ficrescveij);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++)      for(j=1; j<=nlstate;j++){
         fprintf(ficgp,"+$%d",k+i+1);        cptj= (j-1)*nlstate+i;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        for(i2=1; i2<=nlstate;i2++)
                for(j2=1; j2<=nlstate;j2++){
       l=3+(nlstate+ndeath)*cpt;            cptj2= (j2-1)*nlstate+i2;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            if(cptj2 <= cptj)
       for (i=1; i< nlstate ; i ++) {              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
         l=3+(nlstate+ndeath)*cpt;          }
         fprintf(ficgp,"+$%d",l+i+1);      }
       }    fprintf(ficrescveij,"\n");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      
     }    if(estepm < stepm){
   }        printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   /* proba elementaires */    else  hstepm=estepm;   
    for(i=1,jk=1; i <=nlstate; i++){    /* We compute the life expectancy from trapezoids spaced every estepm months
     for(k=1; k <=(nlstate+ndeath); k++){     * This is mainly to measure the difference between two models: for example
       if (k != i) {     * if stepm=24 months pijx are given only every 2 years and by summing them
         for(j=1; j <=ncovmodel; j++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);     * progression in between and thus overestimating or underestimating according
           jk++;     * to the curvature of the survival function. If, for the same date, we 
           fprintf(ficgp,"\n");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         }     * to compare the new estimate of Life expectancy with the same linear 
       }     * hypothesis. A more precise result, taking into account a more precise
     }     * curvature will be obtained if estepm is as small as stepm. */
    }  
     /* For example we decided to compute the life expectancy with the smallest unit */
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      for(jk=1; jk <=m; jk++) {       nhstepm is the number of hstepm from age to agelim 
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);       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,"\nset ylabel \"Quasi-incidence per year\"\n");       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,"\nset title \"Probability\"\n");       survival function given by stepm (the optimization length). Unfortunately it
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);       means that if the survival funtion is printed only each two years of age and if
        i=1;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        for(k2=1; k2<=nlstate; k2++) {       results. So we changed our mind and took the option of the best precision.
          k3=i;    */
          for(k=1; k<=(nlstate+ndeath); k++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
            if (k != k2){  
              if(ng==2)    /* If stepm=6 months */
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    /* nhstepm age range expressed in number of stepm */
              else    agelim=AGESUP;
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
              ij=1;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
              for(j=3; j <=ncovmodel; j++) {    /* if (stepm >= YEARM) hstepm=1;*/
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    
                  ij++;    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                }    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                else    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
              }    gp=matrix(0,nhstepm,1,nlstate*nlstate);
              fprintf(ficgp,")/(1");    gm=matrix(0,nhstepm,1,nlstate*nlstate);
                
              for(k1=1; k1 <=nlstate; k1++){      for (age=bage; age<=fage; age ++){ 
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                ij=1;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                for(j=3; j <=ncovmodel; j++){      /* if (stepm >= YEARM) hstepm=1;*/
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
                    ij++;      /* If stepm=6 months */
                  }      /* Computed by stepm unit matrices, product of hstepma matrices, stored
                  else         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      
                }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                fprintf(ficgp,")");  
              }      /* Computing  Variances of health expectancies */
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");         decrease memory allocation */
              i=i+ncovmodel;      for(theta=1; theta <=npar; theta++){
            }        for(i=1; i<=npar; i++){ 
          } /* end k */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        } /* end k2 */          xm[i] = x[i] - (i==theta ?delti[theta]:0);
      } /* end jk */        }
    } /* end ng */        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
    fclose(ficgp);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
 }  /* end gnuplot */    
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
 /*************** Moving average **************/            for(h=0; h<=nhstepm-1; h++){
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   int i, cpt, cptcod;            }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          }
       for (i=1; i<=nlstate;i++)        }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)       
           mobaverage[(int)agedeb][i][cptcod]=0.;        for(ij=1; ij<= nlstate*nlstate; ij++)
              for(h=0; h<=nhstepm-1; h++){
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
       for (i=1; i<=nlstate;i++){          }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      }/* End theta */
           for (cpt=0;cpt<=4;cpt++){      
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      
           }      for(h=0; h<=nhstepm-1; h++)
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        for(j=1; j<=nlstate*nlstate;j++)
         }          for(theta=1; theta <=npar; theta++)
       }            trgradg[h][j][theta]=gradg[h][theta][j];
     }      
      
 }       for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
 /************** 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){       printf("%d|",(int)age);fflush(stdout);
         fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       for(h=0;h<=nhstepm-1;h++){
   int *popage;        for(k=0;k<=nhstepm-1;k++){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   double *popeffectif,*popcount;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   double ***p3mat;          for(ij=1;ij<=nlstate*nlstate;ij++)
   char fileresf[FILENAMELENGTH];            for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
  agelim=AGESUP;        }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      }
   
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      /* Computing expectancies */
        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
        for(i=1; i<=nlstate;i++)
   strcpy(fileresf,"f");        for(j=1; j<=nlstate;j++)
   strcat(fileresf,fileres);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   if((ficresf=fopen(fileresf,"w"))==NULL) {            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     printf("Problem with forecast resultfile: %s\n", fileresf);            
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);            /* 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]);*/
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);          }
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);  
       fprintf(ficresstdeij,"%3.0f",age );
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      for(i=1; i<=nlstate;i++){
         eip=0.;
   if (mobilav==1) {        vip=0.;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1; j<=nlstate;j++){
     movingaverage(agedeb, fage, ageminpar, mobaverage);          eip += eij[i][j][(int)age];
   }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   if (stepm<=12) stepsize=1;        }
          fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   agelim=AGESUP;      }
        fprintf(ficresstdeij,"\n");
   hstepm=1;  
   hstepm=hstepm/stepm;      fprintf(ficrescveij,"%3.0f",age );
   yp1=modf(dateintmean,&yp);      for(i=1; i<=nlstate;i++)
   anprojmean=yp;        for(j=1; j<=nlstate;j++){
   yp2=modf((yp1*12),&yp);          cptj= (j-1)*nlstate+i;
   mprojmean=yp;          for(i2=1; i2<=nlstate;i2++)
   yp1=modf((yp2*30.5),&yp);            for(j2=1; j2<=nlstate;j2++){
   jprojmean=yp;              cptj2= (j2-1)*nlstate+i2;
   if(jprojmean==0) jprojmean=1;              if(cptj2 <= cptj)
   if(mprojmean==0) jprojmean=1;                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
              }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        }
        fprintf(ficrescveij,"\n");
   for(cptcov=1;cptcov<=i2;cptcov++){     
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }
       k=k+1;    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       fprintf(ficresf,"\n#******");    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       for(j=1;j<=cptcoveff;j++) {    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       }    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficresf,"******\n");    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficresf,"# StartingAge FinalAge");    printf("\n");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    fprintf(ficlog,"\n");
        
          free_vector(xm,1,npar);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    free_vector(xp,1,npar);
         fprintf(ficresf,"\n");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;  /************ Variance ******************/
            void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
           oldm=oldms;savm=savms;    /* Variance of health expectancies */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
            /* double **newm;*/
           for (h=0; h<=nhstepm; h++){    double **dnewm,**doldm;
             if (h==(int) (calagedate+YEARM*cpt)) {    double **dnewmp,**doldmp;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    int i, j, nhstepm, hstepm, h, nstepm ;
             }    int k, cptcode;
             for(j=1; j<=nlstate+ndeath;j++) {    double *xp;
               kk1=0.;kk2=0;    double **gp, **gm;  /* for var eij */
               for(i=1; i<=nlstate;i++) {                  double ***gradg, ***trgradg; /*for var eij */
                 if (mobilav==1)    double **gradgp, **trgradgp; /* for var p point j */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    double *gpp, *gmp; /* for var p point j */
                 else {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double ***p3mat;
                 }    double age,agelim, hf;
                    double ***mobaverage;
               }    int theta;
               if (h==(int)(calagedate+12*cpt)){    char digit[4];
                 fprintf(ficresf," %.3f", kk1);    char digitp[25];
                          
               }    char fileresprobmorprev[FILENAMELENGTH];
             }  
           }    if(popbased==1){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if(mobilav!=0)
         }        strcpy(digitp,"-populbased-mobilav-");
       }      else strcpy(digitp,"-populbased-nomobil-");
     }    }
   }    else 
              strcpy(digitp,"-stablbased-");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     if (mobilav!=0) {
   fclose(ficresf);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 /************** Forecasting ******************/        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 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){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    }
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    strcpy(fileresprobmorprev,"prmorprev"); 
   double *popeffectif,*popcount;    sprintf(digit,"%-d",ij);
   double ***p3mat,***tabpop,***tabpopprev;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   char filerespop[FILENAMELENGTH];    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(fileresprobmorprev,fileres);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   agelim=AGESUP;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     
      fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   strcpy(filerespop,"pop");    pstamp(ficresprobmorprev);
   strcat(filerespop,fileres);    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);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     printf("Problem with forecast resultfile: %s\n", filerespop);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);      fprintf(ficresprobmorprev," p.%-d SE",j);
   }      for(i=1; i<=nlstate;i++)
   printf("Computing forecasting: result on file '%s' \n", filerespop);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);    }  
     fprintf(ficresprobmorprev,"\n");
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   if (mobilav==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");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     movingaverage(agedeb, fage, ageminpar, mobaverage);  /*   } */
   }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   if (stepm<=12) stepsize=1;    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);
   agelim=AGESUP;    else
        fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   hstepm=1;    fprintf(ficresvij,"# Age");
   hstepm=hstepm/stepm;    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
   if (popforecast==1) {        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     if((ficpop=fopen(popfile,"r"))==NULL) {    fprintf(ficresvij,"\n");
       printf("Problem with population file : %s\n",popfile);exit(0);  
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);    xp=vector(1,npar);
     }    dnewm=matrix(1,nlstate,1,npar);
     popage=ivector(0,AGESUP);    doldm=matrix(1,nlstate,1,nlstate);
     popeffectif=vector(0,AGESUP);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     popcount=vector(0,AGESUP);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      
     i=1;      gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    gpp=vector(nlstate+1,nlstate+ndeath);
        gmp=vector(nlstate+1,nlstate+ndeath);
     imx=i;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    
   }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   for(cptcov=1;cptcov<=i2;cptcov++){    }
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    else  hstepm=estepm;   
       k=k+1;    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficrespop,"\n#******");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for(j=1;j<=cptcoveff;j++) {       nhstepm is the number of hstepm from age to agelim 
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       nstepm is the number of stepm from age to agelin. 
       }       Look at function hpijx to understand why (it is linked to memory size questions) */
       fprintf(ficrespop,"******\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fprintf(ficrespop,"# Age");       survival function given by stepm (the optimization length). Unfortunately it
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);       means that if the survival funtion is printed every two years of age and if
       if (popforecast==1)  fprintf(ficrespop," [Population]");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             results. So we changed our mind and took the option of the best precision.
       for (cpt=0; cpt<=0;cpt++) {    */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
            agelim = AGESUP;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           oldm=oldms;savm=savms;      gp=matrix(0,nhstepm,1,nlstate);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        gm=matrix(0,nhstepm,1,nlstate);
          
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {      for(theta=1; theta <=npar; theta++){
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
             }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               for(i=1; i<=nlstate;i++) {                      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        if (popbased==1) {
                 else {          if(mobilav ==0){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            for(i=1; i<=nlstate;i++)
                 }              prlim[i][i]=probs[(int)age][i][ij];
               }          }else{ /* mobilav */ 
               if (h==(int)(calagedate+12*cpt)){            for(i=1; i<=nlstate;i++)
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;              prlim[i][i]=mobaverage[(int)age][i][ij];
                   /*fprintf(ficrespop," %.3f", kk1);          }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        }
               }    
             }        for(j=1; j<= nlstate; j++){
             for(i=1; i<=nlstate;i++){          for(h=0; h<=nhstepm; h++){
               kk1=0.;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                 for(j=1; j<=nlstate;j++){              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          }
                 }        }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        /* This for computing probability of death (h=1 means
             }           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }        }    
       }        /* end probability of death */
    
   /******/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){   
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        if (popbased==1) {
           nhstepm = nhstepm/hstepm;          if(mobilav ==0){
                      for(i=1; i<=nlstate;i++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              prlim[i][i]=probs[(int)age][i][ij];
           oldm=oldms;savm=savms;          }else{ /* mobilav */ 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(i=1; i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){              prlim[i][i]=mobaverage[(int)age][i][ij];
             if (h==(int) (calagedate+YEARM*cpt)) {          }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        }
             }  
             for(j=1; j<=nlstate+ndeath;j++) {        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
               kk1=0.;kk2=0;          for(h=0; h<=nhstepm; h++){
               for(i=1; i<=nlstate;i++) {                          for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  gm[h][j] += prlim[i][i]*p3mat[i][j][h];
               }          }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        }
             }        /* This for computing probability of death (h=1 means
           }           computed over hstepm matrices product = hstepm*stepm months) 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           as a weighted average of prlim.
         }        */
       }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
    }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /* end probability of death */
   
   if (popforecast==1) {        for(j=1; j<= nlstate; j++) /* vareij */
     free_ivector(popage,0,AGESUP);          for(h=0; h<=nhstepm; h++){
     free_vector(popeffectif,0,AGESUP);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     free_vector(popcount,0,AGESUP);          }
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   fclose(ficrespop);        }
 }  
       } /* End theta */
 /***********************************************/  
 /**************** Main Program *****************/      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
 /***********************************************/  
       for(h=0; h<=nhstepm; h++) /* veij */
 int main(int argc, char *argv[])        for(j=1; j<=nlstate;j++)
 {          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  
   double agedeb, agefin,hf;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
   double fret;    
   double **xi,tmp,delta;  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   double dum; /* Dummy variable */      for(i=1;i<=nlstate;i++)
   double ***p3mat;        for(j=1;j<=nlstate;j++)
   int *indx;          vareij[i][j][(int)age] =0.;
   char line[MAXLINE], linepar[MAXLINE];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];      for(h=0;h<=nhstepm;h++){
   int firstobs=1, lastobs=10;        for(k=0;k<=nhstepm;k++){
   int sdeb, sfin; /* Status at beginning and end */          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   int c,  h , cpt,l;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   int ju,jl, mi;          for(i=1;i<=nlstate;i++)
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            for(j=1;j<=nlstate;j++)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   int mobilav=0,popforecast=0;        }
   int hstepm, nhstepm;      }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    
       /* pptj */
   double bage, fage, age, agelim, agebase;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   double ftolpl=FTOL;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   double **prlim;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   double *severity;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   double ***param; /* Matrix of parameters */          varppt[j][i]=doldmp[j][i];
   double  *p;      /* end ppptj */
   double **matcov; /* Matrix of covariance */      /*  x centered again */
   double ***delti3; /* Scale */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   double *delti; /* Scale */      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   double ***eij, ***vareij;   
   double **varpl; /* Variances of prevalence limits by age */      if (popbased==1) {
   double *epj, vepp;        if(mobilav ==0){
   double kk1, kk2;          for(i=1; i<=nlstate;i++)
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;            prlim[i][i]=probs[(int)age][i][ij];
          }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
   char *alph[]={"a","a","b","c","d","e"}, str[4];            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
   char z[1]="c", occ;               
 #include <sys/time.h>      /* This for computing probability of death (h=1 means
 #include <time.h>         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];         as a weighted average of prlim.
        */
   /* long total_usecs;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   struct timeval start_time, end_time;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      }    
   getcwd(pathcd, size);      /* end probability of death */
   
   printf("\n%s",version);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   if(argc <=1){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     printf("\nEnter the parameter file name: ");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     scanf("%s",pathtot);        for(i=1; i<=nlstate;i++){
   }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   else{        }
     strcpy(pathtot,argv[1]);      } 
   }      fprintf(ficresprobmorprev,"\n");
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);      fprintf(ficresvij,"%.0f ",age );
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      for(i=1; i<=nlstate;i++)
   /* cutv(path,optionfile,pathtot,'\\');*/        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        }
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      fprintf(ficresvij,"\n");
   chdir(path);      free_matrix(gp,0,nhstepm,1,nlstate);
   replace(pathc,path);      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
 /*-------- arguments in the command line --------*/      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* Log file */    } /* End age */
   strcat(filelog, optionfilefiname);    free_vector(gpp,nlstate+1,nlstate+ndeath);
   strcat(filelog,".log");    /* */    free_vector(gmp,nlstate+1,nlstate+ndeath);
   if((ficlog=fopen(filelog,"w"))==NULL)    {    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     printf("Problem with logfile %s\n",filelog);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     goto end;    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
   }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   fprintf(ficlog,"Log filename:%s\n",filelog);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   fprintf(ficlog,"\n%s",version);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficlog,"\nEnter the parameter file name: ");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fflush(ficlog);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   /* */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   strcpy(fileres,"r");    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   strcat(fileres, optionfilefiname);    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);
   strcat(fileres,".txt");    /* Other files have txt extension */    /*  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);
   */
   /*---------arguments file --------*/  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);    free_vector(xp,1,npar);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    free_matrix(doldm,1,nlstate,1,nlstate);
     goto end;    free_matrix(dnewm,1,nlstate,1,npar);
   }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   strcpy(filereso,"o");    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcat(filereso,fileres);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if((ficparo=fopen(filereso,"w"))==NULL) {    fclose(ficresprobmorprev);
     printf("Problem with Output resultfile: %s\n", filereso);    fflush(ficgp);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);    fflush(fichtm); 
     goto end;  }  /* end varevsij */
   }  
   /************ Variance of prevlim ******************/
   /* Reads comments: lines beginning with '#' */  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[])
   while((c=getc(ficpar))=='#' && c!= EOF){  {
     ungetc(c,ficpar);    /* Variance of prevalence limit */
     fgets(line, MAXLINE, ficpar);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     puts(line);    double **newm;
     fputs(line,ficparo);    double **dnewm,**doldm;
   }    int i, j, nhstepm, hstepm;
   ungetc(c,ficpar);    int k, cptcode;
     double *xp;
   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);    double *gp, *gm;
   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);    double **gradg, **trgradg;
   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);    double age,agelim;
 while((c=getc(ficpar))=='#' && c!= EOF){    int theta;
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    pstamp(ficresvpl);
     puts(line);    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fputs(line,ficparo);    fprintf(ficresvpl,"# Age");
   }    for(i=1; i<=nlstate;i++)
   ungetc(c,ficpar);        fprintf(ficresvpl," %1d-%1d",i,i);
      fprintf(ficresvpl,"\n");
      
   covar=matrix(0,NCOVMAX,1,n);    xp=vector(1,npar);
   cptcovn=0;    dnewm=matrix(1,nlstate,1,npar);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    doldm=matrix(1,nlstate,1,nlstate);
     
   ncovmodel=2+cptcovn;    hstepm=1*YEARM; /* Every year of age */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
      agelim = AGESUP;
   /* Read guess parameters */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /* Reads comments: lines beginning with '#' */      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   while((c=getc(ficpar))=='#' && c!= EOF){      if (stepm >= YEARM) hstepm=1;
     ungetc(c,ficpar);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     fgets(line, MAXLINE, ficpar);      gradg=matrix(1,npar,1,nlstate);
     puts(line);      gp=vector(1,nlstate);
     fputs(line,ficparo);      gm=vector(1,nlstate);
   }  
   ungetc(c,ficpar);      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for(i=1; i <=nlstate; i++)        }
     for(j=1; j <=nlstate+ndeath-1; j++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fscanf(ficpar,"%1d%1d",&i1,&j1);        for(i=1;i<=nlstate;i++)
       fprintf(ficparo,"%1d%1d",i1,j1);          gp[i] = prlim[i][i];
       if(mle==1)      
         printf("%1d%1d",i,j);        for(i=1; i<=npar; i++) /* Computes gradient */
       fprintf(ficlog,"%1d%1d",i,j);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       for(k=1; k<=ncovmodel;k++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         fscanf(ficpar," %lf",&param[i][j][k]);        for(i=1;i<=nlstate;i++)
         if(mle==1){          gm[i] = prlim[i][i];
           printf(" %lf",param[i][j][k]);  
           fprintf(ficlog," %lf",param[i][j][k]);        for(i=1;i<=nlstate;i++)
         }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         else      } /* End theta */
           fprintf(ficlog," %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);      trgradg =matrix(1,nlstate,1,npar);
       }  
       fscanf(ficpar,"\n");      for(j=1; j<=nlstate;j++)
       if(mle==1)        for(theta=1; theta <=npar; theta++)
         printf("\n");          trgradg[j][theta]=gradg[theta][j];
       fprintf(ficlog,"\n");  
       fprintf(ficparo,"\n");      for(i=1;i<=nlstate;i++)
     }        varpl[i][(int)age] =0.;
        matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
   p=param[1][1];        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    
   /* Reads comments: lines beginning with '#' */      fprintf(ficresvpl,"%.0f ",age );
   while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     fgets(line, MAXLINE, ficpar);      fprintf(ficresvpl,"\n");
     puts(line);      free_vector(gp,1,nlstate);
     fputs(line,ficparo);      free_vector(gm,1,nlstate);
   }      free_matrix(gradg,1,npar,1,nlstate);
   ungetc(c,ficpar);      free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    free_vector(xp,1,npar);
   for(i=1; i <=nlstate; i++){    free_matrix(doldm,1,nlstate,1,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){    free_matrix(dnewm,1,nlstate,1,nlstate);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);  }
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){  /************ Variance of one-step probabilities  ******************/
         fscanf(ficpar,"%le",&delti3[i][j][k]);  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[])
         printf(" %le",delti3[i][j][k]);  {
         fprintf(ficparo," %le",delti3[i][j][k]);    int i, j=0,  i1, k1, l1, t, tj;
       }    int k2, l2, j1,  z1;
       fscanf(ficpar,"\n");    int k=0,l, cptcode;
       printf("\n");    int first=1, first1;
       fprintf(ficparo,"\n");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     }    double **dnewm,**doldm;
   }    double *xp;
   delti=delti3[1][1];    double *gp, *gm;
      double **gradg, **trgradg;
   /* Reads comments: lines beginning with '#' */    double **mu;
   while((c=getc(ficpar))=='#' && c!= EOF){    double age,agelim, cov[NCOVMAX];
     ungetc(c,ficpar);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     fgets(line, MAXLINE, ficpar);    int theta;
     puts(line);    char fileresprob[FILENAMELENGTH];
     fputs(line,ficparo);    char fileresprobcov[FILENAMELENGTH];
   }    char fileresprobcor[FILENAMELENGTH];
   ungetc(c,ficpar);  
      double ***varpij;
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){    strcpy(fileresprob,"prob"); 
     fscanf(ficpar,"%s",&str);    strcat(fileresprob,fileres);
     if(mle==1)    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("%s",str);      printf("Problem with resultfile: %s\n", fileresprob);
     fprintf(ficlog,"%s",str);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     fprintf(ficparo,"%s",str);    }
     for(j=1; j <=i; j++){    strcpy(fileresprobcov,"probcov"); 
       fscanf(ficpar," %le",&matcov[i][j]);    strcat(fileresprobcov,fileres);
       if(mle==1){    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
         printf(" %.5le",matcov[i][j]);      printf("Problem with resultfile: %s\n", fileresprobcov);
         fprintf(ficlog," %.5le",matcov[i][j]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       }    }
       else    strcpy(fileresprobcor,"probcor"); 
         fprintf(ficlog," %.5le",matcov[i][j]);    strcat(fileresprobcor,fileres);
       fprintf(ficparo," %.5le",matcov[i][j]);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobcor);
     fscanf(ficpar,"\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     if(mle==1)    }
       printf("\n");    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"\n");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficparo,"\n");    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);
   for(i=1; i <=npar; i++)    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     for(j=i+1;j<=npar;j++)    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       matcov[i][j]=matcov[j][i];    pstamp(ficresprob);
        fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   if(mle==1)    fprintf(ficresprob,"# Age");
     printf("\n");    pstamp(ficresprobcov);
   fprintf(ficlog,"\n");    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     /*-------- Rewriting paramater file ----------*/    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
      strcpy(rfileres,"r");    /* "Rparameterfile */    fprintf(ficresprobcor,"# Age");
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    for(i=1; i<=nlstate;i++)
     if((ficres =fopen(rfileres,"w"))==NULL) {      for(j=1; j<=(nlstate+ndeath);j++){
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     fprintf(ficres,"#%s\n",version);      }  
       /* fprintf(ficresprob,"\n");
     /*-------- data file ----------*/    fprintf(ficresprobcov,"\n");
     if((fic=fopen(datafile,"r"))==NULL)    {    fprintf(ficresprobcor,"\n");
       printf("Problem with datafile: %s\n", datafile);goto end;   */
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;    xp=vector(1,npar);
     }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     n= lastobs;    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     severity = vector(1,maxwav);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     outcome=imatrix(1,maxwav+1,1,n);    first=1;
     num=ivector(1,n);    fprintf(ficgp,"\n# Routine varprob");
     moisnais=vector(1,n);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     annais=vector(1,n);    fprintf(fichtm,"\n");
     moisdc=vector(1,n);  
     andc=vector(1,n);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     agedc=vector(1,n);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     cod=ivector(1,n);    file %s<br>\n",optionfilehtmcov);
     weight=vector(1,n);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  and drawn. It helps understanding how is the covariance between two incidences.\
     mint=matrix(1,maxwav,1,n);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     anint=matrix(1,maxwav,1,n);    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. \
     s=imatrix(1,maxwav+1,1,n);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     adl=imatrix(1,maxwav+1,1,n);      would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     tab=ivector(1,NCOVMAX);  standard deviations wide on each axis. <br>\
     ncodemax=ivector(1,8);   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>\
     i=1;  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {    cov[1]=1;
            tj=cptcoveff;
         for (j=maxwav;j>=1;j--){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    j1=0;
           strcpy(line,stra);    for(t=1; t<=tj;t++){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for(i1=1; i1<=ncodemax[t];i1++){ 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        j1++;
         }        if  (cptcovn>0) {
                  fprintf(ficresprob, "\n#********** Variable "); 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficresprobcov, "**********\n#\n");
           
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficgp, "\n#********** Variable "); 
         for (j=ncovcol;j>=1;j--){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficgp, "**********\n#\n");
         }          
         num[i]=atol(stra);          
                  fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           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;}*/          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
         i=i+1;          fprintf(ficresprobcor, "\n#********** Variable ");    
       }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresprobcor, "**********\n#");    
     /* printf("ii=%d", ij);        }
        scanf("%d",i);*/        
   imx=i-1; /* Number of individuals */        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
   /* for (i=1; i<=imx; i++){          for (k=1; k<=cptcovn;k++) {
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     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 (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++){            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      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]));}*/          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
            trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
            gp=vector(1,(nlstate)*(nlstate+ndeath));
   /* Calculation of the number of parameter from char model*/          gm=vector(1,(nlstate)*(nlstate+ndeath));
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */      
   Tprod=ivector(1,15);          for(theta=1; theta <=npar; theta++){
   Tvaraff=ivector(1,15);            for(i=1; i<=npar; i++)
   Tvard=imatrix(1,15,1,2);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   Tage=ivector(1,15);                  
                pmij(pmmij,cov,ncovmodel,xp,nlstate);
   if (strlen(model) >1){            
     j=0, j1=0, k1=1, k2=1;            k=0;
     j=nbocc(model,'+');            for(i=1; i<= (nlstate); i++){
     j1=nbocc(model,'*');              for(j=1; j<=(nlstate+ndeath);j++){
     cptcovn=j+1;                k=k+1;
     cptcovprod=j1;                gp[k]=pmmij[i][j];
                  }
     strcpy(modelsav,model);            }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            
       printf("Error. Non available option model=%s ",model);            for(i=1; i<=npar; i++)
       fprintf(ficlog,"Error. Non available option model=%s ",model);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       goto end;      
     }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                k=0;
     for(i=(j+1); i>=1;i--){            for(i=1; i<=(nlstate); i++){
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */              for(j=1; j<=(nlstate+ndeath);j++){
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */                k=k+1;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                gm[k]=pmmij[i][j];
       /*scanf("%d",i);*/              }
       if (strchr(strb,'*')) {  /* Model includes a product */            }
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/       
         if (strcmp(strc,"age")==0) { /* Vn*age */            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
           cptcovprod--;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           cutv(strb,stre,strd,'V');          }
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/  
           cptcovage++;          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             Tage[cptcovage]=i;            for(theta=1; theta <=npar; theta++)
             /*printf("stre=%s ", stre);*/              trgradg[j][theta]=gradg[theta][j];
         }          
         else if (strcmp(strd,"age")==0) { /* or age*Vn */          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           cptcovprod--;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           cutv(strb,stre,strc,'V');          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           Tvar[i]=atoi(stre);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           cptcovage++;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           Tage[cptcovage]=i;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         }  
         else {  /* Age is not in the model */          pmij(pmmij,cov,ncovmodel,x,nlstate);
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/          
           Tvar[i]=ncovcol+k1;          k=0;
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */          for(i=1; i<=(nlstate); i++){
           Tprod[k1]=i;            for(j=1; j<=(nlstate+ndeath);j++){
           Tvard[k1][1]=atoi(strc); /* m*/              k=k+1;
           Tvard[k1][2]=atoi(stre); /* n */              mu[k][(int) age]=pmmij[i][j];
           Tvar[cptcovn+k2]=Tvard[k1][1];            }
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          }
           for (k=1; k<=lastobs;k++)          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
           k1++;              varpij[i][j][(int)age] = doldm[i][j];
           k2=k2+2;  
         }          /*printf("\n%d ",(int)age);
       }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       else { /* no more sum */            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        /*  scanf("%d",i);*/            }*/
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);          fprintf(ficresprob,"\n%d ",(int)age);
       }          fprintf(ficresprobcov,"\n%d ",(int)age);
       strcpy(modelsav,stra);            fprintf(ficresprobcor,"\n%d ",(int)age);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     } /* end of loop + */            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   } /* end model */          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
              fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   printf("cptcovprod=%d ", cptcovprod);          }
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);          i=0;
   scanf("%d ",i);*/          for (k=1; k<=(nlstate);k++){
     fclose(fic);            for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
     /*  if(mle==1){*/              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     if (weightopt != 1) { /* Maximisation without weights*/              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       for(i=1;i<=n;i++) weight[i]=1.0;              for (j=1; j<=i;j++){
     }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     /*-calculation of age at interview from date of interview and age at death -*/                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     agev=matrix(1,maxwav,1,imx);              }
             }
     for (i=1; i<=imx; i++) {          }/* end of loop for state */
       for(m=2; (m<= maxwav); m++) {        } /* end of loop for age */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;        /* Confidence intervalle of pij  */
          s[m][i]=-1;        /*
        }          fprintf(ficgp,"\nunset parametric;unset label");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-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");
     }          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     for (i=1; i<=imx; i++)  {          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       for(m=1; (m<= maxwav); m++){        */
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
             if(agedc[i]>0)        first1=1;
               if(moisdc[i]!=99 && andc[i]!=9999)        for (k2=1; k2<=(nlstate);k2++){
                 agev[m][i]=agedc[i];          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            if(l2==k2) continue;
            else {            j=(k2-1)*(nlstate+ndeath)+l2;
               if (andc[i]!=9999){            for (k1=1; k1<=(nlstate);k1++){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);                if(l1==k1) continue;
               agev[m][i]=-1;                i=(k1-1)*(nlstate+ndeath)+l1;
               }                if(i<=j) continue;
             }                for (age=bage; age<=fage; age ++){ 
           }                  if ((int)age %5==0){
           else if(s[m][i] !=9){ /* Should no more exist */                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
             if(mint[m][i]==99 || anint[m][i]==9999)                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
               agev[m][i]=1;                    mu1=mu[i][(int) age]/stepm*YEARM ;
             else if(agev[m][i] <agemin){                    mu2=mu[j][(int) age]/stepm*YEARM;
               agemin=agev[m][i];                    c12=cv12/sqrt(v1*v2);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/                    /* Computing eigen value of matrix of covariance */
             }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
             else if(agev[m][i] >agemax){                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
               agemax=agev[m][i];                    /* Eigen vectors */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
             }                    /*v21=sqrt(1.-v11*v11); *//* error */
             /*agev[m][i]=anint[m][i]-annais[i];*/                    v21=(lc1-v1)/cv12*v11;
             /*   agev[m][i] = age[i]+2*m;*/                    v12=-v21;
           }                    v22=v11;
           else { /* =9 */                    tnalp=v21/v11;
             agev[m][i]=1;                    if(first1==1){
             s[m][i]=-1;                      first1=0;
           }                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
         }                    }
         else /*= 0 Unknown */                    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);
           agev[m][i]=1;                    /*printf(fignu*/
       }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                        /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     }                    if(first==1){
     for (i=1; i<=imx; i++)  {                      first=0;
       for(m=1; (m<= maxwav); m++){                      fprintf(ficgp,"\nset parametric;unset label");
         if (s[m][i] > (nlstate+ndeath)) {                      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);
           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(ficgp,"\nset ter png small\nset size 0.65,0.65");
           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);                        fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
           goto end;   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
         }  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
       }                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     }                              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);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                      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);
     free_vector(severity,1,maxwav);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     free_imatrix(outcome,1,maxwav+1,1,n);                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     free_vector(moisnais,1,n);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     free_vector(annais,1,n);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     /* free_matrix(mint,1,maxwav,1,n);                    }else{
        free_matrix(anint,1,maxwav,1,n);*/                      first=0;
     free_vector(moisdc,1,n);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
     free_vector(andc,1,n);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                          fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     wav=ivector(1,imx);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     dh=imatrix(1,lastpass-firstpass+1,1,imx);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                    }/* if first */
                      } /* age mod 5 */
     /* Concatenates waves */                } /* end loop age */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
       Tcode=ivector(1,100);            } /* k12 */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          } /*l1 */
       ncodemax[1]=1;        }/* k1 */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      } /* loop covariates */
          }
    codtab=imatrix(1,100,1,10);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
    h=0;    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
    m=pow(2,cptcoveff);    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
    for(k=1;k<=cptcoveff; k++){    free_vector(xp,1,npar);
      for(i=1; i <=(m/pow(2,k));i++){    fclose(ficresprob);
        for(j=1; j <= ncodemax[k]; j++){    fclose(ficresprobcov);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    fclose(ficresprobcor);
            h++;    fflush(ficgp);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    fflush(fichtmcov);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/  }
          }  
        }  
      }  /******************* Printing html file ***********/
    }  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                    int lastpass, int stepm, int weightopt, char model[],\
       codtab[1][2]=1;codtab[2][2]=2; */                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
    /* for(i=1; i <=m ;i++){                    int popforecast, int estepm ,\
       for(k=1; k <=cptcovn; k++){                    double jprev1, double mprev1,double anprev1, \
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                    double jprev2, double mprev2,double anprev2){
       }    int jj1, k1, i1, cpt;
       printf("\n");  
       }     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
       scanf("%d",i);*/     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
      </ul>");
    /* Calculates basic frequencies. Computes observed prevalence at single age     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
        and prints on file fileres'p'. */   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
         fprintf(fichtm,"\
       - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     fprintf(fichtm,"\
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */     fprintf(fichtm,"\
         - (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 Powell, parameters are in a vector p[] starting at p[1]     <a href=\"%s\">%s</a> <br>\n",
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */     fprintf(fichtm,"\
    - Population projections by age and states: \
     if(mle==1){     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
      
     /*--------- results files --------------*/   m=cptcoveff;
     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);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
    jj1=0;
    jk=1;   for(k1=1; k1<=m;k1++){
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");     for(i1=1; i1<=ncodemax[k1];i1++){
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");       jj1++;
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");       if (cptcovn > 0) {
    for(i=1,jk=1; i <=nlstate; i++){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
      for(k=1; k <=(nlstate+ndeath); k++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
        if (k != i)           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
            printf("%d%d ",i,k);       }
            fprintf(ficlog,"%d%d ",i,k);       /* Pij */
            fprintf(ficres,"%1d%1d ",i,k);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
            for(j=1; j <=ncovmodel; j++){  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
              printf("%f ",p[jk]);       /* Quasi-incidences */
              fprintf(ficlog,"%f ",p[jk]);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
              fprintf(ficres,"%f ",p[jk]);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
              jk++;  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
            }         /* Period (stable) prevalence in each health state */
            printf("\n");         for(cpt=1; cpt<nlstate;cpt++){
            fprintf(ficlog,"\n");           fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
            fprintf(ficres,"\n");  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }         }
      }       for(cpt=1; cpt<=nlstate;cpt++) {
    }          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
    if(mle==1){  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
      /* Computing hessian and covariance matrix */       }
      ftolhess=ftol; /* Usually correct */     } /* end i1 */
      hesscov(matcov, p, npar, delti, ftolhess, func);   }/* End k1 */
    }   fprintf(fichtm,"</ul>");
    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");   fprintf(fichtm,"\
    for(i=1,jk=1; i <=nlstate; i++){  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
      for(j=1; j <=nlstate+ndeath; j++){   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
        if (j!=i) {  
          fprintf(ficres,"%1d%1d",i,j);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          printf("%1d%1d",i,j);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
          fprintf(ficlog,"%1d%1d",i,j);   fprintf(fichtm,"\
          for(k=1; k<=ncovmodel;k++){   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            printf(" %.5e",delti[jk]);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
            fprintf(ficlog," %.5e",delti[jk]);  
            fprintf(ficres," %.5e",delti[jk]);   fprintf(fichtm,"\
            jk++;   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          }           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
          printf("\n");   fprintf(fichtm,"\
          fprintf(ficlog,"\n");   - 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): \
          fprintf(ficres,"\n");     <a href=\"%s\">%s</a> <br>\n</li>",
        }             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
      }   fprintf(fichtm,"\
    }   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
         <a href=\"%s\">%s</a> <br>\n</li>",
    k=1;             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    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,"\
    if(mle==1)   - 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",
      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");           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");   fprintf(fichtm,"\
    for(i=1;i<=npar;i++){   - 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",
      /*  if (k>nlstate) k=1;           estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
          i1=(i-1)/(ncovmodel*nlstate)+1;   fprintf(fichtm,"\
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
          printf("%s%d%d",alph[k],i1,tab[i]);*/           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
      fprintf(ficres,"%3d",i);  
      if(mle==1)  /*  if(popforecast==1) fprintf(fichtm,"\n */
        printf("%3d",i);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
      fprintf(ficlog,"%3d",i);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
      for(j=1; j<=i;j++){  /*      <br>",fileres,fileres,fileres,fileres); */
        fprintf(ficres," %.5e",matcov[i][j]);  /*  else  */
        if(mle==1)  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
          printf(" %.5e",matcov[i][j]);   fflush(fichtm);
        fprintf(ficlog," %.5e",matcov[i][j]);   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
      }  
      fprintf(ficres,"\n");   m=cptcoveff;
      if(mle==1)   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
        printf("\n");  
      fprintf(ficlog,"\n");   jj1=0;
      k++;   for(k1=1; k1<=m;k1++){
    }     for(i1=1; i1<=ncodemax[k1];i1++){
           jj1++;
    while((c=getc(ficpar))=='#' && c!= EOF){       if (cptcovn > 0) {
      ungetc(c,ficpar);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
      fgets(line, MAXLINE, ficpar);         for (cpt=1; cpt<=cptcoveff;cpt++) 
      puts(line);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
      fputs(line,ficparo);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
    }       }
    ungetc(c,ficpar);       for(cpt=1; cpt<=nlstate;cpt++) {
    estepm=0;         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
    if (estepm==0 || estepm < stepm) estepm=stepm;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
    if (fage <= 2) {       }
      bage = ageminpar;       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
      fage = agemaxpar;  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
    }  true period expectancies (those weighted with period prevalences are also\
       drawn in addition to the population based expectancies computed using\
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");   observed and cahotic prevalences: %s%d.png<br>\
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);     } /* end i1 */
       }/* End k1 */
    while((c=getc(ficpar))=='#' && c!= EOF){   fprintf(fichtm,"</ul>");
      ungetc(c,ficpar);   fflush(fichtm);
      fgets(line, MAXLINE, ficpar);  }
      puts(line);  
      fputs(line,ficparo);  /******************* Gnuplot file **************/
    }  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    ungetc(c,ficpar);  
      char dirfileres[132],optfileres[132];
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int ng=0;
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
      /*     printf("Problem with file %s",optionfilegnuplot); */
    while((c=getc(ficpar))=='#' && c!= EOF){  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
      ungetc(c,ficpar);  /*   } */
      fgets(line, MAXLINE, ficpar);  
      puts(line);    /*#ifdef windows */
      fputs(line,ficparo);    fprintf(ficgp,"cd \"%s\" \n",pathc);
    }      /*#endif */
    ungetc(c,ficpar);    m=pow(2,cptcoveff);
    
     strcpy(dirfileres,optionfilefiname);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    strcpy(optfileres,"vpl");
    dateprev2=anprev2+mprev2/12.+jprev2/365.;   /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
   fscanf(ficpar,"pop_based=%d\n",&popbased);     for (k1=1; k1<= m ; k1 ++) {
   fprintf(ficparo,"pop_based=%d\n",popbased);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   fprintf(ficres,"pop_based=%d\n",popbased);         fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \n\
   while((c=getc(ficpar))=='#' && c!= EOF){  set ylabel \"Probability\" \n\
     ungetc(c,ficpar);  set ter png small\n\
     fgets(line, MAXLINE, ficpar);  set size 0.65,0.65\n\
     puts(line);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
     fputs(line,ficparo);  
   }       for (i=1; i<= nlstate ; i ++) {
   ungetc(c,ficpar);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);       }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
 while((c=getc(ficpar))=='#' && c!= EOF){       } 
     ungetc(c,ficpar);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
     fgets(line, MAXLINE, ficpar);       for (i=1; i<= nlstate ; i ++) {
     puts(line);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     fputs(line,ficparo);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   }       }  
   ungetc(c,ficpar);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
   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);    /*2 eme*/
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    
     for (k1=1; k1<= m ; k1 ++) { 
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
 /*------------ gnuplot -------------*/      
   strcpy(optionfilegnuplot,optionfilefiname);      for (i=1; i<= nlstate+1 ; i ++) {
   strcat(optionfilegnuplot,".gp");        k=2*i;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     printf("Problem with file %s",optionfilegnuplot);        for (j=1; j<= nlstate+1 ; j ++) {
   }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   fclose(ficgp);          else fprintf(ficgp," \%%*lf (\%%*lf)");
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);        }   
 /*--------- index.htm --------*/        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   strcpy(optionfilehtm,optionfile);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   strcat(optionfilehtm,".htm");        for (j=1; j<= nlstate+1 ; j ++) {
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     printf("Problem with %s \n",optionfilehtm), exit(0);          else fprintf(ficgp," \%%*lf (\%%*lf)");
   }        }   
         fprintf(ficgp,"\" t\"\" w l 0,");
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        for (j=1; j<= nlstate+1 ; j ++) {
 \n          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 Total number of observations=%d <br>\n          else fprintf(ficgp," \%%*lf (\%%*lf)");
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        }   
 <hr  size=\"2\" color=\"#EC5E5E\">        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
  <ul><li><h4>Parameter files</h4>\n        else fprintf(ficgp,"\" t\"\" w l 0,");
  - 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></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);    
   fclose(fichtm);    /*3eme*/
     
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    for (k1=1; k1<= m ; k1 ++) { 
        for (cpt=1; cpt<= nlstate ; cpt ++) {
 /*------------ free_vector  -------------*/        /*       k=2+nlstate*(2*cpt-2); */
  chdir(path);        k=2+(nlstate+1)*(cpt-1);
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
  free_ivector(wav,1,imx);        fprintf(ficgp,"set ter png small\n\
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  set size 0.65,0.65\n\
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    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);
  free_ivector(num,1,n);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
  free_vector(agedc,1,n);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
  fclose(ficparo);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
  fclose(ficres);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
   /*--------------- Prevalence limit --------------*/        */
          for (i=1; i< nlstate ; i ++) {
   strcpy(filerespl,"pl");          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);
   strcat(filerespl,fileres);          /*      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);*/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        } 
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
   }      }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    }
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);    
   fprintf(ficrespl,"#Prevalence limit\n");    /* CV preval stable (period) */
   fprintf(ficrespl,"#Age ");    for (k1=1; k1<= m ; k1 ++) { 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      for (cpt=1; cpt<=nlstate ; cpt ++) {
   fprintf(ficrespl,"\n");        k=3;
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   prlim=matrix(1,nlstate,1,nlstate);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  set ter png small\nset size 0.65,0.65\n\
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  unset log y\n\
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        for (i=1; i< nlstate ; i ++)
   k=0;          fprintf(ficgp,"+$%d",k+i+1);
   agebase=ageminpar;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   agelim=agemaxpar;        
   ftolpl=1.e-10;        l=3+(nlstate+ndeath)*cpt;
   i1=cptcoveff;        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   if (cptcovn < 1){i1=1;}        for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficgp,"+$%d",l+i+1);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
         k=k+1;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      } 
         fprintf(ficrespl,"\n#******");    }  
         printf("\n#******");    
         fprintf(ficlog,"\n#******");    /* proba elementaires */
         for(j=1;j<=cptcoveff;j++) {    for(i=1,jk=1; i <=nlstate; i++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(k=1; k <=(nlstate+ndeath); k++){
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if (k != i) {
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(j=1; j <=ncovmodel; j++){
         }            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
         fprintf(ficrespl,"******\n");            jk++; 
         printf("******\n");            fprintf(ficgp,"\n");
         fprintf(ficlog,"******\n");          }
                }
         for (age=agebase; age<=agelim; age++){      }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     }
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
           fprintf(ficrespl," %.5f", prlim[i][i]);       for(jk=1; jk <=m; jk++) {
           fprintf(ficrespl,"\n");         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
         }         if (ng==2)
       }           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     }         else
   fclose(ficrespl);           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);
   /*------------- h Pij x at various ages ------------*/         i=1;
           for(k2=1; k2<=nlstate; k2++) {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);           k3=i;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {           for(k=1; k<=(nlstate+ndeath); k++) {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;             if (k != k2){
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;               if(ng==2)
   }                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   printf("Computing pij: result on file '%s' \n", filerespij);               else
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 ij=1;
   stepsize=(int) (stepm+YEARM-1)/YEARM;               for(j=3; j <=ncovmodel; j++) {
   /*if (stepm<=24) stepsize=2;*/                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   agelim=AGESUP;                   ij++;
   hstepm=stepsize*YEARM; /* Every year of age */                 }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                 else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   /* hstepm=1;   aff par mois*/               }
                fprintf(ficgp,")/(1");
   k=0;               
   for(cptcov=1;cptcov<=i1;cptcov++){               for(k1=1; k1 <=nlstate; k1++){   
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       k=k+1;                 ij=1;
         fprintf(ficrespij,"\n#****** ");                 for(j=3; j <=ncovmodel; j++){
         for(j=1;j<=cptcoveff;j++)                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
         fprintf(ficrespij,"******\n");                     ij++;
                           }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                   else
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                 }
                  fprintf(ficgp,")");
           /*      nhstepm=nhstepm*YEARM; aff par mois*/               }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           oldm=oldms;savm=savms;               i=i+ncovmodel;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);               }
           fprintf(ficrespij,"# Age");           } /* end k */
           for(i=1; i<=nlstate;i++)         } /* end k2 */
             for(j=1; j<=nlstate+ndeath;j++)       } /* end jk */
               fprintf(ficrespij," %1d-%1d",i,j);     } /* end ng */
           fprintf(ficrespij,"\n");     fflush(ficgp); 
            for (h=0; h<=nhstepm; h++){  }  /* end gnuplot */
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)  /*************** Moving average **************/
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
             fprintf(ficrespij,"\n");  
              }    int i, cpt, cptcod;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int modcovmax =1;
           fprintf(ficrespij,"\n");    int mobilavrange, mob;
         }    double age;
     }  
   }    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   fclose(ficrespij);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
   /*---------- Forecasting ------------------*/      for (age=bage; age<=fage; age++)
   if((stepm == 1) && (strcmp(model,".")==0)){        for (i=1; i<=nlstate;i++)
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   }      /* We keep the original values on the extreme ages bage, fage and for 
   else{         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
     erreur=108;         we use a 5 terms etc. until the borders are no more concerned. 
     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);      for (mob=3;mob <=mobilavrange;mob=mob+2){
   }        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
            for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
   /*---------- Health expectancies and variances ------------*/              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
   strcpy(filerest,"t");                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   strcat(filerest,fileres);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   if((ficrest=fopen(filerest,"w"))==NULL) {                }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;            }
   }          }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        }/* end age */
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);      }/* end mob */
     }else return -1;
     return 0;
   strcpy(filerese,"e");  }/* End movingaverage */
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  /************** Forecasting ******************/
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
   }    /* proj1, year, month, day of starting projection 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       agemin, agemax range of age
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);       dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
   strcpy(fileresv,"v");    */
   strcat(fileresv,fileres);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    int *popage;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    double agec; /* generic age */
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   }    double *popeffectif,*popcount;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    double ***p3mat;
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    double ***mobaverage;
   calagedate=-1;    char fileresf[FILENAMELENGTH];
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
     agelim=AGESUP;
   k=0;    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   for(cptcov=1;cptcov<=i1;cptcov++){   
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    strcpy(fileresf,"f"); 
       k=k+1;    strcat(fileresf,fileres);
       fprintf(ficrest,"\n#****** ");    if((ficresf=fopen(fileresf,"w"))==NULL) {
       for(j=1;j<=cptcoveff;j++)      printf("Problem with forecast resultfile: %s\n", fileresf);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficrest,"******\n");    }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
       fprintf(ficreseij,"\n#****** ");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       fprintf(ficreseij,"******\n");  
     if (mobilav!=0) {
       fprintf(ficresvij,"\n#****** ");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(j=1;j<=cptcoveff;j++)      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       fprintf(ficresvij,"******\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    }
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      stepsize=(int) (stepm+YEARM-1)/YEARM;
      if (stepm<=12) stepsize=1;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    if(estepm < stepm){
       oldm=oldms;savm=savms;      printf ("Problem %d lower than %d\n",estepm, stepm);
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);    }
       if(popbased==1){    else  hstepm=estepm;   
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);  
        }    hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                   fractional in yp1 */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    anprojmean=yp;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    yp2=modf((yp1*12),&yp);
       fprintf(ficrest,"\n");    mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
       epj=vector(1,nlstate+1);    jprojmean=yp;
       for(age=bage; age <=fage ;age++){    if(jprojmean==0) jprojmean=1;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    if(mprojmean==0) jprojmean=1;
         if (popbased==1) {  
           for(i=1; i<=nlstate;i++)    i1=cptcoveff;
             prlim[i][i]=probs[(int)age][i][k];    if (cptcovn < 1){i1=1;}
         }    
            fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
         fprintf(ficrest," %4.0f",age);    
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    fprintf(ficresf,"#****** Routine prevforecast **\n");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  /*            if (h==(int)(YEARM*yearp)){ */
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
           }      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
           epj[nlstate+1] +=epj[j];        k=k+1;
         }        fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
         for(i=1, vepp=0.;i <=nlstate;i++)          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]]);
           for(j=1;j <=nlstate;j++)        }
             vepp += vareij[i][j][(int)age];        fprintf(ficresf,"******\n");
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1;j <=nlstate;j++){        for(j=1; j<=nlstate+ndeath;j++){ 
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));          for(i=1; i<=nlstate;i++)              
         }            fprintf(ficresf," p%d%d",i,j);
         fprintf(ficrest,"\n");          fprintf(ficresf," p.%d",j);
       }        }
     }        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
   }          fprintf(ficresf,"\n");
 free_matrix(mint,1,maxwav,1,n);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
   fclose(ficreseij);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
   fclose(ficresvij);            nhstepm = nhstepm/hstepm; 
   fclose(ficrest);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficpar);            oldm=oldms;savm=savms;
   free_vector(epj,1,nlstate+1);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
            
   /*------- Variance limit prevalence------*/              for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
   strcpy(fileresvpl,"vpl");                fprintf(ficresf,"\n");
   strcat(fileresvpl,fileres);                for(j=1;j<=cptcoveff;j++) 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
     exit(0);              } 
   }              for(j=1; j<=nlstate+ndeath;j++) {
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                ppij=0.;
                 for(i=1; i<=nlstate;i++) {
   k=0;                  if (mobilav==1) 
   for(cptcov=1;cptcov<=i1;cptcov++){                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                  else {
       k=k+1;                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
       fprintf(ficresvpl,"\n#****** ");                  }
       for(j=1;j<=cptcoveff;j++)                  if (h*hstepm/YEARM*stepm== yearp) {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
       fprintf(ficresvpl,"******\n");                  }
                      } /* end i */
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                if (h*hstepm/YEARM*stepm==yearp) {
       oldm=oldms;savm=savms;                  fprintf(ficresf," %.3f", ppij);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                }
     }              }/* end j */
  }            } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficresvpl);          } /* end agec */
         } /* end yearp */
   /*---------- End : free ----------------*/      } /* end cptcod */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    } /* end  cptcov */
           
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
      fclose(ficresf);
    }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  /************** Forecasting *****not tested NB*************/
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  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){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    
      int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   free_matrix(matcov,1,npar,1,npar);    int *popage;
   free_vector(delti,1,npar);    double calagedatem, agelim, kk1, kk2;
   free_matrix(agev,1,maxwav,1,imx);    double *popeffectif,*popcount;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
   fprintf(fichtm,"\n</body>");    char filerespop[FILENAMELENGTH];
   fclose(fichtm);  
   fclose(ficgp);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
   if(erreur >0){    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     printf("End of Imach with error or warning %d\n",erreur);    
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   }else{    
    printf("End of Imach\n");    
    fprintf(ficlog,"End of Imach\n");    strcpy(filerespop,"pop"); 
   }    strcat(filerespop,fileres);
   printf("See log file on %s\n",filelog);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   fclose(ficlog);      printf("Problem with forecast resultfile: %s\n", filerespop);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
      }
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    printf("Computing forecasting: result on file '%s' \n", filerespop);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   /*------ End -----------*/  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
  end:    if (mobilav!=0) {
 #ifdef windows      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /* chdir(pathcd);*/      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
 #endif        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  /*system("wgnuplot graph.plt");*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      }
  /*system("cd ../gp37mgw");*/    }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    stepsize=(int) (stepm+YEARM-1)/YEARM;
  strcat(plotcmd," ");    if (stepm<=12) stepsize=1;
  strcat(plotcmd,optionfilegnuplot);    
  system(plotcmd);    agelim=AGESUP;
     
 #ifdef windows    hstepm=1;
   while (z[0] != 'q') {    hstepm=hstepm/stepm; 
     /* chdir(path); */    
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    if (popforecast==1) {
     scanf("%s",z);      if((ficpop=fopen(popfile,"r"))==NULL) {
     if (z[0] == 'c') system("./imach");        printf("Problem with population file : %s\n",popfile);exit(0);
     else if (z[0] == 'e') system(optionfilehtm);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
     else if (z[0] == 'g') system(plotcmd);      } 
     else if (z[0] == 'q') exit(0);      popage=ivector(0,AGESUP);
   }      popeffectif=vector(0,AGESUP);
 #endif      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 %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);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.1.52  
changed lines
  Added in v.1.133


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