Diff for /imach/src/imach.c between versions 1.50 and 1.167

version 1.50, 2002/06/26 23:25:02 version 1.167, 2014/12/22 13:50:56
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.167  2014/12/22 13:50:56  brouard
      Summary: Testing uname and compiler version and if compiled 32 or 64
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Testing on Linux 64
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.166  2014/12/22 11:40:47  brouard
   case of a health survey which is our main interest) -2- at least a    *** empty log message ***
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.165  2014/12/16 11:20:36  brouard
   computed from the time spent in each health state according to a    Summary: After compiling on Visual C
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    * imach.c (Module): Merging 1.61 to 1.162
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Revision 1.164  2014/12/16 10:52:11  brouard
   conditional to be observed in state i at the first wave. Therefore    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    * imach.c (Module): Merging 1.61 to 1.162
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.163  2014/12/16 10:30:11  brouard
   you to do it.  More covariates you add, slower the    * imach.c (Module): Merging 1.61 to 1.162
   convergence.  
     Revision 1.162  2014/09/25 11:43:39  brouard
   The advantage of this computer programme, compared to a simple    Summary: temporary backup 0.99!
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.1  2014/09/16 11:06:58  brouard
   intermediate interview, the information is lost, but taken into    Summary: With some code (wrong) for nlopt
   account using an interpolation or extrapolation.    
     Author:
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.161  2014/09/15 20:41:41  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Summary: Problem with macro SQR on Intel compiler
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.160  2014/09/02 09:24:05  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    *** empty log message ***
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.159  2014/09/01 10:34:10  brouard
     Summary: WIN32
   Also this programme outputs the covariance matrix of the parameters but also    Author: Brouard
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.158  2014/08/27 17:11:51  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    *** empty log message ***
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.157  2014/08/27 16:26:55  brouard
   from the European Union.    Summary: Preparing windows Visual studio version
   It is copyrighted identically to a GNU software product, ie programme and    Author: Brouard
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    In order to compile on Visual studio, time.h is now correct and time_t
   **********************************************************************/    and tm struct should be used. difftime should be used but sometimes I
      just make the differences in raw time format (time(&now).
 #include <math.h>    Trying to suppress #ifdef LINUX
 #include <stdio.h>    Add xdg-open for __linux in order to open default browser.
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.156  2014/08/25 20:10:10  brouard
     *** empty log message ***
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "gnuplot"    Revision 1.155  2014/08/25 18:32:34  brouard
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Summary: New compile, minor changes
 #define FILENAMELENGTH 80    Author: Brouard
 /*#define DEBUG*/  
 #define windows    Revision 1.154  2014/06/20 17:32:08  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Summary: Outputs now all graphs of convergence to period prevalence
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.153  2014/06/20 16:45:46  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: If 3 live state, convergence to period prevalence on same graph
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Author: Brouard
   
 #define NINTERVMAX 8    Revision 1.152  2014/06/18 17:54:09  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.151  2014/06/18 16:43:30  brouard
 #define MAXN 20000    *** empty log message ***
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.150  2014/06/18 16:42:35  brouard
 #define AGEBASE 40    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 #ifdef windows    Author: brouard
 #define DIRSEPARATOR '\\'  
 #define ODIRSEPARATOR '/'    Revision 1.149  2014/06/18 15:51:14  brouard
 #else    Summary: Some fixes in parameter files errors
 #define DIRSEPARATOR '/'    Author: Nicolas Brouard
 #define ODIRSEPARATOR '\\'  
 #endif    Revision 1.148  2014/06/17 17:38:48  brouard
     Summary: Nothing new
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Author: Brouard
 int erreur; /* Error number */  
 int nvar;    Just a new packaging for OS/X version 0.98nS
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.147  2014/06/16 10:33:11  brouard
 int nlstate=2; /* Number of live states */    *** empty log message ***
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.146  2014/06/16 10:20:28  brouard
 int popbased=0;    Summary: Merge
     Author: Brouard
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Merge, before building revised version.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.145  2014/06/10 21:23:15  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Summary: Debugging with valgrind
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Author: Nicolas Brouard
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Lot of changes in order to output the results with some covariates
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    After the Edimburgh REVES conference 2014, it seems mandatory to
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    improve the code.
 FILE *ficlog;    No more memory valgrind error but a lot has to be done in order to
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    continue the work of splitting the code into subroutines.
 FILE *ficresprobmorprev;    Also, decodemodel has been improved. Tricode is still not
 FILE *fichtm; /* Html File */    optimal. nbcode should be improved. Documentation has been added in
 FILE *ficreseij;    the source code.
 char filerese[FILENAMELENGTH];  
 FILE  *ficresvij;    Revision 1.143  2014/01/26 09:45:38  brouard
 char fileresv[FILENAMELENGTH];    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 char title[MAXLINE];    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    Revision 1.142  2014/01/26 03:57:36  brouard
     Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
 char filelog[FILENAMELENGTH]; /* Log file */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    Revision 1.141  2014/01/26 02:42:01  brouard
 char popfile[FILENAMELENGTH];    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Revision 1.140  2011/09/02 10:37:54  brouard
     Summary: times.h is ok with mingw32 now.
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.139  2010/06/14 07:50:17  brouard
 #define FTOL 1.0e-10    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
     I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 #define NRANSI  
 #define ITMAX 200    Revision 1.138  2010/04/30 18:19:40  brouard
     *** empty log message ***
 #define TOL 2.0e-4  
     Revision 1.137  2010/04/29 18:11:38  brouard
 #define CGOLD 0.3819660    (Module): Checking covariates for more complex models
 #define ZEPS 1.0e-10    than V1+V2. A lot of change to be done. Unstable.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.136  2010/04/26 20:30:53  brouard
 #define GOLD 1.618034    (Module): merging some libgsl code. Fixing computation
 #define GLIMIT 100.0    of likelione (using inter/intrapolation if mle = 0) in order to
 #define TINY 1.0e-20    get same likelihood as if mle=1.
     Some cleaning of code and comments added.
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.135  2009/10/29 15:33:14  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.134  2009/10/29 13:18:53  brouard
 #define rint(a) floor(a+0.5)    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
 static double sqrarg;    Revision 1.133  2009/07/06 10:21:25  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    just nforces
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.132  2009/07/06 08:22:05  brouard
 int imx;    Many tings
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
 int m,nb;    lot of cleaning with variables initialized to 0. Trying to make
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.129  2007/08/31 13:49:27  lievre
 double dateintmean=0;    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   
 double *weight;    Revision 1.128  2006/06/30 13:02:05  brouard
 int **s; /* Status */    (Module): Clarifications on computing e.j
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    imach-114 because nhstepm was no more computed in the age
 double ftolhess; /* Tolerance for computing hessian */    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
 /**************** split *************************/    compute health expectancies (without variances) in a first step
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    and then all the health expectancies with variances or standard
 {    deviation (needs data from the Hessian matrices) which slows the
    char *s;                             /* pointer */    computation.
    int  l1, l2;                         /* length counters */    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.126  2006/04/28 17:23:28  brouard
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    (Module): Yes the sum of survivors was wrong since
    if ( s == NULL ) {                   /* no directory, so use current */    imach-114 because nhstepm was no more computed in the age
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    loop. Now we define nhstepma in the age loop.
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    Version 0.98h
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
       if ( getwd( dirc ) == NULL ) {    Forecasting file added.
 #else  
       extern char       *getcwd( );    Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    The log-likelihood is printed in the log file
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.123  2006/03/20 10:52:43  brouard
       }    * imach.c (Module): <title> changed, corresponds to .htm file
       strcpy( name, path );             /* we've got it */    name. <head> headers where missing.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    * imach.c (Module): Weights can have a decimal point as for
       l2 = strlen( s );                 /* length of filename */    English (a comma might work with a correct LC_NUMERIC environment,
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    otherwise the weight is truncated).
       strcpy( name, s );                /* save file name */    Modification of warning when the covariates values are not 0 or
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    1.
       dirc[l1-l2] = 0;                  /* add zero */    Version 0.98g
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.122  2006/03/20 09:45:41  brouard
 #ifdef windows    (Module): Weights can have a decimal point as for
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    English (a comma might work with a correct LC_NUMERIC environment,
 #else    otherwise the weight is truncated).
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Modification of warning when the covariates values are not 0 or
 #endif    1.
    s = strrchr( name, '.' );            /* find last / */    Version 0.98g
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.121  2006/03/16 17:45:01  lievre
    l1= strlen( name);    * imach.c (Module): Comments concerning covariates added
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    * imach.c (Module): refinements in the computation of lli if
    finame[l1-l2]= 0;    status=-2 in order to have more reliable computation if stepm is
    return( 0 );                         /* we're done */    not 1 month. Version 0.98f
 }  
     Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
 /******************************************/    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 void replace(char *s, char*t)  
 {    Revision 1.119  2006/03/15 17:42:26  brouard
   int i;    (Module): Bug if status = -2, the loglikelihood was
   int lg=20;    computed as likelihood omitting the logarithm. Version O.98e
   i=0;  
   lg=strlen(t);    Revision 1.118  2006/03/14 18:20:07  brouard
   for(i=0; i<= lg; i++) {    (Module): varevsij Comments added explaining the second
     (s[i] = t[i]);    table of variances if popbased=1 .
     if (t[i]== '\\') s[i]='/';    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   }    (Module): Function pstamp added
 }    (Module): Version 0.98d
   
 int nbocc(char *s, char occ)    Revision 1.117  2006/03/14 17:16:22  brouard
 {    (Module): varevsij Comments added explaining the second
   int i,j=0;    table of variances if popbased=1 .
   int lg=20;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   i=0;    (Module): Function pstamp added
   lg=strlen(s);    (Module): Version 0.98d
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    Revision 1.116  2006/03/06 10:29:27  brouard
   }    (Module): Variance-covariance wrong links and
   return j;    varian-covariance of ej. is needed (Saito).
 }  
     Revision 1.115  2006/02/27 12:17:45  brouard
 void cutv(char *u,char *v, char*t, char occ)    (Module): One freematrix added in mlikeli! 0.98c
 {  
   /* cuts string t into u and v where u is ended by char occ excluding it    Revision 1.114  2006/02/26 12:57:58  brouard
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    (Module): Some improvements in processing parameter
      gives u="abcedf" and v="ghi2j" */    filename with strsep.
   int i,lg,j,p=0;  
   i=0;    Revision 1.113  2006/02/24 14:20:24  brouard
   for(j=0; j<=strlen(t)-1; j++) {    (Module): Memory leaks checks with valgrind and:
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    datafile was not closed, some imatrix were not freed and on matrix
   }    allocation too.
   
   lg=strlen(t);    Revision 1.112  2006/01/30 09:55:26  brouard
   for(j=0; j<p; j++) {    (Module): Back to gnuplot.exe instead of wgnuplot.exe
     (u[j] = t[j]);  
   }    Revision 1.111  2006/01/25 20:38:18  brouard
      u[p]='\0';    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
    for(j=0; j<= lg; j++) {    can be a simple dot '.'.
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.110  2006/01/25 00:51:50  brouard
 }    (Module): Lots of cleaning and bugs added (Gompertz)
   
 /********************** nrerror ********************/    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
 void nrerror(char error_text[])  
 {    Revision 1.108  2006/01/19 18:05:42  lievre
   fprintf(stderr,"ERREUR ...\n");    Gnuplot problem appeared...
   fprintf(stderr,"%s\n",error_text);    To be fixed
   exit(1);  
 }    Revision 1.107  2006/01/19 16:20:37  brouard
 /*********************** vector *******************/    Test existence of gnuplot in imach path
 double *vector(int nl, int nh)  
 {    Revision 1.106  2006/01/19 13:24:36  brouard
   double *v;    Some cleaning and links added in html output
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Revision 1.105  2006/01/05 20:23:19  lievre
   return v-nl+NR_END;    *** empty log message ***
 }  
     Revision 1.104  2005/09/30 16:11:43  lievre
 /************************ free vector ******************/    (Module): sump fixed, loop imx fixed, and simplifications.
 void free_vector(double*v, int nl, int nh)    (Module): If the status is missing at the last wave but we know
 {    that the person is alive, then we can code his/her status as -2
   free((FREE_ARG)(v+nl-NR_END));    (instead of missing=-1 in earlier versions) and his/her
 }    contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
 /************************ivector *******************************/    the healthy state at last known wave). Version is 0.98
 int *ivector(long nl,long nh)  
 {    Revision 1.103  2005/09/30 15:54:49  lievre
   int *v;    (Module): sump fixed, loop imx fixed, and simplifications.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Revision 1.102  2004/09/15 17:31:30  brouard
   return v-nl+NR_END;    Add the possibility to read data file including tab characters.
 }  
     Revision 1.101  2004/09/15 10:38:38  brouard
 /******************free ivector **************************/    Fix on curr_time
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.100  2004/07/12 18:29:06  brouard
   free((FREE_ARG)(v+nl-NR_END));    Add version for Mac OS X. Just define UNIX in Makefile
 }  
     Revision 1.99  2004/06/05 08:57:40  brouard
 /******************* imatrix *******************************/    *** empty log message ***
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.98  2004/05/16 15:05:56  brouard
 {    New version 0.97 . First attempt to estimate force of mortality
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    directly from the data i.e. without the need of knowing the health
   int **m;    state at each age, but using a Gompertz model: log u =a + b*age .
      This is the basic analysis of mortality and should be done before any
   /* allocate pointers to rows */    other analysis, in order to test if the mortality estimated from the
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    cross-longitudinal survey is different from the mortality estimated
   if (!m) nrerror("allocation failure 1 in matrix()");    from other sources like vital statistic data.
   m += NR_END;  
   m -= nrl;    The same imach parameter file can be used but the option for mle should be -3.
    
      Agnès, who wrote this part of the code, tried to keep most of the
   /* allocate rows and set pointers to them */    former routines in order to include the new code within the former code.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    The output is very simple: only an estimate of the intercept and of
   m[nrl] += NR_END;    the slope with 95% confident intervals.
   m[nrl] -= ncl;  
      Current limitations:
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    A) Even if you enter covariates, i.e. with the
      model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   /* return pointer to array of pointers to rows */    B) There is no computation of Life Expectancy nor Life Table.
   return m;  
 }    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
 /****************** free_imatrix *************************/    suppressed.
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Revision 1.96  2003/07/15 15:38:55  brouard
       long nch,ncl,nrh,nrl;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
      /* free an int matrix allocated by imatrix() */    rewritten within the same printf. Workaround: many printfs.
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Revision 1.95  2003/07/08 07:54:34  brouard
   free((FREE_ARG) (m+nrl-NR_END));    * imach.c (Repository):
 }    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.94  2003/06/27 13:00:02  brouard
 {    Just cleaning
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    exist so I changed back to asctime which exists.
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Version 0.96b
   m += NR_END;  
   m -= nrl;    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    exist so I changed back to asctime which exists.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.91  2003/06/25 15:30:29  brouard
   m[nrl] -= ncl;    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    helps to forecast when convergence will be reached. Elapsed time
   return m;    is stamped in powell.  We created a new html file for the graphs
 }    concerning matrix of covariance. It has extension -cov.htm.
   
 /*************************free matrix ************************/    Revision 1.90  2003/06/24 12:34:15  brouard
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    of the covariance matrix to be input.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 /******************* ma3x *******************************/    mle=-1 a template is output in file "or"mypar.txt with the design
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    of the covariance matrix to be input.
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.88  2003/06/23 17:54:56  brouard
   double ***m;    * 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.
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.87  2003/06/18 12:26:01  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    Version 0.96
   m += NR_END;  
   m -= nrl;    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    routine fileappend.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.85  2003/06/17 13:12:43  brouard
   m[nrl] -= ncl;    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    assuming that the date of death was just one stepm after the
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    interview.
   m[nrl][ncl] += NR_END;    (Repository): Because some people have very long ID (first column)
   m[nrl][ncl] -= nll;    we changed int to long in num[] and we added a new lvector for
   for (j=ncl+1; j<=nch; j++)    memory allocation. But we also truncated to 8 characters (left
     m[nrl][j]=m[nrl][j-1]+nlay;    truncation)
      (Repository): No more line truncation errors.
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Revision 1.84  2003/06/13 21:44:43  brouard
     for (j=ncl+1; j<=nch; j++)    * imach.c (Repository): Replace "freqsummary" at a correct
       m[i][j]=m[i][j-1]+nlay;    place. It differs from routine "prevalence" which may be called
   }    many times. Probs is memory consuming and must be used with
   return m;    parcimony.
 }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 /*************************free ma3x ************************/    Revision 1.83  2003/06/10 13:39:11  lievre
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    *** empty log message ***
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Revision 1.82  2003/06/05 15:57:20  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Add log in  imach.c and  fullversion number is now printed.
   free((FREE_ARG)(m+nrl-NR_END));  
 }  */
   /*
 /***************** f1dim *************************/     Interpolated Markov Chain
 extern int ncom;  
 extern double *pcom,*xicom;    Short summary of the programme:
 extern double (*nrfunc)(double []);    
      This program computes Healthy Life Expectancies from
 double f1dim(double x)    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 {    first survey ("cross") where individuals from different ages are
   int j;    interviewed on their health status or degree of disability (in the
   double f;    case of a health survey which is our main interest) -2- at least a
   double *xt;    second wave of interviews ("longitudinal") which measure each change
      (if any) in individual health status.  Health expectancies are
   xt=vector(1,ncom);    computed from the time spent in each health state according to a
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    model. More health states you consider, more time is necessary to reach the
   f=(*nrfunc)(xt);    Maximum Likelihood of the parameters involved in the model.  The
   free_vector(xt,1,ncom);    simplest model is the multinomial logistic model where pij is the
   return f;    probability to be observed in state j at the second wave
 }    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 /*****************brent *************************/    'age' is age and 'sex' is a covariate. If you want to have a more
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    complex model than "constant and age", you should modify the program
 {    where the markup *Covariates have to be included here again* invites
   int iter;    you to do it.  More covariates you add, slower the
   double a,b,d,etemp;    convergence.
   double fu,fv,fw,fx;  
   double ftemp;    The advantage of this computer programme, compared to a simple
   double p,q,r,tol1,tol2,u,v,w,x,xm;    multinomial logistic model, is clear when the delay between waves is not
   double e=0.0;    identical for each individual. Also, if a individual missed an
      intermediate interview, the information is lost, but taken into
   a=(ax < cx ? ax : cx);    account using an interpolation or extrapolation.  
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    hPijx is the probability to be observed in state i at age x+h
   fw=fv=fx=(*f)(x);    conditional to the observed state i at age x. The delay 'h' can be
   for (iter=1;iter<=ITMAX;iter++) {    split into an exact number (nh*stepm) of unobserved intermediate
     xm=0.5*(a+b);    states. This elementary transition (by month, quarter,
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    semester or year) is modelled as a multinomial logistic.  The hPx
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    matrix is simply the matrix product of nh*stepm elementary matrices
     printf(".");fflush(stdout);    and the contribution of each individual to the likelihood is simply
     fprintf(ficlog,".");fflush(ficlog);    hPijx.
 #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);    Also this programme outputs the covariance matrix of the parameters but also
     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);    of the life expectancies. It also computes the period (stable) prevalence. 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    
 #endif    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){             Institut national d'études démographiques, Paris.
       *xmin=x;    This software have been partly granted by Euro-REVES, a concerted action
       return fx;    from the European Union.
     }    It is copyrighted identically to a GNU software product, ie programme and
     ftemp=fu;    software can be distributed freely for non commercial use. Latest version
     if (fabs(e) > tol1) {    can be accessed at http://euroreves.ined.fr/imach .
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       p=(x-v)*q-(x-w)*r;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       q=2.0*(q-r);    
       if (q > 0.0) p = -p;    **********************************************************************/
       q=fabs(q);  /*
       etemp=e;    main
       e=d;    read parameterfile
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    read datafile
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    concatwav
       else {    freqsummary
         d=p/q;    if (mle >= 1)
         u=x+d;      mlikeli
         if (u-a < tol2 || b-u < tol2)    print results files
           d=SIGN(tol1,xm-x);    if mle==1 
       }       computes hessian
     } else {    read end of parameter file: agemin, agemax, bage, fage, estepm
       d=CGOLD*(e=(x >= xm ? a-x : b-x));        begin-prev-date,...
     }    open gnuplot file
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    open html file
     fu=(*f)(u);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
     if (fu <= fx) {     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
       if (u >= x) a=x; else b=x;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
       SHFT(v,w,x,u)      freexexit2 possible for memory heap.
         SHFT(fv,fw,fx,fu)  
         } else {    h Pij x                         | pij_nom  ficrestpij
           if (u < x) a=u; else b=u;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
           if (fu <= fw || w == x) {         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
             v=w;         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
             w=u;  
             fv=fw;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
             fw=fu;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
           } else if (fu <= fv || v == x || v == w) {    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
             v=u;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
             fv=fu;     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
           }  
         }    forecasting if prevfcast==1 prevforecast call prevalence()
   }    health expectancies
   nrerror("Too many iterations in brent");    Variance-covariance of DFLE
   *xmin=x;    prevalence()
   return fx;     movingaverage()
 }    varevsij() 
     if popbased==1 varevsij(,popbased)
 /****************** mnbrak ***********************/    total life expectancies
     Variance of period (stable) prevalence
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,   end
             double (*func)(double))  */
 {  
   double ulim,u,r,q, dum;  #define POWELL /* Instead of NLOPT */
   double fu;  
    #include <math.h>
   *fa=(*func)(*ax);  #include <stdio.h>
   *fb=(*func)(*bx);  #include <stdlib.h>
   if (*fb > *fa) {  #include <string.h>
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  #ifdef _WIN32
       }  #include <io.h>
   *cx=(*bx)+GOLD*(*bx-*ax);  #else
   *fc=(*func)(*cx);  #include <unistd.h>
   while (*fb > *fc) {  #endif
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  #include <limits.h>
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #include <sys/types.h>
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #include <sys/utsname.h>
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #include <sys/stat.h>
     if ((*bx-u)*(u-*cx) > 0.0) {  #include <errno.h>
       fu=(*func)(u);  /* extern int errno; */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  /* #ifdef LINUX */
       if (fu < *fc) {  /* #include <time.h> */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /* #include "timeval.h" */
           SHFT(*fb,*fc,fu,(*func)(u))  /* #else */
           }  /* #include <sys/time.h> */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  /* #endif */
       u=ulim;  
       fu=(*func)(u);  #include <time.h>
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);  #ifdef GSL
       fu=(*func)(u);  #include <gsl/gsl_errno.h>
     }  #include <gsl/gsl_multimin.h>
     SHFT(*ax,*bx,*cx,u)  #endif
       SHFT(*fa,*fb,*fc,fu)  
       }  
 }  #ifdef NLOPT
   #include <nlopt.h>
 /*************** linmin ************************/  typedef struct {
     double (* function)(double [] );
 int ncom;  } myfunc_data ;
 double *pcom,*xicom;  #endif
 double (*nrfunc)(double []);  
    /* #include <libintl.h> */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /* #define _(String) gettext (String) */
 {  
   double brent(double ax, double bx, double cx,  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  #define GNUPLOTPROGRAM "gnuplot"
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
               double *fc, double (*func)(double));  #define FILENAMELENGTH 132
   int j;  
   double xx,xmin,bx,ax;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   double fx,fb,fa;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    
   ncom=n;  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   pcom=vector(1,n);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   xicom=vector(1,n);  
   nrfunc=func;  #define NINTERVMAX 8
   for (j=1;j<=n;j++) {  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
     pcom[j]=p[j];  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     xicom[j]=xi[j];  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   }  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   ax=0.0;  #define MAXN 20000
   xx=1.0;  #define YEARM 12. /**< Number of months per year */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define AGESUP 130
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #define AGEBASE 40
 #ifdef DEBUG  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #ifdef _WIN32
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #define DIRSEPARATOR '\\'
 #endif  #define CHARSEPARATOR "\\"
   for (j=1;j<=n;j++) {  #define ODIRSEPARATOR '/'
     xi[j] *= xmin;  #else
     p[j] += xi[j];  #define DIRSEPARATOR '/'
   }  #define CHARSEPARATOR "/"
   free_vector(xicom,1,n);  #define ODIRSEPARATOR '\\'
   free_vector(pcom,1,n);  #endif
 }  
   /* $Id$ */
 /*************** powell ************************/  /* $State$ */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 {  char fullversion[]="$Revision$ $Date$"; 
   void linmin(double p[], double xi[], int n, double *fret,  char strstart[80];
               double (*func)(double []));  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   int i,ibig,j;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double del,t,*pt,*ptt,*xit;  int nvar=0, nforce=0; /* Number of variables, number of forces */
   double fp,fptt;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   double *xits;  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   pt=vector(1,n);  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   ptt=vector(1,n);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   xit=vector(1,n);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   xits=vector(1,n);  int cptcovprodnoage=0; /**< Number of covariate products without age */   
   *fret=(*func)(p);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   for (j=1;j<=n;j++) pt[j]=p[j];  int cptcov=0; /* Working variable */
   for (*iter=1;;++(*iter)) {  int npar=NPARMAX;
     fp=(*fret);  int nlstate=2; /* Number of live states */
     ibig=0;  int ndeath=1; /* Number of dead states */
     del=0.0;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  int popbased=0;
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  int *wav; /* Number of waves for this individuual 0 is possible */
       printf(" %d %.12f",i, p[i]);  int maxwav=0; /* Maxim number of waves */
     fprintf(ficlog," %d %.12f",i, p[i]);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     printf("\n");  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     fprintf(ficlog,"\n");  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     for (i=1;i<=n;i++) {                     to the likelihood and the sum of weights (done by funcone)*/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  int mle=1, weightopt=0;
       fptt=(*fret);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #ifdef DEBUG  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       printf("fret=%lf \n",*fret);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       fprintf(ficlog,"fret=%lf \n",*fret);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 #endif  int countcallfunc=0;  /* Count the number of calls to func */
       printf("%d",i);fflush(stdout);  double jmean=1; /* Mean space between 2 waves */
       fprintf(ficlog,"%d",i);fflush(ficlog);  double **matprod2(); /* test */
       linmin(p,xit,n,fret,func);  double **oldm, **newm, **savm; /* Working pointers to matrices */
       if (fabs(fptt-(*fret)) > del) {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
         del=fabs(fptt-(*fret));  /*FILE *fic ; */ /* Used in readdata only */
         ibig=i;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       }  FILE *ficlog, *ficrespow;
 #ifdef DEBUG  int globpr=0; /* Global variable for printing or not */
       printf("%d %.12e",i,(*fret));  double fretone; /* Only one call to likelihood */
       fprintf(ficlog,"%d %.12e",i,(*fret));  long ipmx=0; /* Number of contributions */
       for (j=1;j<=n;j++) {  double sw; /* Sum of weights */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  char filerespow[FILENAMELENGTH];
         printf(" x(%d)=%.12e",j,xit[j]);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  FILE *ficresilk;
       }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       for(j=1;j<=n;j++) {  FILE *ficresprobmorprev;
         printf(" p=%.12e",p[j]);  FILE *fichtm, *fichtmcov; /* Html File */
         fprintf(ficlog," p=%.12e",p[j]);  FILE *ficreseij;
       }  char filerese[FILENAMELENGTH];
       printf("\n");  FILE *ficresstdeij;
       fprintf(ficlog,"\n");  char fileresstde[FILENAMELENGTH];
 #endif  FILE *ficrescveij;
     }  char filerescve[FILENAMELENGTH];
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  FILE  *ficresvij;
 #ifdef DEBUG  char fileresv[FILENAMELENGTH];
       int k[2],l;  FILE  *ficresvpl;
       k[0]=1;  char fileresvpl[FILENAMELENGTH];
       k[1]=-1;  char title[MAXLINE];
       printf("Max: %.12e",(*func)(p));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       fprintf(ficlog,"Max: %.12e",(*func)(p));  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       for (j=1;j<=n;j++) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
         printf(" %.12e",p[j]);  char command[FILENAMELENGTH];
         fprintf(ficlog," %.12e",p[j]);  int  outcmd=0;
       }  
       printf("\n");  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       fprintf(ficlog,"\n");  
       for(l=0;l<=1;l++) {  char filelog[FILENAMELENGTH]; /* Log file */
         for (j=1;j<=n;j++) {  char filerest[FILENAMELENGTH];
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  char fileregp[FILENAMELENGTH];
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  char popfile[FILENAMELENGTH];
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
       }  /* struct timezone tzp; */
 #endif  /* extern int gettimeofday(); */
   struct tm tml, *gmtime(), *localtime();
   
       free_vector(xit,1,n);  extern time_t time();
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  struct tm start_time, end_time, curr_time, last_time, forecast_time;
       free_vector(pt,1,n);  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
       return;  struct tm tm;
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  char strcurr[80], strfor[80];
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  char *endptr;
       xit[j]=p[j]-pt[j];  long lval;
       pt[j]=p[j];  double dval;
     }  
     fptt=(*func)(ptt);  #define NR_END 1
     if (fptt < fp) {  #define FREE_ARG char*
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #define FTOL 1.0e-10
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  #define NRANSI 
         for (j=1;j<=n;j++) {  #define ITMAX 200 
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  #define TOL 2.0e-4 
         }  
 #ifdef DEBUG  #define CGOLD 0.3819660 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define ZEPS 1.0e-10 
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
         for(j=1;j<=n;j++){  
           printf(" %.12e",xit[j]);  #define GOLD 1.618034 
           fprintf(ficlog," %.12e",xit[j]);  #define GLIMIT 100.0 
         }  #define TINY 1.0e-20 
         printf("\n");  
         fprintf(ficlog,"\n");  static double maxarg1,maxarg2;
 #endif  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     }    
   }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 }  #define rint(a) floor(a+0.5)
   /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
 /**** Prevalence limit ****************/  /* #define mytinydouble 1.0e-16 */
   /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
 {  /* static double dsqrarg; */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
      matrix by transitions matrix until convergence is reached */  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   int i, ii,j,k;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   double min, max, maxmin, maxmax,sumnew=0.;  int agegomp= AGEGOMP;
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  int imx; 
   double **newm;  int stepm=1;
   double agefin, delaymax=50 ; /* Max number of years to converge */  /* Stepm, step in month: minimum step interpolation*/
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  int estepm;
     for (j=1;j<=nlstate+ndeath;j++){  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  int m,nb;
   long *num;
    cov[1]=1.;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
    double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  double **pmmij, ***probs;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  double *ageexmed,*agecens;
     newm=savm;  double dateintmean=0;
     /* Covariates have to be included here again */  
      cov[2]=agefin;  double *weight;
    int **s; /* Status */
       for (k=1; k<=cptcovn;k++) {  double *agedc;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
         /*      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]]);*/                    * covar=matrix(0,NCOVMAX,1,n); 
       }                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  double  idx; 
       for (k=1; k<=cptcovprod;k++)  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  int *Ndum; /** Freq of modality (tricode */
   int **codtab; /**< codtab=imatrix(1,100,1,10); */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  double *lsurv, *lpop, *tpop;
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   double ftolhess; /**< Tolerance for computing hessian */
     savm=oldm;  
     oldm=newm;  /**************** split *************************/
     maxmax=0.;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     for(j=1;j<=nlstate;j++){  {
       min=1.;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       max=0.;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       for(i=1; i<=nlstate; i++) {    */ 
         sumnew=0;    char  *ss;                            /* pointer */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    int   l1, l2;                         /* length counters */
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);    l1 = strlen(path );                   /* length of path */
         min=FMIN(min,prlim[i][j]);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       maxmin=max-min;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       maxmax=FMAX(maxmax,maxmin);      strcpy( name, path );               /* we got the fullname name because no directory */
     }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     if(maxmax < ftolpl){        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       return prlim;      /* get current working directory */
     }      /*    extern  char* getcwd ( char *buf , int len);*/
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 }        return( GLOCK_ERROR_GETCWD );
       }
 /*************** transition probabilities ***************/      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   double s1, s2;      l2 = strlen( ss );                  /* length of filename */
   /*double t34;*/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i,j,j1, nc, ii, jj;      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
     for(i=1; i<= nlstate; i++){      dirc[l1-l2] = 0;                    /* add zero */
     for(j=1; j<i;j++){      printf(" DIRC2 = %s \n",dirc);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    }
         /*s2 += param[i][j][nc]*cov[nc];*/    /* We add a separator at the end of dirc if not exists */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    l1 = strlen( dirc );                  /* length of directory */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    if( dirc[l1-1] != DIRSEPARATOR ){
       }      dirc[l1] =  DIRSEPARATOR;
       ps[i][j]=s2;      dirc[l1+1] = 0; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      printf(" DIRC3 = %s \n",dirc);
     }    }
     for(j=i+1; j<=nlstate+ndeath;j++){    ss = strrchr( name, '.' );            /* find last / */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if (ss >0){
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      ss++;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      strcpy(ext,ss);                     /* save extension */
       }      l1= strlen( name);
       ps[i][j]=s2;      l2= strlen(ss)+1;
     }      strncpy( finame, name, l1-l2);
   }      finame[l1-l2]= 0;
     /*ps[3][2]=1;*/    }
   
   for(i=1; i<= nlstate; i++){    return( 0 );                          /* we're done */
      s1=0;  }
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  /******************************************/
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);  void replace_back_to_slash(char *s, char*t)
     for(j=1; j<i; j++)  {
       ps[i][j]= exp(ps[i][j])*ps[i][i];    int i;
     for(j=i+1; j<=nlstate+ndeath; j++)    int lg=0;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    i=0;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    lg=strlen(t);
   } /* end i */    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      if (t[i]== '\\') s[i]='/';
     for(jj=1; jj<= nlstate+ndeath; jj++){    }
       ps[ii][jj]=0;  }
       ps[ii][ii]=1;  
     }  char *trimbb(char *out, char *in)
   }  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     char *s;
     s=out;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    while (*in != '\0'){
     for(jj=1; jj<= nlstate+ndeath; jj++){      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
      printf("%lf ",ps[ii][jj]);        in++;
    }      }
     printf("\n ");      *out++ = *in++;
     }    }
     printf("\n ");printf("%lf ",cov[2]);*/    *out='\0';
 /*    return s;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  }
   goto end;*/  
     return ps;  char *cutl(char *blocc, char *alocc, char *in, char occ)
 }  {
     /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
 /**************** Product of 2 matrices ******************/       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)       If occ is not found blocc is null and alocc is equal to in. Returns blocc
 {    */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    char *s, *t;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    t=in;s=in;
   /* in, b, out are matrice of pointers which should have been initialized    while ((*in != occ) && (*in != '\0')){
      before: only the contents of out is modified. The function returns      *alocc++ = *in++;
      a pointer to pointers identical to out */    }
   long i, j, k;    if( *in == occ){
   for(i=nrl; i<= nrh; i++)      *(alocc)='\0';
     for(k=ncolol; k<=ncoloh; k++)      s=++in;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    }
         out[i][k] +=in[i][j]*b[j][k];   
     if (s == t) {/* occ not found */
   return out;      *(alocc-(in-s))='\0';
 }      in=s;
     }
     while ( *in != '\0'){
 /************* Higher Matrix Product ***************/      *blocc++ = *in++;
     }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {    *blocc='\0';
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    return t;
      duration (i.e. until  }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  char *cutv(char *blocc, char *alocc, char *in, char occ)
      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).    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
      Model is determined by parameters x and covariates have to be       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
      included manually here.       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns alocc
      */    */
     char *s, *t;
   int i, j, d, h, k;    t=in;s=in;
   double **out, cov[NCOVMAX];    while (*in != '\0'){
   double **newm;      while( *in == occ){
         *blocc++ = *in++;
   /* Hstepm could be zero and should return the unit matrix */        s=in;
   for (i=1;i<=nlstate+ndeath;i++)      }
     for (j=1;j<=nlstate+ndeath;j++){      *blocc++ = *in++;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    }
       po[i][j][0]=(i==j ? 1.0 : 0.0);    if (s == t) /* occ not found */
     }      *(blocc-(in-s))='\0';
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    else
   for(h=1; h <=nhstepm; h++){      *(blocc-(in-s)-1)='\0';
     for(d=1; d <=hstepm; d++){    in=s;
       newm=savm;    while ( *in != '\0'){
       /* Covariates have to be included here again */      *alocc++ = *in++;
       cov[1]=1.;    }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    *alocc='\0';
       for (k=1; k<=cptcovage;k++)    return s;
         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]]];  int nbocc(char *s, char occ)
   {
     int i,j=0;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    int lg=20;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    i=0;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    lg=strlen(s);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    for(i=0; i<= lg; i++) {
       savm=oldm;    if  (s[i] == occ ) j++;
       oldm=newm;    }
     }    return j;
     for(i=1; i<=nlstate+ndeath; i++)  }
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  /* void cutv(char *u,char *v, char*t, char occ) */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /* { */
          */  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       }  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   } /* end h */  /*      gives u="abcdef2ghi" and v="j" *\/ */
   return po;  /*   int i,lg,j,p=0; */
 }  /*   i=0; */
   /*   lg=strlen(t); */
   /*   for(j=0; j<=lg-1; j++) { */
 /*************** log-likelihood *************/  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
 double func( double *x)  /*   } */
 {  
   int i, ii, j, k, mi, d, kk;  /*   for(j=0; j<p; j++) { */
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*     (u[j] = t[j]); */
   double **out;  /*   } */
   double sw; /* Sum of weights */  /*      u[p]='\0'; */
   double lli; /* Individual log likelihood */  
   long ipmx;  /*    for(j=0; j<= lg; j++) { */
   /*extern weight */  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /* We are differentiating ll according to initial status */  /*   } */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  /* } */
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);  #ifdef _WIN32
   */  char * strsep(char **pp, const char *delim)
   cov[1]=1.;  {
     char *p, *q;
   for(k=1; k<=nlstate; k++) ll[k]=0.;           
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    if ((p = *pp) == NULL)
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      return 0;
     for(mi=1; mi<= wav[i]-1; mi++){    if ((q = strpbrk (p, delim)) != NULL)
       for (ii=1;ii<=nlstate+ndeath;ii++)    {
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      *pp = q + 1;
       for(d=0; d<dh[mi][i]; d++){      *q = '\0';
         newm=savm;    }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    else
         for (kk=1; kk<=cptcovage;kk++) {      *pp = 0;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    return p;
         }  }
          #endif
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /********************** nrerror ********************/
         savm=oldm;  
         oldm=newm;  void nrerror(char error_text[])
          {
            fprintf(stderr,"ERREUR ...\n");
       } /* end mult */    fprintf(stderr,"%s\n",error_text);
          exit(EXIT_FAILURE);
       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]]);*/  /*********************** vector *******************/
       ipmx +=1;  double *vector(int nl, int nh)
       sw += weight[i];  {
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    double *v;
     } /* end of wave */    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   } /* end of individual */    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  }
   /* 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 */  /************************ free vector ******************/
   return -l;  void free_vector(double*v, int nl, int nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
   }
 /*********** Maximum Likelihood Estimation ***************/  
   /************************ivector *******************************/
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  int *ivector(long nl,long nh)
 {  {
   int i,j, iter;    int *v;
   double **xi,*delti;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   double fret;    if (!v) nrerror("allocation failure in ivector");
   xi=matrix(1,npar,1,npar);    return v-nl+NR_END;
   for (i=1;i<=npar;i++)  }
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);  /******************free ivector **************************/
   printf("Powell\n");  fprintf(ficlog,"Powell\n");  void free_ivector(int *v, long nl, long nh)
   powell(p,xi,npar,ftol,&iter,&fret,func);  {
     free((FREE_ARG)(v+nl-NR_END));
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  }
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  /************************lvector *******************************/
   long *lvector(long nl,long nh)
 }  {
     long *v;
 /**** Computes Hessian and covariance matrix ***/    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    if (!v) nrerror("allocation failure in ivector");
 {    return v-nl+NR_END;
   double  **a,**y,*x,pd;  }
   double **hess;  
   int i, j,jk;  /******************free lvector **************************/
   int *indx;  void free_lvector(long *v, long nl, long nh)
   {
   double hessii(double p[], double delta, int theta, double delti[]);    free((FREE_ARG)(v+nl-NR_END));
   double hessij(double p[], double delti[], int i, int j);  }
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
   hess=matrix(1,npar,1,npar);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
   printf("\nCalculation of the hessian matrix. Wait...\n");    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    int **m; 
   for (i=1;i<=npar;i++){    
     printf("%d",i);fflush(stdout);    /* allocate pointers to rows */ 
     fprintf(ficlog,"%d",i);fflush(ficlog);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    if (!m) nrerror("allocation failure 1 in matrix()"); 
     /*printf(" %f ",p[i]);*/    m += NR_END; 
     /*printf(" %lf ",hess[i][i]);*/    m -= nrl; 
   }    
      
   for (i=1;i<=npar;i++) {    /* allocate rows and set pointers to them */ 
     for (j=1;j<=npar;j++)  {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       if (j>i) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         printf(".%d%d",i,j);fflush(stdout);    m[nrl] += NR_END; 
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    m[nrl] -= ncl; 
         hess[i][j]=hessij(p,delti,i,j);    
         hess[j][i]=hess[i][j];        for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         /*printf(" %lf ",hess[i][j]);*/    
       }    /* return pointer to array of pointers to rows */ 
     }    return m; 
   }  } 
   printf("\n");  
   fprintf(ficlog,"\n");  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        int **m;
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");        long nch,ncl,nrh,nrl; 
         /* free an int matrix allocated by imatrix() */ 
   a=matrix(1,npar,1,npar);  { 
   y=matrix(1,npar,1,npar);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   x=vector(1,npar);    free((FREE_ARG) (m+nrl-NR_END)); 
   indx=ivector(1,npar);  } 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /******************* matrix *******************************/
   ludcmp(a,npar,indx,&pd);  double **matrix(long nrl, long nrh, long ncl, long nch)
   {
   for (j=1;j<=npar;j++) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     for (i=1;i<=npar;i++) x[i]=0;    double **m;
     x[j]=1;  
     lubksb(a,npar,indx,x);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for (i=1;i<=npar;i++){    if (!m) nrerror("allocation failure 1 in matrix()");
       matcov[i][j]=x[i];    m += NR_END;
     }    m -= nrl;
   }  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   printf("\n#Hessian matrix#\n");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   fprintf(ficlog,"\n#Hessian matrix#\n");    m[nrl] += NR_END;
   for (i=1;i<=npar;i++) {    m[nrl] -= ncl;
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       fprintf(ficlog,"%.3e ",hess[i][j]);    return m;
     }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     printf("\n");  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     fprintf(ficlog,"\n");  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   }     */
   }
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  /*************************free matrix ************************/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   ludcmp(a,npar,indx,&pd);  {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
   /*  printf("\n#Hessian matrix recomputed#\n");    free((FREE_ARG)(m+nrl-NR_END));
   }
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /******************* ma3x *******************************/
     x[j]=1;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     lubksb(a,npar,indx,x);  {
     for (i=1;i<=npar;i++){    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       y[i][j]=x[i];    double ***m;
       printf("%.3e ",y[i][j]);  
       fprintf(ficlog,"%.3e ",y[i][j]);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
     printf("\n");    m += NR_END;
     fprintf(ficlog,"\n");    m -= nrl;
   }  
   */    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free_matrix(a,1,npar,1,npar);    m[nrl] += NR_END;
   free_matrix(y,1,npar,1,npar);    m[nrl] -= ncl;
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   free_matrix(hess,1,npar,1,npar);  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 }    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
 /*************** hessian matrix ****************/    for (j=ncl+1; j<=nch; j++) 
 double hessii( double x[], double delta, int theta, double delti[])      m[nrl][j]=m[nrl][j-1]+nlay;
 {    
   int i;    for (i=nrl+1; i<=nrh; i++) {
   int l=1, lmax=20;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   double k1,k2;      for (j=ncl+1; j<=nch; j++) 
   double p2[NPARMAX+1];        m[i][j]=m[i][j-1]+nlay;
   double res;    }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    return m; 
   double fx;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   int k=0,kmax=10;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   double l1;    */
   }
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];  /*************************free ma3x ************************/
   for(l=0 ; l <=lmax; l++){  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     l1=pow(10,l);  {
     delts=delt;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for(k=1 ; k <kmax; k=k+1){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       delt = delta*(l1*k);    free((FREE_ARG)(m+nrl-NR_END));
       p2[theta]=x[theta] +delt;  }
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;  /*************** function subdirf ***********/
       k2=func(p2)-fx;  char *subdirf(char fileres[])
       /*res= (k1-2.0*fx+k2)/delt/delt; */  {
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    /* Caution optionfilefiname is hidden */
          strcpy(tmpout,optionfilefiname);
 #ifdef DEBUG    strcat(tmpout,"/"); /* Add to the right */
       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);    strcat(tmpout,fileres);
       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);    return tmpout;
 #endif  }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  /*************** function subdirf2 ***********/
         k=kmax;  char *subdirf2(char fileres[], char *preop)
       }  {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    
         k=kmax; l=lmax*10.;    /* Caution optionfilefiname is hidden */
       }    strcpy(tmpout,optionfilefiname);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    strcat(tmpout,"/");
         delts=delt;    strcat(tmpout,preop);
       }    strcat(tmpout,fileres);
     }    return tmpout;
   }  }
   delti[theta]=delts;  
   return res;  /*************** function subdirf3 ***********/
    char *subdirf3(char fileres[], char *preop, char *preop2)
 }  {
     
 double hessij( double x[], double delti[], int thetai,int thetaj)    /* Caution optionfilefiname is hidden */
 {    strcpy(tmpout,optionfilefiname);
   int i;    strcat(tmpout,"/");
   int l=1, l1, lmax=20;    strcat(tmpout,preop);
   double k1,k2,k3,k4,res,fx;    strcat(tmpout,preop2);
   double p2[NPARMAX+1];    strcat(tmpout,fileres);
   int k;    return tmpout;
   }
   fx=func(x);  
   for (k=1; k<=2; k++) {  char *asc_diff_time(long time_sec, char ascdiff[])
     for (i=1;i<=npar;i++) p2[i]=x[i];  {
     p2[thetai]=x[thetai]+delti[thetai]/k;    long sec_left, days, hours, minutes;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    days = (time_sec) / (60*60*24);
     k1=func(p2)-fx;    sec_left = (time_sec) % (60*60*24);
      hours = (sec_left) / (60*60) ;
     p2[thetai]=x[thetai]+delti[thetai]/k;    sec_left = (sec_left) %(60*60);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    minutes = (sec_left) /60;
     k2=func(p2)-fx;    sec_left = (sec_left) % (60);
      sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     p2[thetai]=x[thetai]-delti[thetai]/k;    return ascdiff;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  }
     k3=func(p2)-fx;  
    /***************** f1dim *************************/
     p2[thetai]=x[thetai]-delti[thetai]/k;  extern int ncom; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  extern double *pcom,*xicom;
     k4=func(p2)-fx;  extern double (*nrfunc)(double []); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */   
 #ifdef DEBUG  double f1dim(double x) 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  { 
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    int j; 
 #endif    double f;
   }    double *xt; 
   return res;   
 }    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 /************** Inverse of matrix **************/    f=(*nrfunc)(xt); 
 void ludcmp(double **a, int n, int *indx, double *d)    free_vector(xt,1,ncom); 
 {    return f; 
   int i,imax,j,k;  } 
   double big,dum,sum,temp;  
   double *vv;  /*****************brent *************************/
    double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   vv=vector(1,n);  { 
   *d=1.0;    int iter; 
   for (i=1;i<=n;i++) {    double a,b,d,etemp;
     big=0.0;    double fu=0,fv,fw,fx;
     for (j=1;j<=n;j++)    double ftemp=0.;
       if ((temp=fabs(a[i][j])) > big) big=temp;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    double e=0.0; 
     vv[i]=1.0/big;   
   }    a=(ax < cx ? ax : cx); 
   for (j=1;j<=n;j++) {    b=(ax > cx ? ax : cx); 
     for (i=1;i<j;i++) {    x=w=v=bx; 
       sum=a[i][j];    fw=fv=fx=(*f)(x); 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    for (iter=1;iter<=ITMAX;iter++) { 
       a[i][j]=sum;      xm=0.5*(a+b); 
     }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     big=0.0;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for (i=j;i<=n;i++) {      printf(".");fflush(stdout);
       sum=a[i][j];      fprintf(ficlog,".");fflush(ficlog);
       for (k=1;k<j;k++)  #ifdef DEBUGBRENT
         sum -= a[i][k]*a[k][j];      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);
       a[i][j]=sum;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       if ( (dum=vv[i]*fabs(sum)) >= big) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         big=dum;  #endif
         imax=i;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       }        *xmin=x; 
     }        return fx; 
     if (j != imax) {      } 
       for (k=1;k<=n;k++) {      ftemp=fu;
         dum=a[imax][k];      if (fabs(e) > tol1) { 
         a[imax][k]=a[j][k];        r=(x-w)*(fx-fv); 
         a[j][k]=dum;        q=(x-v)*(fx-fw); 
       }        p=(x-v)*q-(x-w)*r; 
       *d = -(*d);        q=2.0*(q-r); 
       vv[imax]=vv[j];        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
     indx[j]=imax;        etemp=e; 
     if (a[j][j] == 0.0) a[j][j]=TINY;        e=d; 
     if (j != n) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       dum=1.0/(a[j][j]);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        else { 
     }          d=p/q; 
   }          u=x+d; 
   free_vector(vv,1,n);  /* Doesn't work */          if (u-a < tol2 || b-u < tol2) 
 ;            d=SIGN(tol1,xm-x); 
 }        } 
       } else { 
 void lubksb(double **a, int n, int *indx, double b[])        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 {      } 
   int i,ii=0,ip,j;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double sum;      fu=(*f)(u); 
        if (fu <= fx) { 
   for (i=1;i<=n;i++) {        if (u >= x) a=x; else b=x; 
     ip=indx[i];        SHFT(v,w,x,u) 
     sum=b[ip];          SHFT(fv,fw,fx,fu) 
     b[ip]=b[i];          } else { 
     if (ii)            if (u < x) a=u; else b=u; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            if (fu <= fw || w == x) { 
     else if (sum) ii=i;              v=w; 
     b[i]=sum;              w=u; 
   }              fv=fw; 
   for (i=n;i>=1;i--) {              fw=fu; 
     sum=b[i];            } else if (fu <= fv || v == x || v == w) { 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];              v=u; 
     b[i]=sum/a[i][i];              fv=fu; 
   }            } 
 }          } 
     } 
 /************ Frequencies ********************/    nrerror("Too many iterations in brent"); 
 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)    *xmin=x; 
 {  /* Some frequencies */    return fx; 
    } 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   int first;  /****************** mnbrak ***********************/
   double ***freq; /* Frequencies */  
   double *pp;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double pos, k2, dateintsum=0,k2cpt=0;              double (*func)(double)) 
   FILE *ficresp;  { 
   char fileresp[FILENAMELENGTH];    double ulim,u,r,q, dum;
      double fu; 
   pp=vector(1,nlstate);   
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    *fa=(*func)(*ax); 
   strcpy(fileresp,"p");    *fb=(*func)(*bx); 
   strcat(fileresp,fileres);    if (*fb > *fa) { 
   if((ficresp=fopen(fileresp,"w"))==NULL) {      SHFT(dum,*ax,*bx,dum) 
     printf("Problem with prevalence resultfile: %s\n", fileresp);        SHFT(dum,*fb,*fa,dum) 
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);        } 
     exit(0);    *cx=(*bx)+GOLD*(*bx-*ax); 
   }    *fc=(*func)(*cx); 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    while (*fb > *fc) { /* Declining fa, fb, fc */
   j1=0;      r=(*bx-*ax)*(*fb-*fc); 
        q=(*bx-*cx)*(*fb-*fa); 
   j=cptcoveff;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
       ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
   first=1;      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
         fu=(*func)(u); 
   for(k1=1; k1<=j;k1++){  #ifdef DEBUG
     for(i1=1; i1<=ncodemax[k1];i1++){        /* f(x)=A(x-u)**2+f(u) */
       j1++;        double A, fparabu; 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         scanf("%d", i);*/        fparabu= *fa - A*(*ax-u)*(*ax-u);
       for (i=-1; i<=nlstate+ndeath; i++)          printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
         for (jk=-1; jk<=nlstate+ndeath; jk++)          fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
           for(m=agemin; m <= agemax+3; m++)  #endif 
             freq[i][jk][m]=0;      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
              fu=(*func)(u); 
       dateintsum=0;        if (fu < *fc) { 
       k2cpt=0;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for (i=1; i<=imx; i++) {            SHFT(*fb,*fc,fu,(*func)(u)) 
         bool=1;            } 
         if  (cptcovn>0) {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
           for (z1=1; z1<=cptcoveff; z1++)        u=ulim; 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        fu=(*func)(u); 
               bool=0;      } else { 
         }        u=(*cx)+GOLD*(*cx-*bx); 
         if (bool==1) {        fu=(*func)(u); 
           for(m=firstpass; m<=lastpass; m++){      } 
             k2=anint[m][i]+(mint[m][i]/12.);      SHFT(*ax,*bx,*cx,u) 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        SHFT(*fa,*fb,*fc,fu) 
               if(agev[m][i]==0) agev[m][i]=agemax+1;        } 
               if(agev[m][i]==1) agev[m][i]=agemax+2;  } 
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /*************** linmin ************************/
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
               }  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
                and replaces xi by the actual vector displacement that p was moved. Also returns as fret
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  the value of func at the returned location p . This is actually all accomplished by calling the
                 dateintsum=dateintsum+k2;  routines mnbrak and brent .*/
                 k2cpt++;  int ncom; 
               }  double *pcom,*xicom;
             }  double (*nrfunc)(double []); 
           }   
         }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       }  { 
            double brent(double ax, double bx, double cx, 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
       if  (cptcovn>0) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         fprintf(ficresp, "\n#********** Variable ");                double *fc, double (*func)(double)); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    int j; 
         fprintf(ficresp, "**********\n#");    double xx,xmin,bx,ax; 
       }    double fx,fb,fa;
       for(i=1; i<=nlstate;i++)   
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    ncom=n; 
       fprintf(ficresp, "\n");    pcom=vector(1,n); 
          xicom=vector(1,n); 
       for(i=(int)agemin; i <= (int)agemax+3; i++){    nrfunc=func; 
         if(i==(int)agemax+3){    for (j=1;j<=n;j++) { 
           fprintf(ficlog,"Total");      pcom[j]=p[j]; 
         }else{      xicom[j]=xi[j]; 
           if(first==1){    } 
             first=0;    ax=0.0; 
             printf("See log file for details...\n");    xx=1.0; 
           }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
           fprintf(ficlog,"Age %d", i);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
         }  #ifdef DEBUG
         for(jk=1; jk <=nlstate ; jk++){    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
             pp[jk] += freq[jk][m][i];  #endif
         }    for (j=1;j<=n;j++) { 
         for(jk=1; jk <=nlstate ; jk++){      xi[j] *= xmin; 
           for(m=-1, pos=0; m <=0 ; m++)      p[j] += xi[j]; 
             pos += freq[jk][m][i];    } 
           if(pp[jk]>=1.e-10){    free_vector(xicom,1,n); 
             if(first==1){    free_vector(pcom,1,n); 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  } 
             }  
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
           }else{  /*************** powell ************************/
             if(first==1)  /*
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  Minimization of a function func of n variables. Input consists of an initial starting point
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
           }  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
         }  such that failure to decrease by more than this amount on one iteration signals doneness. On
   output, p is set to the best point found, xi is the then-current direction set, fret is the returned
         for(jk=1; jk <=nlstate ; jk++){  function value at p , and iter is the number of iterations taken. The routine linmin is used.
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)   */
             pp[jk] += freq[jk][m][i];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         }              double (*func)(double [])) 
   { 
         for(jk=1,pos=0; jk <=nlstate ; jk++)    void linmin(double p[], double xi[], int n, double *fret, 
           pos += pp[jk];                double (*func)(double [])); 
         for(jk=1; jk <=nlstate ; jk++){    int i,ibig,j; 
           if(pos>=1.e-5){    double del,t,*pt,*ptt,*xit;
             if(first==1)    double fp,fptt;
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    double *xits;
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    int niterf, itmp;
           }else{  
             if(first==1)    pt=vector(1,n); 
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    ptt=vector(1,n); 
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    xit=vector(1,n); 
           }    xits=vector(1,n); 
           if( i <= (int) agemax){    *fret=(*func)(p); 
             if(pos>=1.e-5){    for (j=1;j<=n;j++) pt[j]=p[j]; 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      rcurr_time = time(NULL);  
               probs[i][jk][j1]= pp[jk]/pos;    for (*iter=1;;++(*iter)) { 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      fp=(*fret); 
             }      ibig=0; 
             else      del=0.0; 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      rlast_time=rcurr_time;
           }      /* (void) gettimeofday(&curr_time,&tzp); */
         }      rcurr_time = time(NULL);  
              curr_time = *localtime(&rcurr_time);
         for(jk=-1; jk <=nlstate+ndeath; jk++)      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
           for(m=-1; m <=nlstate+ndeath; m++)      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
             if(freq[jk][m][i] !=0 ) {  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
             if(first==1)     for (i=1;i<=n;i++) {
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        printf(" %d %.12f",i, p[i]);
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);        fprintf(ficlog," %d %.12lf",i, p[i]);
             }        fprintf(ficrespow," %.12lf", p[i]);
         if(i <= (int) agemax)      }
           fprintf(ficresp,"\n");      printf("\n");
         if(first==1)      fprintf(ficlog,"\n");
           printf("Others in log...\n");      fprintf(ficrespow,"\n");fflush(ficrespow);
         fprintf(ficlog,"\n");      if(*iter <=3){
       }        tml = *localtime(&rcurr_time);
     }        strcpy(strcurr,asctime(&tml));
   }        rforecast_time=rcurr_time; 
   dateintmean=dateintsum/k2cpt;        itmp = strlen(strcurr);
          if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   fclose(ficresp);          strcurr[itmp-1]='\0';
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   free_vector(pp,1,nlstate);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
          for(niterf=10;niterf<=30;niterf+=10){
   /* End of Freq */          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
 }          forecast_time = *localtime(&rforecast_time);
           strcpy(strfor,asctime(&forecast_time));
 /************ Prevalence ********************/          itmp = strlen(strfor);
 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)          if(strfor[itmp-1]=='\n')
 {  /* Some frequencies */          strfor[itmp-1]='\0';
            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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
   double ***freq; /* Frequencies */        }
   double *pp;      }
   double pos, k2;      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   pp=vector(1,nlstate);        fptt=(*fret); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  #ifdef DEBUG
              printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   j1=0;  #endif
          printf("%d",i);fflush(stdout);
   j=cptcoveff;        fprintf(ficlog,"%d",i);fflush(ficlog);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        linmin(p,xit,n,fret,func); 
          if (fabs(fptt-(*fret)) > del) { 
   for(k1=1; k1<=j;k1++){          del=fabs(fptt-(*fret)); 
     for(i1=1; i1<=ncodemax[k1];i1++){          ibig=i; 
       j1++;        } 
        #ifdef DEBUG
       for (i=-1; i<=nlstate+ndeath; i++)          printf("%d %.12e",i,(*fret));
         for (jk=-1; jk<=nlstate+ndeath; jk++)          fprintf(ficlog,"%d %.12e",i,(*fret));
           for(m=agemin; m <= agemax+3; m++)        for (j=1;j<=n;j++) {
             freq[i][jk][m]=0;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
                printf(" x(%d)=%.12e",j,xit[j]);
       for (i=1; i<=imx; i++) {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         bool=1;        }
         if  (cptcovn>0) {        for(j=1;j<=n;j++) {
           for (z1=1; z1<=cptcoveff; z1++)          printf(" p(%d)=%.12e",j,p[j]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
               bool=0;        }
         }        printf("\n");
         if (bool==1) {        fprintf(ficlog,"\n");
           for(m=firstpass; m<=lastpass; m++){  #endif
             k2=anint[m][i]+(mint[m][i]/12.);      } /* end i */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
               if(agev[m][i]==0) agev[m][i]=agemax+1;  #ifdef DEBUG
               if(agev[m][i]==1) agev[m][i]=agemax+2;        int k[2],l;
               if (m<lastpass) {        k[0]=1;
                 if (calagedate>0)        k[1]=-1;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        printf("Max: %.12e",(*func)(p));
                 else        fprintf(ficlog,"Max: %.12e",(*func)(p));
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for (j=1;j<=n;j++) {
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          printf(" %.12e",p[j]);
               }          fprintf(ficlog," %.12e",p[j]);
             }        }
           }        printf("\n");
         }        fprintf(ficlog,"\n");
       }        for(l=0;l<=1;l++) {
       for(i=(int)agemin; i <= (int)agemax+3; i++){          for (j=1;j<=n;j++) {
         for(jk=1; jk <=nlstate ; jk++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             pp[jk] += freq[jk][m][i];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         }          }
         for(jk=1; jk <=nlstate ; jk++){          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           for(m=-1, pos=0; m <=0 ; m++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
             pos += freq[jk][m][i];        }
         }  #endif
          
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        free_vector(xit,1,n); 
             pp[jk] += freq[jk][m][i];        free_vector(xits,1,n); 
         }        free_vector(ptt,1,n); 
                free_vector(pt,1,n); 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        return; 
              } 
         for(jk=1; jk <=nlstate ; jk++){          if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
           if( i <= (int) agemax){      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
             if(pos>=1.e-5){        ptt[j]=2.0*p[j]-pt[j]; 
               probs[i][jk][j1]= pp[jk]/pos;        xit[j]=p[j]-pt[j]; 
             }        pt[j]=p[j]; 
           }      } 
         }/* end jk */      fptt=(*func)(ptt); 
       }/* end i */      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
     } /* end i1 */        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
   } /* end k1 */        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
         /* Let f"(x2) be the 2nd derivative equal everywhere.  */
          /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
   free_vector(pp,1,nlstate);        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
          /* Thus we compare delta(2h) with observed f1-f3 */
 }  /* End of Freq */        /* or best gain on one ancient line 'del' with total  */
         /* gain f1-f2 = f1 - f2 - 'del' with del  */
 /************* Waves Concatenation ***************/        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
 {        t= t- del*SQR(fp-fptt);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
      Death is a valid wave (if date is known).        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  #ifdef DEBUG
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
      and mw[mi+1][i]. dh depends on stepm.               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
      */        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   int i, mi, m;        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
      double sum=0., jmean=0.;*/  #endif
   int first;        if (t < 0.0) { /* Then we use it for last direction */
   int j, k=0,jk, ju, jl;          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
   double sum=0.;          for (j=1;j<=n;j++) { 
   first=0;            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
   jmin=1e+5;            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
   jmax=-1;          }
   jmean=0.;          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   for(i=1; i<=imx; i++){          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
     mi=0;  
     m=firstpass;  #ifdef DEBUG
     while(s[m][i] <= nlstate){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       if(s[m][i]>=1)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         mw[++mi][i]=m;          for(j=1;j<=n;j++){
       if(m >=lastpass)            printf(" %.12e",xit[j]);
         break;            fprintf(ficlog," %.12e",xit[j]);
       else          }
         m++;          printf("\n");
     }/* end while */          fprintf(ficlog,"\n");
     if (s[m][i] > nlstate){  #endif
       mi++;     /* Death is another wave */        } /* end of t negative */
       /* if(mi==0)  never been interviewed correctly before death */      } /* end if (fptt < fp)  */
          /* Only death is a correct wave */    } 
       mw[mi][i]=m;  } 
     }  
   /**** Prevalence limit (stable or period prevalence)  ****************/
     wav[i]=mi;  
     if(mi==0){  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       if(first==0){  {
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         first=1;       matrix by transitions matrix until convergence is reached */
       }  
       if(first==1){    int i, ii,j,k;
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);    double min, max, maxmin, maxmax,sumnew=0.;
       }    /* double **matprod2(); */ /* test */
     } /* end mi==0 */    double **out, cov[NCOVMAX+1], **pmij();
   }    double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){    for (ii=1;ii<=nlstate+ndeath;ii++)
       if (stepm <=0)      for (j=1;j<=nlstate+ndeath;j++){
         dh[mi][i]=1;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       else{      }
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {     cov[1]=1.;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);   
           if(j==0) j=1;  /* Survives at least one month after exam */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           k=k+1;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
           if (j >= jmax) jmax=j;      newm=savm;
           if (j <= jmin) jmin=j;      /* Covariates have to be included here again */
           sum=sum+j;      cov[2]=agefin;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      
           }      for (k=1; k<=cptcovn;k++) {
         }        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         else{        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      }
           k=k+1;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           if (j >= jmax) jmax=j;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
           else if (j <= jmin)jmin=j;      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      
           sum=sum+j;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         }      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         jk= j/stepm;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         jl= j -jk*stepm;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         ju= j -(jk+1)*stepm;      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
         if(jl <= -ju)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           dh[mi][i]=jk;      
         else      savm=oldm;
           dh[mi][i]=jk+1;      oldm=newm;
         if(dh[mi][i]==0)      maxmax=0.;
           dh[mi][i]=1; /* At least one step */      for(j=1;j<=nlstate;j++){
       }        min=1.;
     }        max=0.;
   }        for(i=1; i<=nlstate; i++) {
   jmean=sum/k;          sumnew=0;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          prlim[i][j]= newm[i][j]/(1-sumnew);
  }          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           max=FMAX(max,prlim[i][j]);
 /*********** Tricode ****************************/          min=FMIN(min,prlim[i][j]);
 void tricode(int *Tvar, int **nbcode, int imx)        }
 {        maxmin=max-min;
   int Ndum[20],ij=1, k, j, i;        maxmax=FMAX(maxmax,maxmin);
   int cptcode=0;      }
   cptcoveff=0;      if(maxmax < ftolpl){
          return prlim;
   for (k=0; k<19; k++) Ndum[k]=0;      }
   for (k=1; k<=7; k++) ncodemax[k]=0;    }
   }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {  /*************** transition probabilities ***************/ 
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  {
       if (ij > cptcode) cptcode=ij;    /* According to parameters values stored in x and the covariate's values stored in cov,
     }       computes the probability to be observed in state j being in state i by appying the
        model to the ncovmodel covariates (including constant and age).
     for (i=0; i<=cptcode; i++) {       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
       if(Ndum[i]!=0) ncodemax[j]++;       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
     }       ncth covariate in the global vector x is given by the formula:
     ij=1;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
        j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     for (i=1; i<=ncodemax[j]; i++) {       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
       for (k=0; k<=19; k++) {       Outputs ps[i][j] the probability to be observed in j being in j according to
         if (Ndum[k] != 0) {       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
           nbcode[Tvar[j]][ij]=k;    */
              double s1, lnpijopii;
           ij++;    /*double t34;*/
         }    int i,j, nc, ii, jj;
         if (ij > ncodemax[j]) break;  
       }        for(i=1; i<= nlstate; i++){
     }        for(j=1; j<i;j++){
   }            for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += param[i][j][nc]*cov[nc];*/
  for (k=0; k<19; k++) Ndum[k]=0;            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
  for (i=1; i<=ncovmodel-2; i++) {          }
    ij=Tvar[i];          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
    Ndum[ij]++;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
  }        }
         for(j=i+1; j<=nlstate+ndeath;j++){
  ij=1;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
  for (i=1; i<=10; i++) {            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
    if((Ndum[i]!=0) && (i<=ncovcol)){            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
      Tvaraff[ij]=i;  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
      ij++;          }
    }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
  }        }
        }
  cptcoveff=ij-1;      
 }      for(i=1; i<= nlstate; i++){
         s1=0;
 /*********** Health Expectancies ****************/        for(j=1; j<i; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
 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 )          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
 {        for(j=i+1; j<=nlstate+ndeath; j++){
   /* Health expectancies */          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   double age, agelim, hf;        }
   double ***p3mat,***varhe;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   double **dnewm,**doldm;        ps[i][i]=1./(s1+1.);
   double *xp;        /* Computing other pijs */
   double **gp, **gm;        for(j=1; j<i; j++)
   double ***gradg, ***trgradg;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   int theta;        for(j=i+1; j<=nlstate+ndeath; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   xp=vector(1,npar);      } /* end i */
   dnewm=matrix(1,nlstate*2,1,npar);      
   doldm=matrix(1,nlstate*2,1,nlstate*2);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
          for(jj=1; jj<= nlstate+ndeath; jj++){
   fprintf(ficreseij,"# Health expectancies\n");          ps[ii][jj]=0;
   fprintf(ficreseij,"# Age");          ps[ii][ii]=1;
   for(i=1; i<=nlstate;i++)        }
     for(j=1; j<=nlstate;j++)      }
       fprintf(ficreseij," %1d-%1d (SE)",i,j);      
   fprintf(ficreseij,"\n");      
       /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   if(estepm < stepm){      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     printf ("Problem %d lower than %d\n",estepm, stepm);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   }      /*   } */
   else  hstepm=estepm;        /*   printf("\n "); */
   /* We compute the life expectancy from trapezoids spaced every estepm months      /* } */
    * This is mainly to measure the difference between two models: for example      /* printf("\n ");printf("%lf ",cov[2]);*/
    * if stepm=24 months pijx are given only every 2 years and by summing them      /*
    * we are calculating an estimate of the Life Expectancy assuming a linear        for(i=1; i<= npar; i++) printf("%f ",x[i]);
    * progression inbetween and thus overestimating or underestimating according        goto end;*/
    * to the curvature of the survival function. If, for the same date, we      return ps;
    * 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  /**************** Product of 2 matrices ******************/
    * curvature will be obtained if estepm is as small as stepm. */  
   double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   /* For example we decided to compute the life expectancy with the smallest unit */  {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
      nhstepm is the number of hstepm from age to agelim       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      nstepm is the number of stepm from age to agelin.    /* in, b, out are matrice of pointers which should have been initialized 
      Look at hpijx to understand the reason of that which relies in memory size       before: only the contents of out is modified. The function returns
      and note for a fixed period like estepm months */       a pointer to pointers identical to out */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    int i, j, k;
      survival function given by stepm (the optimization length). Unfortunately it    for(i=nrl; i<= nrh; i++)
      means that if the survival funtion is printed only each two years of age and if      for(k=ncolol; k<=ncoloh; k++){
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        out[i][k]=0.;
      results. So we changed our mind and took the option of the best precision.        for(j=ncl; j<=nch; j++)
   */          out[i][k] +=in[i][j]*b[j][k];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      }
     return out;
   agelim=AGESUP;  }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     /* nhstepm age range expressed in number of stepm */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  /************* Higher Matrix Product ***************/
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  
     /* if (stepm >= YEARM) hstepm=1;*/  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* Computes the transition matrix starting at age 'age' over 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);       'nhstepm*hstepm*stepm' months (i.e. until
     gp=matrix(0,nhstepm,1,nlstate*2);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     gm=matrix(0,nhstepm,1,nlstate*2);       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored       (typically every 2 years instead of every month which is too big 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */       for the memory).
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);         Model is determined by parameters x and covariates have to be 
         included manually here. 
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */       */
   
     /* Computing Variances of health expectancies */    int i, j, d, h, k;
     double **out, cov[NCOVMAX+1];
      for(theta=1; theta <=npar; theta++){    double **newm;
       for(i=1; i<=npar; i++){  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /* Hstepm could be zero and should return the unit matrix */
       }    for (i=1;i<=nlstate+ndeath;i++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (j=1;j<=nlstate+ndeath;j++){
          oldm[i][j]=(i==j ? 1.0 : 0.0);
       cptj=0;        po[i][j][0]=(i==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++){      }
         for(i=1; i<=nlstate; i++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           cptj=cptj+1;    for(h=1; h <=nhstepm; h++){
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      for(d=1; d <=hstepm; d++){
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        newm=savm;
           }        /* Covariates have to be included here again */
         }        cov[1]=1.;
       }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
              for (k=1; k<=cptcovn;k++) 
                cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for(i=1; i<=npar; i++)        for (k=1; k<=cptcovage;k++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
                cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       cptj=0;  
       for(j=1; j<= nlstate; j++){  
         for(i=1;i<=nlstate;i++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
           cptj=cptj+1;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
           }        savm=oldm;
         }        oldm=newm;
       }      }
       for(j=1; j<= nlstate*2; j++)      for(i=1; i<=nlstate+ndeath; i++)
         for(h=0; h<=nhstepm-1; h++){        for(j=1;j<=nlstate+ndeath;j++) {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          po[i][j][h]=newm[i][j];
         }          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
      }        }
          /*printf("h=%d ",h);*/
 /* End theta */    } /* end h */
   /*     printf("\n H=%d \n",h); */
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    return po;
   }
      for(h=0; h<=nhstepm-1; h++)  
       for(j=1; j<=nlstate*2;j++)  #ifdef NLOPT
         for(theta=1; theta <=npar; theta++)    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
           trgradg[h][j][theta]=gradg[h][theta][j];    double fret;
          double *xt;
     int j;
      for(i=1;i<=nlstate*2;i++)    myfunc_data *d2 = (myfunc_data *) pd;
       for(j=1;j<=nlstate*2;j++)  /* xt = (p1-1); */
         varhe[i][j][(int)age] =0.;    xt=vector(1,n); 
     for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
      printf("%d|",(int)age);fflush(stdout);  
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
      for(h=0;h<=nhstepm-1;h++){    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
       for(k=0;k<=nhstepm-1;k++){    printf("Function = %.12lf ",fret);
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    printf("\n");
         for(i=1;i<=nlstate*2;i++)   free_vector(xt,1,n);
           for(j=1;j<=nlstate*2;j++)    return fret;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  }
       }  #endif
     }  
     /* Computing expectancies */  /*************** log-likelihood *************/
     for(i=1; i<=nlstate;i++)  double func( double *x)
       for(j=1; j<=nlstate;j++)  {
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    int i, ii, j, k, mi, d, kk;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
              double **out;
 /* 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]);*/    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
         }    int s1, s2;
     double bbh, survp;
     fprintf(ficreseij,"%3.0f",age );    long ipmx;
     cptj=0;    /*extern weight */
     for(i=1; i<=nlstate;i++)    /* We are differentiating ll according to initial status */
       for(j=1; j<=nlstate;j++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         cptj++;    /*for(i=1;i<imx;i++) 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      printf(" %d\n",s[4][i]);
       }    */
     fprintf(ficreseij,"\n");  
        ++countcallfunc;
     free_matrix(gm,0,nhstepm,1,nlstate*2);  
     free_matrix(gp,0,nhstepm,1,nlstate*2);    cov[1]=1.;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    for(k=1; k<=nlstate; k++) ll[k]=0.;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }    if(mle==1){
   printf("\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficlog,"\n");        /* Computes the values of the ncovmodel covariates of the model
            depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   free_vector(xp,1,npar);           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   free_matrix(dnewm,1,nlstate*2,1,npar);           to be observed in j being in i according to the model.
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);         */
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
 }          cov[2+k]=covar[Tvar[k]][i];
         }
 /************ Variance ******************/        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
 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)           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
 {           has been calculated etc */
   /* Variance of health expectancies */        for(mi=1; mi<= wav[i]-1; mi++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for (ii=1;ii<=nlstate+ndeath;ii++)
   /* double **newm;*/            for (j=1;j<=nlstate+ndeath;j++){
   double **dnewm,**doldm;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **dnewmp,**doldmp;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j, nhstepm, hstepm, h, nstepm ;            }
   int k, cptcode;          for(d=0; d<dh[mi][i]; d++){
   double *xp;            newm=savm;
   double **gp, **gm;  /* for var eij */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***gradg, ***trgradg; /*for var eij */            for (kk=1; kk<=cptcovage;kk++) {
   double **gradgp, **trgradgp; /* for var p point j */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
   double *gpp, *gmp; /* for var p point j */            }
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***p3mat;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double age,agelim, hf;            savm=oldm;
   int theta;            oldm=newm;
   char digit[4];          } /* end mult */
   char digitp[16];        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   char fileresprobmorprev[FILENAMELENGTH];          /* But now since version 0.9 we anticipate for bias at large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
   if(popbased==1)           * (in months) between two waves is not a multiple of stepm, we rounded to 
     strcpy(digitp,"-populbased-");           * 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
     strcpy(digitp,"-stablbased-");           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
   strcpy(fileresprobmorprev,"prmorprev");           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   sprintf(digit,"%-d",ij);           * -stepm/2 to stepm/2 .
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/           * For stepm=1 the results are the same as for previous versions of Imach.
   strcat(fileresprobmorprev,digit); /* Tvar to be done */           * For stepm > 1 the results are less biased than in previous versions. 
   strcat(fileresprobmorprev,digitp); /* Popbased or not */           */
   strcat(fileresprobmorprev,fileres);          s1=s[mw[mi][i]][i];
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {          s2=s[mw[mi+1][i]][i];
     printf("Problem with resultfile: %s\n", fileresprobmorprev);          bbh=(double)bh[mi][i]/(double)stepm; 
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);          /* bias bh is positive if real duration
   }           * is higher than the multiple of stepm and negative otherwise.
   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);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");          if( s2 > nlstate){ 
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);            /* i.e. if s2 is a death state and if the date of death is known 
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){               then the contribution to the likelihood is the probability to 
     fprintf(ficresprobmorprev," p.%-d SE",j);               die between last step unit time and current  step unit time, 
     for(i=1; i<=nlstate;i++)               which is also equal to probability to die before dh 
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);               minus probability to die before dh-stepm . 
   }                 In version up to 0.92 likelihood was computed
   fprintf(ficresprobmorprev,"\n");          as if date of death was unknown. Death was treated as any other
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          health state: the date of the interview describes the actual state
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          and not the date of a change in health state. The former idea was
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);          to consider that at each interview the state was recorded
     exit(0);          (healthy, disable or death) and IMaCh was corrected; but when we
   }          introduced the exact date of death then we should have modified
   else{          the contribution of an exact death to the likelihood. This new
     fprintf(ficgp,"\n# Routine varevsij");          contribution is smaller and very dependent of the step unit
   }          stepm. It is no more the probability to die between last interview
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {          and month of death but the probability to survive from last
     printf("Problem with html file: %s\n", optionfilehtm);          interview up to one month before death multiplied by the
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);          probability to die within a month. Thanks to Chris
     exit(0);          Jackson for correcting this bug.  Former versions increased
   }          mortality artificially. The bad side is that we add another loop
   else{          which slows down the processing. The difference can be up to 10%
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");          lower mortality.
   }            */
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            lli=log(out[s1][s2] - savm[s1][s2]);
   
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");  
   fprintf(ficresvij,"# Age");          } else if  (s2==-2) {
   for(i=1; i<=nlstate;i++)            for (j=1,survp=0. ; j<=nlstate; j++) 
     for(j=1; j<=nlstate;j++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            /*survp += out[s1][j]; */
   fprintf(ficresvij,"\n");            lli= log(survp);
           }
   xp=vector(1,npar);          
   dnewm=matrix(1,nlstate,1,npar);          else if  (s2==-4) { 
   doldm=matrix(1,nlstate,1,nlstate);            for (j=3,survp=0. ; j<=nlstate; j++)  
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            lli= log(survp); 
           } 
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);  
   gpp=vector(nlstate+1,nlstate+ndeath);          else if  (s2==-5) { 
   gmp=vector(nlstate+1,nlstate+ndeath);            for (j=1,survp=0. ; j<=2; j++)  
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
              lli= log(survp); 
   if(estepm < stepm){          } 
     printf ("Problem %d lower than %d\n",estepm, stepm);          
   }          else{
   else  hstepm=estepm;              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   /* For example we decided to compute the life expectancy with the smallest unit */            /*  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 */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          } 
      nhstepm is the number of hstepm from age to agelim          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
      nstepm is the number of stepm from age to agelin.          /*if(lli ==000.0)*/
      Look at hpijx to understand the reason of that which relies in memory size          /*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); */
      and note for a fixed period like k years */          ipmx +=1;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          sw += weight[i];
      survival function given by stepm (the optimization length). Unfortunately it          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      means that if the survival funtion is printed only each two years of age and if        } /* end of wave */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      } /* end of individual */
      results. So we changed our mind and took the option of the best precision.    }  else if(mle==2){
   */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   agelim = AGESUP;        for(mi=1; mi<= wav[i]-1; mi++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for (ii=1;ii<=nlstate+ndeath;ii++)
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            for (j=1;j<=nlstate+ndeath;j++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            }
     gp=matrix(0,nhstepm,1,nlstate);          for(d=0; d<=dh[mi][i]; d++){
     gm=matrix(0,nhstepm,1,nlstate);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for(theta=1; theta <=npar; theta++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(i=1; i<=npar; i++){ /* Computes gradient */            }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              savm=oldm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            oldm=newm;
           } /* end mult */
       if (popbased==1) {        
         for(i=1; i<=nlstate;i++)          s1=s[mw[mi][i]][i];
           prlim[i][i]=probs[(int)age][i][ij];          s2=s[mw[mi+1][i]][i];
       }          bbh=(double)bh[mi][i]/(double)stepm; 
            lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       for(j=1; j<= nlstate; j++){          ipmx +=1;
         for(h=0; h<=nhstepm; h++){          sw += weight[i];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        } /* end of wave */
         }      } /* end of individual */
       }    }  else if(mle==3){  /* exponential inter-extrapolation */
       /* This for computing forces of mortality (h=1)as a weighted average */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(i=1; i<= nlstate; i++)        for(mi=1; mi<= wav[i]-1; mi++){
           gpp[j] += prlim[i][i]*p3mat[i][j][1];          for (ii=1;ii<=nlstate+ndeath;ii++)
       }                for (j=1;j<=nlstate+ndeath;j++){
       /* end force of mortality */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++) /* Computes gradient */            }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for(d=0; d<dh[mi][i]; d++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              newm=savm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
       if (popbased==1) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(i=1; i<=nlstate;i++)            }
           prlim[i][i]=probs[(int)age][i][ij];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
       for(j=1; j<= nlstate; j++){            oldm=newm;
         for(h=0; h<=nhstepm; h++){          } /* end mult */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
       }          bbh=(double)bh[mi][i]/(double)stepm; 
       /* This for computing force of mortality (h=1)as a weighted average */          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 */
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){          ipmx +=1;
         for(i=1; i<= nlstate; i++)          sw += weight[i];
           gmp[j] += prlim[i][i]*p3mat[i][j][1];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }            } /* end of wave */
       /* end force of mortality */      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for(j=1; j<= nlstate; j++) /* vareij */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(h=0; h<=nhstepm; h++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */            for (j=1;j<=nlstate+ndeath;j++){
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     } /* End theta */          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for(h=0; h<=nhstepm; h++) /* veij */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<=nlstate;j++)            }
         for(theta=1; theta <=npar; theta++)          
           trgradg[h][j][theta]=gradg[h][theta][j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */            savm=oldm;
       for(theta=1; theta <=npar; theta++)            oldm=newm;
         trgradgp[j][theta]=gradgp[theta][j];          } /* end mult */
         
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          s1=s[mw[mi][i]][i];
     for(i=1;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       for(j=1;j<=nlstate;j++)          if( s2 > nlstate){ 
         vareij[i][j][(int)age] =0.;            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
     for(h=0;h<=nhstepm;h++){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for(k=0;k<=nhstepm;k++){          }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          ipmx +=1;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          sw += weight[i];
         for(i=1;i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(j=1;j<=nlstate;j++)  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        } /* 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++){
     /* pptj */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);        for(mi=1; mi<= wav[i]-1; mi++){
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(j=nlstate+1;j<=nlstate+ndeath;j++)            for (j=1;j<=nlstate+ndeath;j++){
       for(i=nlstate+1;i<=nlstate+ndeath;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         varppt[j][i]=doldmp[j][i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* end ppptj */            }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);            for(d=0; d<dh[mi][i]; d++){
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (popbased==1) {            for (kk=1; kk<=cptcovage;kk++) {
       for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         prlim[i][i]=probs[(int)age][i][ij];            }
     }          
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     /* This for computing force of mortality (h=1)as a weighted average */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){            savm=oldm;
       for(i=1; i<= nlstate; i++)            oldm=newm;
         gmp[j] += prlim[i][i]*p3mat[i][j][1];          } /* end mult */
     }            
     /* end force of mortality */          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){          ipmx +=1;
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));          sw += weight[i];
       for(i=1; i<=nlstate;i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);          /*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 */
     fprintf(ficresprobmorprev,"\n");    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     fprintf(ficresvij,"%.0f ",age );    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for(i=1; i<=nlstate;i++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       for(j=1; j<=nlstate;j++){    return -l;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  }
       }  
     fprintf(ficresvij,"\n");  /*************** log-likelihood *************/
     free_matrix(gp,0,nhstepm,1,nlstate);  double funcone( double *x)
     free_matrix(gm,0,nhstepm,1,nlstate);  {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    /* Same as likeli but slower because of a lot of printf and if */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    int i, ii, j, k, mi, d, kk;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   } /* End age */    double **out;
   free_vector(gpp,nlstate+1,nlstate+ndeath);    double lli; /* Individual log likelihood */
   free_vector(gmp,nlstate+1,nlstate+ndeath);    double llt;
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);    int s1, s2;
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    double bbh, survp;
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");    /*extern weight */
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    /* We are differentiating ll according to initial status */
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);    /*for(i=1;i<imx;i++) 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);      printf(" %d\n",s[4][i]);
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);    */
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);    cov[1]=1.;
   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);  
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   free_vector(xp,1,npar);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_matrix(doldm,1,nlstate,1,nlstate);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_matrix(dnewm,1,nlstate,1,npar);      for(mi=1; mi<= wav[i]-1; mi++){
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        for (ii=1;ii<=nlstate+ndeath;ii++)
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);          for (j=1;j<=nlstate+ndeath;j++){
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fclose(ficresprobmorprev);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fclose(ficgp);          }
   fclose(fichtm);        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
 }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
 /************ Variance of prevlim ******************/            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 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)          }
 {          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   /* Variance of prevalence limit */          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double **newm;          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
   double **dnewm,**doldm;          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
   int i, j, nhstepm, hstepm;          savm=oldm;
   int k, cptcode;          oldm=newm;
   double *xp;        } /* end mult */
   double *gp, *gm;        
   double **gradg, **trgradg;        s1=s[mw[mi][i]][i];
   double age,agelim;        s2=s[mw[mi+1][i]][i];
   int theta;        bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias is positive if real duration
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");         * is higher than the multiple of stepm and negative otherwise.
   fprintf(ficresvpl,"# Age");         */
   for(i=1; i<=nlstate;i++)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       fprintf(ficresvpl," %1d-%1d",i,i);          lli=log(out[s1][s2] - savm[s1][s2]);
   fprintf(ficresvpl,"\n");        } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++) 
   xp=vector(1,npar);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   dnewm=matrix(1,nlstate,1,npar);          lli= log(survp);
   doldm=matrix(1,nlstate,1,nlstate);        }else if (mle==1){
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   hstepm=1*YEARM; /* Every year of age */        } else if(mle==2){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          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 */
   agelim = AGESUP;        } else if(mle==3){  /* exponential inter-extrapolation */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          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 */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     if (stepm >= YEARM) hstepm=1;          lli=log(out[s1][s2]); /* Original formula */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        } else{  /* mle=0 back to 1 */
     gradg=matrix(1,npar,1,nlstate);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     gp=vector(1,nlstate);          /*lli=log(out[s1][s2]); */ /* Original formula */
     gm=vector(1,nlstate);        } /* End of if */
         ipmx +=1;
     for(theta=1; theta <=npar; theta++){        sw += weight[i];
       for(i=1; i<=npar; i++){ /* Computes gradient */        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       }        if(globpr){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       for(i=1;i<=nlstate;i++)   %11.6f %11.6f %11.6f ", \
         gp[i] = prlim[i][i];                  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(i=1; i<=npar; i++) /* Computes gradient */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            llt +=ll[k]*gipmx/gsw;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       for(i=1;i<=nlstate;i++)          }
         gm[i] = prlim[i][i];          fprintf(ficresilk," %10.6f\n", -llt);
         }
       for(i=1;i<=nlstate;i++)      } /* end of wave */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    } /* end of individual */
     } /* End theta */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     trgradg =matrix(1,nlstate,1,npar);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
     for(j=1; j<=nlstate;j++)      gipmx=ipmx;
       for(theta=1; theta <=npar; theta++)      gsw=sw;
         trgradg[j][theta]=gradg[theta][j];    }
     return -l;
     for(i=1;i<=nlstate;i++)  }
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  /*************** function likelione ***********/
     for(i=1;i<=nlstate;i++)  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  {
     /* This routine should help understanding what is done with 
     fprintf(ficresvpl,"%.0f ",age );       the selection of individuals/waves and
     for(i=1; i<=nlstate;i++)       to check the exact contribution to the likelihood.
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));       Plotting could be done.
     fprintf(ficresvpl,"\n");     */
     free_vector(gp,1,nlstate);    int k;
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);    if(*globpri !=0){ /* Just counts and sums, no printings */
     free_matrix(trgradg,1,nlstate,1,npar);      strcpy(fileresilk,"ilk"); 
   } /* End age */      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   free_vector(xp,1,npar);        printf("Problem with resultfile: %s\n", fileresilk);
   free_matrix(doldm,1,nlstate,1,npar);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   free_matrix(dnewm,1,nlstate,1,nlstate);      }
       fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
 }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
 /************ Variance of one-step probabilities  ******************/      for(k=1; k<=nlstate; 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)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 {      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   int i, j=0,  i1, k1, l1, t, tj;    }
   int k2, l2, j1,  z1;  
   int k=0,l, cptcode;    *fretone=(*funcone)(p);
   int first=1, first1;    if(*globpri !=0){
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;      fclose(ficresilk);
   double **dnewm,**doldm;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   double *xp;      fflush(fichtm); 
   double *gp, *gm;    } 
   double **gradg, **trgradg;    return;
   double **mu;  }
   double age,agelim, cov[NCOVMAX];  
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */  
   int theta;  /*********** Maximum Likelihood Estimation ***************/
   char fileresprob[FILENAMELENGTH];  
   char fileresprobcov[FILENAMELENGTH];  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   char fileresprobcor[FILENAMELENGTH];  {
     int i,j, iter=0;
   double ***varpij;    double **xi;
     double fret;
   strcpy(fileresprob,"prob");    double fretone; /* Only one call to likelihood */
   strcat(fileresprob,fileres);    /*  char filerespow[FILENAMELENGTH];*/
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);  #ifdef NLOPT
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);    int creturn;
   }    nlopt_opt opt;
   strcpy(fileresprobcov,"probcov");    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
   strcat(fileresprobcov,fileres);    double *lb;
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    double minf; /* the minimum objective value, upon return */
     printf("Problem with resultfile: %s\n", fileresprobcov);    double * p1; /* Shifted parameters from 0 instead of 1 */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    myfunc_data dinst, *d = &dinst;
   }  #endif
   strcpy(fileresprobcor,"probcor");  
   strcat(fileresprobcor,fileres);  
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    xi=matrix(1,npar,1,npar);
     printf("Problem with resultfile: %s\n", fileresprobcor);    for (i=1;i<=npar;i++)
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);      for (j=1;j<=npar;j++)
   }        xi[i][j]=(i==j ? 1.0 : 0.0);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    strcpy(filerespow,"pow"); 
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    strcat(filerespow,fileres);
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);      printf("Problem with resultfile: %s\n", filerespow);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      }
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   fprintf(ficresprob,"# Age");    for (i=1;i<=nlstate;i++)
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");      for(j=1;j<=nlstate+ndeath;j++)
   fprintf(ficresprobcov,"# Age");        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    fprintf(ficrespow,"\n");
   fprintf(ficresprobcov,"# Age");  #ifdef POWELL
     powell(p,xi,npar,ftol,&iter,&fret,func);
   #endif
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=(nlstate+ndeath);j++){  #ifdef NLOPT
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  #ifdef NEWUOA
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  #else
     }      opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   fprintf(ficresprob,"\n");  #endif
   fprintf(ficresprobcov,"\n");    lb=vector(0,npar-1);
   fprintf(ficresprobcor,"\n");    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
   xp=vector(1,npar);    nlopt_set_lower_bounds(opt, lb);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    nlopt_set_initial_step1(opt, 0.1);
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    d->function = func;
   first=1;    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    nlopt_set_min_objective(opt, myfunc, d);
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    nlopt_set_xtol_rel(opt, ftol);
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
     exit(0);      printf("nlopt failed! %d\n",creturn); 
   }    }
   else{    else {
     fprintf(ficgp,"\n# Routine varprob");      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
   }      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {      iter=1; /* not equal */
     printf("Problem with html file: %s\n", optionfilehtm);    }
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    nlopt_destroy(opt);
     exit(0);  #endif
   }    free_matrix(xi,1,npar,1,npar);
   else{    fclose(ficrespow);
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fprintf(fichtm,"\n");    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     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");  
   /**** 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;
   cov[1]=1;    double **hess;
   tj=cptcoveff;    int i, j;
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    int *indx;
   j1=0;  
   for(t=1; t<=tj;t++){    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     for(i1=1; i1<=ncodemax[t];i1++){    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       j1++;    void lubksb(double **a, int npar, int *indx, double b[]) ;
          void ludcmp(double **a, int npar, int *indx, double *d) ;
       if  (cptcovn>0) {    double gompertz(double p[]);
         fprintf(ficresprob, "\n#********** Variable ");    hess=matrix(1,npar,1,npar);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresprob, "**********\n#");    printf("\nCalculation of the hessian matrix. Wait...\n");
         fprintf(ficresprobcov, "\n#********** Variable ");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (i=1;i<=npar;i++){
         fprintf(ficresprobcov, "**********\n#");      printf("%d",i);fflush(stdout);
              fprintf(ficlog,"%d",i);fflush(ficlog);
         fprintf(ficgp, "\n#********** Variable ");     
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         fprintf(ficgp, "**********\n#");      
              /*  printf(" %f ",p[i]);
                  printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");    }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");    for (i=1;i<=npar;i++) {
              for (j=1;j<=npar;j++)  {
         fprintf(ficresprobcor, "\n#********** Variable ");            if (j>i) { 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          printf(".%d%d",i,j);fflush(stdout);
         fprintf(ficgp, "**********\n#");              fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       }          hess[i][j]=hessij(p,delti,i,j,func,npar);
                
       for (age=bage; age<=fage; age ++){          hess[j][i]=hess[i][j];    
         cov[2]=age;          /*printf(" %lf ",hess[i][j]);*/
         for (k=1; k<=cptcovn;k++) {        }
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];      }
         }    }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    printf("\n");
         for (k=1; k<=cptcovprod;k++)    fprintf(ficlog,"\n");
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
            printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    
         gp=vector(1,(nlstate)*(nlstate+ndeath));    a=matrix(1,npar,1,npar);
         gm=vector(1,(nlstate)*(nlstate+ndeath));    y=matrix(1,npar,1,npar);
        x=vector(1,npar);
         for(theta=1; theta <=npar; theta++){    indx=ivector(1,npar);
           for(i=1; i<=npar; i++)    for (i=1;i<=npar;i++)
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
              ludcmp(a,npar,indx,&pd);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
              for (j=1;j<=npar;j++) {
           k=0;      for (i=1;i<=npar;i++) x[i]=0;
           for(i=1; i<= (nlstate); i++){      x[j]=1;
             for(j=1; j<=(nlstate+ndeath);j++){      lubksb(a,npar,indx,x);
               k=k+1;      for (i=1;i<=npar;i++){ 
               gp[k]=pmmij[i][j];        matcov[i][j]=x[i];
             }      }
           }    }
            
           for(i=1; i<=npar; i++)    printf("\n#Hessian matrix#\n");
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    fprintf(ficlog,"\n#Hessian matrix#\n");
        for (i=1;i<=npar;i++) { 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (j=1;j<=npar;j++) { 
           k=0;        printf("%.3e ",hess[i][j]);
           for(i=1; i<=(nlstate); i++){        fprintf(ficlog,"%.3e ",hess[i][j]);
             for(j=1; j<=(nlstate+ndeath);j++){      }
               k=k+1;      printf("\n");
               gm[k]=pmmij[i][j];      fprintf(ficlog,"\n");
             }    }
           }  
          /* Recompute Inverse */
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    for (i=1;i<=npar;i++)
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         }    ludcmp(a,npar,indx,&pd);
   
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)    /*  printf("\n#Hessian matrix recomputed#\n");
           for(theta=1; theta <=npar; theta++)  
             trgradg[j][theta]=gradg[theta][j];    for (j=1;j<=npar;j++) {
              for (i=1;i<=npar;i++) x[i]=0;
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);      x[j]=1;
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);      lubksb(a,npar,indx,x);
              for (i=1;i<=npar;i++){ 
         pmij(pmmij,cov,ncovmodel,x,nlstate);        y[i][j]=x[i];
                printf("%.3e ",y[i][j]);
         k=0;        fprintf(ficlog,"%.3e ",y[i][j]);
         for(i=1; i<=(nlstate); i++){      }
           for(j=1; j<=(nlstate+ndeath);j++){      printf("\n");
             k=k+1;      fprintf(ficlog,"\n");
             mu[k][(int) age]=pmmij[i][j];    }
           }    */
         }  
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    free_matrix(a,1,npar,1,npar);
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    free_matrix(y,1,npar,1,npar);
             varpij[i][j][(int)age] = doldm[i][j];    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
         /*printf("\n%d ",(int)age);    free_matrix(hess,1,npar,1,npar);
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  }
      }*/  
   /*************** hessian matrix ****************/
         fprintf(ficresprob,"\n%d ",(int)age);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         fprintf(ficresprobcov,"\n%d ",(int)age);  {
         fprintf(ficresprobcor,"\n%d ",(int)age);    int i;
     int l=1, lmax=20;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    double k1,k2;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));    double p2[MAXPARM+1]; /* identical to x */
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    double res;
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);    double fx;
         }    int k=0,kmax=10;
         i=0;    double l1;
         for (k=1; k<=(nlstate);k++){  
           for (l=1; l<=(nlstate+ndeath);l++){    fx=func(x);
             i=i++;    for (i=1;i<=npar;i++) p2[i]=x[i];
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);      l1=pow(10,l);
             for (j=1; j<=i;j++){      delts=delt;
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);      for(k=1 ; k <kmax; k=k+1){
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));        delt = delta*(l1*k);
             }        p2[theta]=x[theta] +delt;
           }        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
         }/* end of loop for state */        p2[theta]=x[theta]-delt;
       } /* end of loop for age */        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
       /* Confidence intervalle of pij  */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       /*        
       fprintf(ficgp,"\nset noparametric;unset label");  #ifdef DEBUGHESS
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);  #endif
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);          k=kmax;
       */        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/          k=kmax; l=lmax*10;
       first1=1;        }
       for (k1=1; k1<=(nlstate);k1++){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         for (l1=1; l1<=(nlstate+ndeath);l1++){          delts=delt;
           if(l1==k1) continue;        }
           i=(k1-1)*(nlstate+ndeath)+l1;      }
           for (k2=1; k2<=(nlstate);k2++){    }
             for (l2=1; l2<=(nlstate+ndeath);l2++){    delti[theta]=delts;
               if(l2==k2) continue;    return res; 
               j=(k2-1)*(nlstate+ndeath)+l2;    
               if(j<=i) continue;  }
               for (age=bage; age<=fage; age ++){  
                 if ((int)age %5==0){  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;  {
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    int i;
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    int l=1, lmax=20;
                   mu1=mu[i][(int) age]/stepm*YEARM ;    double k1,k2,k3,k4,res,fx;
                   mu2=mu[j][(int) age]/stepm*YEARM;    double p2[MAXPARM+1];
                   /* Computing eigen value of matrix of covariance */    int k;
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));  
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    fx=func(x);
                   if(first1==1){    for (k=1; k<=2; k++) {
                     first1=0;      for (i=1;i<=npar;i++) p2[i]=x[i];
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);      p2[thetai]=x[thetai]+delti[thetai]/k;
                   }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);      k1=func(p2)-fx;
                   /* Eigen vectors */    
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));      p2[thetai]=x[thetai]+delti[thetai]/k;
                   v21=sqrt(1.-v11*v11);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                   v12=-v21;      k2=func(p2)-fx;
                   v22=v11;    
                   /*printf(fignu*/      p2[thetai]=x[thetai]-delti[thetai]/k;
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */      k3=func(p2)-fx;
                   if(first==1){    
                     first=0;      p2[thetai]=x[thetai]-delti[thetai]/k;
                     fprintf(ficgp,"\nset parametric;set nolabel");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);      k4=func(p2)-fx;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
                     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>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);  #ifdef DEBUG
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  #endif
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    }
                     /*              fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    return res;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  }
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  
                     */  /************** Inverse of matrix **************/
                     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",\  void ludcmp(double **a, int n, int *indx, double *d) 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  { 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));    int i,imax,j,k; 
                   }else{    double big,dum,sum,temp; 
                     first=0;    double *vv; 
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);   
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    vv=vector(1,n); 
                     /*    *d=1.0; 
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    for (i=1;i<=n;i++) { 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      big=0.0; 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);      for (j=1;j<=n;j++) 
                     */        if ((temp=fabs(a[i][j])) > big) big=temp; 
                     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",\      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      vv[i]=1.0/big; 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));    } 
                   }/* if first */    for (j=1;j<=n;j++) { 
                 } /* age mod 5 */      for (i=1;i<j;i++) { 
               } /* end loop age */        sum=a[i][j]; 
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
               first=1;        a[i][j]=sum; 
             } /*l12 */      } 
           } /* k12 */      big=0.0; 
         } /*l1 */      for (i=j;i<=n;i++) { 
       }/* k1 */        sum=a[i][j]; 
     } /* loop covariates */        for (k=1;k<j;k++) 
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);          sum -= a[i][k]*a[k][j]; 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        a[i][j]=sum; 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);          big=dum; 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          imax=i; 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        } 
   }      } 
   free_vector(xp,1,npar);      if (j != imax) { 
   fclose(ficresprob);        for (k=1;k<=n;k++) { 
   fclose(ficresprobcov);          dum=a[imax][k]; 
   fclose(ficresprobcor);          a[imax][k]=a[j][k]; 
   fclose(ficgp);          a[j][k]=dum; 
   fclose(fichtm);        } 
 }        *d = -(*d); 
         vv[imax]=vv[j]; 
       } 
 /******************* Printing html file ***********/      indx[j]=imax; 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      if (a[j][j] == 0.0) a[j][j]=TINY; 
                   int lastpass, int stepm, int weightopt, char model[],\      if (j != n) { 
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\        dum=1.0/(a[j][j]); 
                   int popforecast, int estepm ,\        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
                   double jprev1, double mprev1,double anprev1, \      } 
                   double jprev2, double mprev2,double anprev2){    } 
   int jj1, k1, i1, cpt;    free_vector(vv,1,n);  /* Doesn't work */
   /*char optionfilehtm[FILENAMELENGTH];*/  ;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {  } 
     printf("Problem with %s \n",optionfilehtm), exit(0);  
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);  void lubksb(double **a, int n, int *indx, double b[]) 
   }  { 
     int i,ii=0,ip,j; 
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n    double sum; 
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n   
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    for (i=1;i<=n;i++) { 
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n      ip=indx[i]; 
  - Life expectancies by age and initial health status (estepm=%2d months):      sum=b[ip]; 
    <a href=\"e%s\">e%s</a> <br>\n</li>", \      b[ip]=b[i]; 
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");      else if (sum) ii=i; 
       b[i]=sum; 
  m=cptcoveff;    } 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    for (i=n;i>=1;i--) { 
       sum=b[i]; 
  jj1=0;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
  for(k1=1; k1<=m;k1++){      b[i]=sum/a[i][i]; 
    for(i1=1; i1<=ncodemax[k1];i1++){    } 
      jj1++;  } 
      if (cptcovn > 0) {  
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  void pstamp(FILE *fichier)
        for (cpt=1; cpt<=cptcoveff;cpt++)  {
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  }
      }  
      /* Pij */  /************ Frequencies ********************/
      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>  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[])
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      {  /* Some frequencies */
      /* 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>    int i, m, jk, j1, bool, z1,j;
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    int first;
        /* Stable prevalence in each health state */    double ***freq; /* Frequencies */
        for(cpt=1; cpt<nlstate;cpt++){    double *pp, **prop;
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    double pos,posprop, k2, dateintsum=0,k2cpt=0;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    char fileresp[FILENAMELENGTH];
        }    
      for(cpt=1; cpt<=nlstate;cpt++) {    pp=vector(1,nlstate);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    prop=matrix(1,nlstate,iagemin,iagemax+3);
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    strcpy(fileresp,"p");
      }    strcat(fileresp,fileres);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    if((ficresp=fopen(fileresp,"w"))==NULL) {
 health expectancies in states (1) and (2): e%s%d.png<br>      printf("Problem with prevalence resultfile: %s\n", fileresp);
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
    } /* end i1 */      exit(0);
  }/* End k1 */    }
  fprintf(fichtm,"</ul>");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
     
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    j=cptcoveff;
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    if (cptcovn<1) {j=1;ncodemax[1]=1;}
  - 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    first=1;
  - 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    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
  - 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);    /*    j1++;
   */
  if(popforecast==1) fprintf(fichtm,"\n    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          scanf("%d", i);*/
         <br>",fileres,fileres,fileres,fileres);        for (i=-5; i<=nlstate+ndeath; i++)  
  else          for (jk=-5; jk<=nlstate+ndeath; jk++)  
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);            for(m=iagemin; m <= iagemax+3; m++)
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");              freq[i][jk][m]=0;
         
  m=cptcoveff;        for (i=1; i<=nlstate; i++)  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0;
  jj1=0;        
  for(k1=1; k1<=m;k1++){        dateintsum=0;
    for(i1=1; i1<=ncodemax[k1];i1++){        k2cpt=0;
      jj1++;        for (i=1; i<=imx; i++) {
      if (cptcovn > 0) {          bool=1;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
        for (cpt=1; cpt<=cptcoveff;cpt++)            for (z1=1; z1<=cptcoveff; z1++)       
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
      }                bool=0;
      for(cpt=1; cpt<=nlstate;cpt++) {                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
 interval) in state (%d): v%s%d%d.png <br>                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                  /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
      }              } 
    } /* end i1 */          }
  }/* End k1 */   
  fprintf(fichtm,"</ul>");          if (bool==1){
 fclose(fichtm);            for(m=firstpass; m<=lastpass; m++){
 }              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 /******************* Gnuplot file **************/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;                if (m<lastpass) {
   int ng;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     printf("Problem with file %s",optionfilegnuplot);                }
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);                
   }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
 #ifdef windows                  k2cpt++;
     fprintf(ficgp,"cd \"%s\" \n",pathc);                }
 #endif                /*}*/
 m=pow(2,cptcoveff);            }
            }
  /* 1eme*/        } /* end i */
   for (cpt=1; cpt<= nlstate ; cpt ++) {         
    for (k1=1; k1<= m ; k1 ++) {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         pstamp(ficresp);
 #ifdef windows        if  (cptcovn>0) {
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          fprintf(ficresp, "\n#********** Variable "); 
      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);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 #endif          fprintf(ficresp, "**********\n#");
 #ifdef unix          fprintf(ficlog, "\n#********** Variable "); 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          fprintf(ficlog, "**********\n#");
 #endif        }
         for(i=1; i<=nlstate;i++) 
 for (i=1; i<= nlstate ; i ++) {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficresp, "\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");        
 }        for(i=iagemin; i <= iagemax+3; i++){
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          if(i==iagemax+3){
     for (i=1; i<= nlstate ; i ++) {            fprintf(ficlog,"Total");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }else{
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if(first==1){
 }              first=0;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);              printf("See log file for details...\n");
      for (i=1; i<= nlstate ; i ++) {            }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            fprintf(ficlog,"Age %d", i);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }            for(jk=1; jk <=nlstate ; jk++){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 #ifdef unix              pp[jk] += freq[jk][m][i]; 
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");          }
 #endif          for(jk=1; jk <=nlstate ; jk++){
    }            for(m=-1, pos=0; m <=0 ; m++)
   }              pos += freq[jk][m][i];
   /*2 eme*/            if(pp[jk]>=1.e-10){
               if(first==1){
   for (k1=1; k1<= m ; k1 ++) {                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     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(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                }else{
     for (i=1; i<= nlstate+1 ; i ++) {              if(first==1)
       k=2*i;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for (j=1; j<= nlstate+1 ; j ++) {            }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }            for(jk=1; jk <=nlstate ; jk++){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              pp[jk] += freq[jk][m][i];
     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 ++) {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            pos += pp[jk];
         else fprintf(ficgp," \%%*lf (\%%*lf)");            posprop += prop[jk][i];
 }            }
       fprintf(ficgp,"\" t\"\" w l 0,");          for(jk=1; jk <=nlstate ; jk++){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            if(pos>=1.e-5){
       for (j=1; j<= nlstate+1 ; j ++) {              if(first==1)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 }              }else{
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              if(first==1)
       else fprintf(ficgp,"\" t\"\" w l 0,");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   }            }
              if( i <= iagemax){
   /*3eme*/              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   for (k1=1; k1<= m ; k1 ++) {                /*probs[i][jk][j1]= pp[jk]/pos;*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       k=2+nlstate*(2*cpt-2);              }
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);              else
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          for(jk=-1; jk <=nlstate+ndeath; jk++)
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            for(m=-1; m <=nlstate+ndeath; m++)
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);              if(freq[jk][m][i] !=0 ) {
               if(first==1)
 */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       for (i=1; i< nlstate ; i ++) {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);              }
           if(i <= iagemax)
       }            fprintf(ficresp,"\n");
     }          if(first==1)
   }            printf("Others in log...\n");
            fprintf(ficlog,"\n");
   /* CV preval stat */        }
     for (k1=1; k1<= m ; k1 ++) {        /*}*/
     for (cpt=1; cpt<nlstate ; cpt ++) {    }
       k=3;    dateintmean=dateintsum/k2cpt; 
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);   
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    fclose(ficresp);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       for (i=1; i< nlstate ; i ++)    free_vector(pp,1,nlstate);
         fprintf(ficgp,"+$%d",k+i+1);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    /* End of Freq */
        }
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  /************ Prevalence ********************/
       for (i=1; i< nlstate ; i ++) {  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
         l=3+(nlstate+ndeath)*cpt;  {  
         fprintf(ficgp,"+$%d",l+i+1);    /* 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).
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);         We still use firstpass and lastpass as another selection.
     }    */
   }     
      int i, m, jk, j1, bool, z1,j;
   /* proba elementaires */  
    for(i=1,jk=1; i <=nlstate; i++){    double **prop;
     for(k=1; k <=(nlstate+ndeath); k++){    double posprop; 
       if (k != i) {    double  y2; /* in fractional years */
         for(j=1; j <=ncovmodel; j++){    int iagemin, iagemax;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    int first; /** to stop verbosity which is redirected to log file */
           jk++;  
           fprintf(ficgp,"\n");    iagemin= (int) agemin;
         }    iagemax= (int) agemax;
       }    /*pp=vector(1,nlstate);*/
     }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
    }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    
      for(jk=1; jk <=m; jk++) {    /*j=cptcoveff;*/
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
        if (ng==2)    
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    first=1;
        else    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
          fprintf(ficgp,"\nset title \"Probability\"\n");      /*for(i1=1; i1<=ncodemax[k1];i1++){
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        j1++;*/
        i=1;        
        for(k2=1; k2<=nlstate; k2++) {        for (i=1; i<=nlstate; i++)  
          k3=i;          for(m=iagemin; m <= iagemax+3; m++)
          for(k=1; k<=(nlstate+ndeath); k++) {            prop[i][m]=0.0;
            if (k != k2){       
              if(ng==2)        for (i=1; i<=imx; i++) { /* Each individual */
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          bool=1;
              else          if  (cptcovn>0) {
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            for (z1=1; z1<=cptcoveff; z1++) 
              ij=1;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
              for(j=3; j <=ncovmodel; j++) {                bool=0;
                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]]]);          if (bool==1) { 
                  ij++;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                else              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
              }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
              fprintf(ficgp,")/(1");                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); 
                              if (s[m][i]>0 && s[m][i]<=nlstate) { 
              for(k1=1; k1 <=nlstate; k1++){                    /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                ij=1;                  prop[s[m][i]][iagemax+3] += weight[i]; 
                for(j=3; j <=ncovmodel; j++){                } 
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              }
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            } /* end selection of waves */
                    ij++;          }
                  }        }
                  else        for(i=iagemin; i <= iagemax+3; i++){  
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                }            posprop += prop[jk][i]; 
                fprintf(ficgp,")");          } 
              }          
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);          for(jk=1; jk <=nlstate ; jk++){     
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            if( i <=  iagemax){ 
              i=i+ncovmodel;              if(posprop>=1.e-5){ 
            }                probs[i][jk][j1]= prop[jk][i]/posprop;
          } /* end k */              } else{
        } /* end k2 */                if(first==1){
      } /* end jk */                  first=0;
    } /* end ng */                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
    fclose(ficgp);                }
 }  /* end gnuplot */              }
             } 
           }/* end jk */ 
 /*************** Moving average **************/        }/* end i */ 
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      /*} *//* end i1 */
     } /* end j1 */
   int i, cpt, cptcod;    
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       for (i=1; i<=nlstate;i++)    /*free_vector(pp,1,nlstate);*/
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           mobaverage[(int)agedeb][i][cptcod]=0.;  }  /* End of prevalence */
      
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  /************* Waves Concatenation ***************/
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
           for (cpt=0;cpt<=4;cpt++){  {
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           }       Death is a valid wave (if date is known).
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       }       and mw[mi+1][i]. dh depends on stepm.
     }       */
      
 }    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
 /************** Forecasting ******************/    int first;
 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){    int j, k=0,jk, ju, jl;
      double sum=0.;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    first=0;
   int *popage;    jmin=100000;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    jmax=-1;
   double *popeffectif,*popcount;    jmean=0.;
   double ***p3mat;    for(i=1; i<=imx; i++){
   char fileresf[FILENAMELENGTH];      mi=0;
       m=firstpass;
  agelim=AGESUP;      while(s[m][i] <= nlstate){
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           mw[++mi][i]=m;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        if(m >=lastpass)
            break;
          else
   strcpy(fileresf,"f");          m++;
   strcat(fileresf,fileres);      }/* end while */
   if((ficresf=fopen(fileresf,"w"))==NULL) {      if (s[m][i] > nlstate){
     printf("Problem with forecast resultfile: %s\n", fileresf);        mi++;     /* Death is another wave */
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);        /* if(mi==0)  never been interviewed correctly before death */
   }           /* Only death is a correct wave */
   printf("Computing forecasting: result on file '%s' \n", fileresf);        mw[mi][i]=m;
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);      }
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      wav[i]=mi;
       if(mi==0){
   if (mobilav==1) {        nbwarn++;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        if(first==0){
     movingaverage(agedeb, fage, ageminpar, mobaverage);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   }          first=1;
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;        if(first==1){
   if (stepm<=12) stepsize=1;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
          }
   agelim=AGESUP;      } /* end mi==0 */
      } /* End individuals */
   hstepm=1;  
   hstepm=hstepm/stepm;    for(i=1; i<=imx; i++){
   yp1=modf(dateintmean,&yp);      for(mi=1; mi<wav[i];mi++){
   anprojmean=yp;        if (stepm <=0)
   yp2=modf((yp1*12),&yp);          dh[mi][i]=1;
   mprojmean=yp;        else{
   yp1=modf((yp2*30.5),&yp);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   jprojmean=yp;            if (agedc[i] < 2*AGESUP) {
   if(jprojmean==0) jprojmean=1;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   if(mprojmean==0) jprojmean=1;              if(j==0) j=1;  /* Survives at least one month after exam */
                else if(j<0){
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);                nberr++;
                  printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   for(cptcov=1;cptcov<=i2;cptcov++){                j=1; /* Temporary Dangerous patch */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                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);
       k=k+1;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficresf,"\n#******");                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(j=1;j<=cptcoveff;j++) {              }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              k=k+1;
       }              if (j >= jmax){
       fprintf(ficresf,"******\n");                jmax=j;
       fprintf(ficresf,"# StartingAge FinalAge");                ijmax=i;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);              }
                    if (j <= jmin){
                      jmin=j;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {                ijmin=i;
         fprintf(ficresf,"\n");              }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            }
           nhstepm = nhstepm/hstepm;          }
                    else{
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           oldm=oldms;savm=savms;  /*        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]); */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
                    k=k+1;
           for (h=0; h<=nhstepm; h++){            if (j >= jmax) {
             if (h==(int) (calagedate+YEARM*cpt)) {              jmax=j;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);              ijmax=i;
             }            }
             for(j=1; j<=nlstate+ndeath;j++) {            else if (j <= jmin){
               kk1=0.;kk2=0;              jmin=j;
               for(i=1; i<=nlstate;i++) {                            ijmin=i;
                 if (mobilav==1)            }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                 else {            /*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]);*/
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            if(j<0){
                 }              nberr++;
                              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               if (h==(int)(calagedate+12*cpt)){            }
                 fprintf(ficresf," %.3f", kk1);            sum=sum+j;
                                  }
               }          jk= j/stepm;
             }          jl= j -jk*stepm;
           }          ju= j -(jk+1)*stepm;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         }            if(jl==0){
       }              dh[mi][i]=jk;
     }              bh[mi][i]=0;
   }            }else{ /* We want a negative bias in order to only have interpolation ie
                            * to avoid the price of an extra matrix product in likelihood */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   fclose(ficresf);            }
 }          }else{
 /************** Forecasting ******************/            if(jl <= -ju){
 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){              dh[mi][i]=jk;
                bh[mi][i]=jl;       /* bias is positive if real duration
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                                   * is higher than the multiple of stepm and negative otherwise.
   int *popage;                                   */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            }
   double *popeffectif,*popcount;            else{
   double ***p3mat,***tabpop,***tabpopprev;              dh[mi][i]=jk+1;
   char filerespop[FILENAMELENGTH];              bh[mi][i]=ju;
             }
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            if(dh[mi][i]==0){
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              dh[mi][i]=1; /* At least one step */
   agelim=AGESUP;              bh[mi][i]=ju; /* At least one step */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;              /*  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);*/
              }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          } /* end if mle */
          }
        } /* end wave */
   strcpy(filerespop,"pop");    }
   strcat(filerespop,fileres);    jmean=sum/k;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    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);
     printf("Problem with forecast resultfile: %s\n", filerespop);    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);   }
   }  
   printf("Computing forecasting: result on file '%s' \n", filerespop);  /*********** Tricode ****************************/
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
     /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   if (mobilav==1) {    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     movingaverage(agedeb, fage, ageminpar, mobaverage);    /* nbcode[Tvar[j]][1]= 
   }    */
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   if (stepm<=12) stepsize=1;    int modmaxcovj=0; /* Modality max of covariates j */
      int cptcode=0; /* Modality max of covariates j */
   agelim=AGESUP;    int modmincovj=0; /* Modality min of covariates j */
    
   hstepm=1;  
   hstepm=hstepm/stepm;    cptcoveff=0; 
     
   if (popforecast==1) {    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     if((ficpop=fopen(popfile,"r"))==NULL) {    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
       printf("Problem with population file : %s\n",popfile);exit(0);  
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);    /* Loop on covariates without age and products */
     }    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
     popage=ivector(0,AGESUP);      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
     popeffectif=vector(0,AGESUP);                                 modality of this covariate Vj*/ 
     popcount=vector(0,AGESUP);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                          * If product of Vn*Vm, still boolean *:
     i=1;                                        * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
            /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
     imx=i;                                        modality of the nth covariate of individual i. */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        if (ij > modmaxcovj)
   }          modmaxcovj=ij; 
         else if (ij < modmincovj) 
   for(cptcov=1;cptcov<=i2;cptcov++){          modmincovj=ij; 
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        if ((ij < -1) && (ij > NCOVMAX)){
       k=k+1;          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
       fprintf(ficrespop,"\n#******");          exit(1);
       for(j=1;j<=cptcoveff;j++) {        }else
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
       }        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
       fprintf(ficrespop,"******\n");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       fprintf(ficrespop,"# Age");        /* getting the maximum value of the modality of the covariate
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
       if (popforecast==1)  fprintf(ficrespop," [Population]");           female is 1, then modmaxcovj=1.*/
            }
       for (cpt=0; cpt<=0;cpt++) {      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        cptcode=modmaxcovj;
              /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){     /*for (i=0; i<=cptcode; i++) {*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
           nhstepm = nhstepm/hstepm;        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
                  if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
           oldm=oldms;savm=savms;        }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
                   historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
           for (h=0; h<=nhstepm; h++){      } /* Ndum[-1] number of undefined modalities */
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
             }      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
             for(j=1; j<=nlstate+ndeath;j++) {      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
               kk1=0.;kk2=0;         modmincovj=3; modmaxcovj = 7;
               for(i=1; i<=nlstate;i++) {                       There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
                 if (mobilav==1)         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];         variables V1_1 and V1_2.
                 else {         nbcode[Tvar[j]][ij]=k;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];         nbcode[Tvar[j]][1]=0;
                 }         nbcode[Tvar[j]][2]=1;
               }         nbcode[Tvar[j]][3]=2;
               if (h==(int)(calagedate+12*cpt)){      */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      ij=1; /* ij is similar to i but can jumps over null modalities */
                   /*fprintf(ficrespop," %.3f", kk1);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
               }          /*recode from 0 */
             }          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             for(i=1; i<=nlstate;i++){            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
               kk1=0.;                                       k is a modality. If we have model=V1+V1*sex 
                 for(j=1; j<=nlstate;j++){                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];            ij++;
                 }          }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          if (ij > ncodemax[j]) break; 
             }        }  /* end of loop on */
       } /* end of loop on modality */ 
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    
           }   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
         }    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
       }     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
       ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
   /******/     Ndum[ij]++; 
    } 
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     ij=1;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
           nhstepm = nhstepm/hstepm;     if((Ndum[i]!=0) && (i<=ncovcol)){
                 /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       Tvaraff[ij]=i; /*For printing (unclear) */
           oldm=oldms;savm=savms;       ij++;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       }else
           for (h=0; h<=nhstepm; h++){         Tvaraff[ij]=0;
             if (h==(int) (calagedate+YEARM*cpt)) {   }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);   ij--;
             }   cptcoveff=ij; /*Number of total covariates*/
             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];      
               }  /*********** Health Expectancies ****************/
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  
             }  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
         }    /* Health expectancies, no variances */
       }    int i, j, nhstepm, hstepm, h, nstepm;
    }    int nhstepma, nstepma; /* Decreasing with age */
   }    double age, agelim, hf;
      double ***p3mat;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double eip;
   
   if (popforecast==1) {    pstamp(ficreseij);
     free_ivector(popage,0,AGESUP);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     free_vector(popeffectif,0,AGESUP);    fprintf(ficreseij,"# Age");
     free_vector(popcount,0,AGESUP);    for(i=1; i<=nlstate;i++){
   }      for(j=1; j<=nlstate;j++){
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficreseij," e%1d%1d ",i,j);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      }
   fclose(ficrespop);      fprintf(ficreseij," e%1d. ",i);
 }    }
     fprintf(ficreseij,"\n");
 /***********************************************/  
 /**************** Main Program *****************/    
 /***********************************************/    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
 int main(int argc, char *argv[])    }
 {    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;     * This is mainly to measure the difference between two models: for example
   double agedeb, agefin,hf;     * if stepm=24 months pijx are given only every 2 years and by summing them
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   double fret;     * to the curvature of the survival function. If, for the same date, we 
   double **xi,tmp,delta;     * 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 
   double dum; /* Dummy variable */     * hypothesis. A more precise result, taking into account a more precise
   double ***p3mat;     * curvature will be obtained if estepm is as small as stepm. */
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];    /* For example we decided to compute the life expectancy with the smallest unit */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   int firstobs=1, lastobs=10;       nhstepm is the number of hstepm from age to agelim 
   int sdeb, sfin; /* Status at beginning and end */       nstepm is the number of stepm from age to agelin. 
   int c,  h , cpt,l;       Look at hpijx to understand the reason of that which relies in memory size
   int ju,jl, mi;       and note for a fixed period like estepm months */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;       survival function given by stepm (the optimization length). Unfortunately it
   int mobilav=0,popforecast=0;       means that if the survival funtion is printed only each two years of age and if
   int hstepm, nhstepm;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;       results. So we changed our mind and took the option of the best precision.
     */
   double bage, fage, age, agelim, agebase;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double ftolpl=FTOL;  
   double **prlim;    agelim=AGESUP;
   double *severity;    /* If stepm=6 months */
   double ***param; /* Matrix of parameters */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   double  *p;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   double **matcov; /* Matrix of covariance */      
   double ***delti3; /* Scale */  /* nhstepm age range expressed in number of stepm */
   double *delti; /* Scale */    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   double ***eij, ***vareij;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   double **varpl; /* Variances of prevalence limits by age */    /* if (stepm >= YEARM) hstepm=1;*/
   double *epj, vepp;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double kk1, kk2;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
      for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   char *alph[]={"a","a","b","c","d","e"}, str[4];      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   char z[1]="c", occ;  
 #include <sys/time.h>      /* If stepm=6 months */
 #include <time.h>      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
        
   /* long total_usecs;      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   struct timeval start_time, end_time;      
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      
   getcwd(pathcd, size);      printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   printf("\n%s",version);      
   if(argc <=1){      /* Computing expectancies */
     printf("\nEnter the parameter file name: ");      for(i=1; i<=nlstate;i++)
     scanf("%s",pathtot);        for(j=1; j<=nlstate;j++)
   }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   else{            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     strcpy(pathtot,argv[1]);            
   }            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   /*if(getcwd(pathcd, 80)!= 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,'\\');*/      fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        eip=0;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        for(j=1; j<=nlstate;j++){
   chdir(path);          eip +=eij[i][j][(int)age];
   replace(pathc,path);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
 /*-------- arguments in the command line --------*/        fprintf(ficreseij,"%9.4f", eip );
       }
   /* Log file */      fprintf(ficreseij,"\n");
   strcat(filelog, optionfilefiname);      
   strcat(filelog,".log");    /* */    }
   if((ficlog=fopen(filelog,"w"))==NULL)    {    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with logfile %s\n",filelog);    printf("\n");
     goto end;    fprintf(ficlog,"\n");
   }    
   fprintf(ficlog,"Log filename:%s\n",filelog);  }
   fprintf(ficlog,"\n%s",version);  
   fprintf(ficlog,"\nEnter the parameter file name: ");  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[] )
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   fflush(ficlog);  {
     /* Covariances of health expectancies eij and of total life expectancies according
   /* */     to initial status i, ei. .
   strcpy(fileres,"r");    */
   strcat(fileres, optionfilefiname);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   strcat(fileres,".txt");    /* Other files have txt extension */    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
   /*---------arguments file --------*/    double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    double *xp, *xm;
     printf("Problem with optionfile %s\n",optionfile);    double **gp, **gm;
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    double ***gradg, ***trgradg;
     goto end;    int theta;
   }  
     double eip, vip;
   strcpy(filereso,"o");  
   strcat(filereso,fileres);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   if((ficparo=fopen(filereso,"w"))==NULL) {    xp=vector(1,npar);
     printf("Problem with Output resultfile: %s\n", filereso);    xm=vector(1,npar);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     goto end;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   }    
     pstamp(ficresstdeij);
   /* Reads comments: lines beginning with '#' */    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresstdeij,"# Age");
     ungetc(c,ficpar);    for(i=1; i<=nlstate;i++){
     fgets(line, MAXLINE, ficpar);      for(j=1; j<=nlstate;j++)
     puts(line);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     fputs(line,ficparo);      fprintf(ficresstdeij," e%1d. ",i);
   }    }
   ungetc(c,ficpar);    fprintf(ficresstdeij,"\n");
   
   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);    pstamp(ficrescveij);
   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(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   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(ficrescveij,"# Age");
 while((c=getc(ficpar))=='#' && c!= EOF){    for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);      for(j=1; j<=nlstate;j++){
     fgets(line, MAXLINE, ficpar);        cptj= (j-1)*nlstate+i;
     puts(line);        for(i2=1; i2<=nlstate;i2++)
     fputs(line,ficparo);          for(j2=1; j2<=nlstate;j2++){
   }            cptj2= (j2-1)*nlstate+i2;
   ungetc(c,ficpar);            if(cptj2 <= cptj)
                fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
              }
   covar=matrix(0,NCOVMAX,1,n);      }
   cptcovn=0;    fprintf(ficrescveij,"\n");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    
     if(estepm < stepm){
   ncovmodel=2+cptcovn;      printf ("Problem %d lower than %d\n",estepm, stepm);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    }
      else  hstepm=estepm;   
   /* Read guess parameters */    /* We compute the life expectancy from trapezoids spaced every estepm months
   /* Reads comments: lines beginning with '#' */     * This is mainly to measure the difference between two models: for example
   while((c=getc(ficpar))=='#' && c!= EOF){     * if stepm=24 months pijx are given only every 2 years and by summing them
     ungetc(c,ficpar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
     fgets(line, MAXLINE, ficpar);     * progression in between and thus overestimating or underestimating according
     puts(line);     * to the curvature of the survival function. If, for the same date, we 
     fputs(line,ficparo);     * 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 
   ungetc(c,ficpar);     * hypothesis. A more precise result, taking into account a more precise
       * curvature will be obtained if estepm is as small as stepm. */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)    /* For example we decided to compute the life expectancy with the smallest unit */
     for(j=1; j <=nlstate+ndeath-1; j++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fscanf(ficpar,"%1d%1d",&i1,&j1);       nhstepm is the number of hstepm from age to agelim 
       fprintf(ficparo,"%1d%1d",i1,j1);       nstepm is the number of stepm from age to agelin. 
       if(mle==1)       Look at hpijx to understand the reason of that which relies in memory size
         printf("%1d%1d",i,j);       and note for a fixed period like estepm months */
       fprintf(ficlog,"%1d%1d",i,j);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       for(k=1; k<=ncovmodel;k++){       survival function given by stepm (the optimization length). Unfortunately it
         fscanf(ficpar," %lf",&param[i][j][k]);       means that if the survival funtion is printed only each two years of age and if
         if(mle==1){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           printf(" %lf",param[i][j][k]);       results. So we changed our mind and took the option of the best precision.
           fprintf(ficlog," %lf",param[i][j][k]);    */
         }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         else  
           fprintf(ficlog," %lf",param[i][j][k]);    /* If stepm=6 months */
         fprintf(ficparo," %lf",param[i][j][k]);    /* nhstepm age range expressed in number of stepm */
       }    agelim=AGESUP;
       fscanf(ficpar,"\n");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
       if(mle==1)    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         printf("\n");    /* if (stepm >= YEARM) hstepm=1;*/
       fprintf(ficlog,"\n");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fprintf(ficparo,"\n");    
     }    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   p=param[1][1];    gp=matrix(0,nhstepm,1,nlstate*nlstate);
      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    for (age=bage; age<=fage; age ++){ 
     ungetc(c,ficpar);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     fgets(line, MAXLINE, ficpar);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     puts(line);      /* if (stepm >= YEARM) hstepm=1;*/
     fputs(line,ficparo);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   }  
   ungetc(c,ficpar);      /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      
   for(i=1; i <=nlstate; i++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);      /* Computing  Variances of health expectancies */
       printf("%1d%1d",i,j);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       fprintf(ficparo,"%1d%1d",i1,j1);         decrease memory allocation */
       for(k=1; k<=ncovmodel;k++){      for(theta=1; theta <=npar; theta++){
         fscanf(ficpar,"%le",&delti3[i][j][k]);        for(i=1; i<=npar; i++){ 
         printf(" %le",delti3[i][j][k]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         fprintf(ficparo," %le",delti3[i][j][k]);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       }        }
       fscanf(ficpar,"\n");        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       printf("\n");        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       fprintf(ficparo,"\n");    
     }        for(j=1; j<= nlstate; j++){
   }          for(i=1; i<=nlstate; i++){
   delti=delti3[1][1];            for(h=0; h<=nhstepm-1; h++){
                gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
   /* Reads comments: lines beginning with '#' */              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);       
     fputs(line,ficparo);        for(ij=1; ij<= nlstate*nlstate; ij++)
   }          for(h=0; h<=nhstepm-1; h++){
   ungetc(c,ficpar);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
            }
   matcov=matrix(1,npar,1,npar);      }/* End theta */
   for(i=1; i <=npar; i++){      
     fscanf(ficpar,"%s",&str);      
     if(mle==1)      for(h=0; h<=nhstepm-1; h++)
       printf("%s",str);        for(j=1; j<=nlstate*nlstate;j++)
     fprintf(ficlog,"%s",str);          for(theta=1; theta <=npar; theta++)
     fprintf(ficparo,"%s",str);            trgradg[h][j][theta]=gradg[h][theta][j];
     for(j=1; j <=i; j++){      
       fscanf(ficpar," %le",&matcov[i][j]);  
       if(mle==1){       for(ij=1;ij<=nlstate*nlstate;ij++)
         printf(" %.5le",matcov[i][j]);        for(ji=1;ji<=nlstate*nlstate;ji++)
         fprintf(ficlog," %.5le",matcov[i][j]);          varhe[ij][ji][(int)age] =0.;
       }  
       else       printf("%d|",(int)age);fflush(stdout);
         fprintf(ficlog," %.5le",matcov[i][j]);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fprintf(ficparo," %.5le",matcov[i][j]);       for(h=0;h<=nhstepm-1;h++){
     }        for(k=0;k<=nhstepm-1;k++){
     fscanf(ficpar,"\n");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     if(mle==1)          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       printf("\n");          for(ij=1;ij<=nlstate*nlstate;ij++)
     fprintf(ficlog,"\n");            for(ji=1;ji<=nlstate*nlstate;ji++)
     fprintf(ficparo,"\n");              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   }        }
   for(i=1; i <=npar; i++)      }
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];      /* Computing expectancies */
          hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   if(mle==1)      for(i=1; i<=nlstate;i++)
     printf("\n");        for(j=1; j<=nlstate;j++)
   fprintf(ficlog,"\n");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
     /*-------- Rewriting paramater file ----------*/            /* 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]);*/
      strcpy(rfileres,"r");    /* "Rparameterfile */  
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          }
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      fprintf(ficresstdeij,"%3.0f",age );
     if((ficres =fopen(rfileres,"w"))==NULL) {      for(i=1; i<=nlstate;i++){
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        eip=0.;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;        vip=0.;
     }        for(j=1; j<=nlstate;j++){
     fprintf(ficres,"#%s\n",version);          eip += eij[i][j][(int)age];
              for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     /*-------- data file ----------*/            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     if((fic=fopen(datafile,"r"))==NULL)    {          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       printf("Problem with datafile: %s\n", datafile);goto end;        }
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     }      }
       fprintf(ficresstdeij,"\n");
     n= lastobs;  
     severity = vector(1,maxwav);      fprintf(ficrescveij,"%3.0f",age );
     outcome=imatrix(1,maxwav+1,1,n);      for(i=1; i<=nlstate;i++)
     num=ivector(1,n);        for(j=1; j<=nlstate;j++){
     moisnais=vector(1,n);          cptj= (j-1)*nlstate+i;
     annais=vector(1,n);          for(i2=1; i2<=nlstate;i2++)
     moisdc=vector(1,n);            for(j2=1; j2<=nlstate;j2++){
     andc=vector(1,n);              cptj2= (j2-1)*nlstate+i2;
     agedc=vector(1,n);              if(cptj2 <= cptj)
     cod=ivector(1,n);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
     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);      fprintf(ficrescveij,"\n");
     anint=matrix(1,maxwav,1,n);     
     s=imatrix(1,maxwav+1,1,n);    }
     adl=imatrix(1,maxwav+1,1,n);        free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     tab=ivector(1,NCOVMAX);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     ncodemax=ivector(1,8);    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     i=1;    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     while (fgets(line, MAXLINE, fic) != NULL)    {    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if ((i >= firstobs) && (i <=lastobs)) {    printf("\n");
            fprintf(ficlog,"\n");
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    free_vector(xm,1,npar);
           strcpy(line,stra);    free_vector(xp,1,npar);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
         }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
          }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  /************ 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[])
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  {
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    /* double **newm;*/
         for (j=ncovcol;j>=1;j--){    double **dnewm,**doldm;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double **dnewmp,**doldmp;
         }    int i, j, nhstepm, hstepm, h, nstepm ;
         num[i]=atol(stra);    int k;
            double *xp;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    double **gp, **gm;  /* for var eij */
           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;}*/    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
         i=i+1;    double *gpp, *gmp; /* for var p point j */
       }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     }    double ***p3mat;
     /* printf("ii=%d", ij);    double age,agelim, hf;
        scanf("%d",i);*/    double ***mobaverage;
   imx=i-1; /* Number of individuals */    int theta;
     char digit[4];
   /* for (i=1; i<=imx; i++){    char digitp[25];
     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;    char fileresprobmorprev[FILENAMELENGTH];
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  
     }*/    if(popbased==1){
    /*  for (i=1; i<=imx; i++){      if(mobilav!=0)
      if (s[4][i]==9)  s[4][i]=-1;        strcpy(digitp,"-populbased-mobilav-");
      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]));}*/      else strcpy(digitp,"-populbased-nomobil-");
      }
      else 
   /* Calculation of the number of parameter from char model*/      strcpy(digitp,"-stablbased-");
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */  
   Tprod=ivector(1,15);    if (mobilav!=0) {
   Tvaraff=ivector(1,15);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   Tvard=imatrix(1,15,1,2);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   Tage=ivector(1,15);              fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
            printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if (strlen(model) >1){      }
     j=0, j1=0, k1=1, k2=1;    }
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');    strcpy(fileresprobmorprev,"prmorprev"); 
     cptcovn=j+1;    sprintf(digit,"%-d",ij);
     cptcovprod=j1;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
        strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcpy(modelsav,model);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    strcat(fileresprobmorprev,fileres);
       printf("Error. Non available option model=%s ",model);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       fprintf(ficlog,"Error. Non available option model=%s ",model);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       goto end;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }    }
        printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     for(i=(j+1); i>=1;i--){   
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */    pstamp(ficresprobmorprev);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    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);
       /*scanf("%d",i);*/    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       if (strchr(strb,'*')) {  /* Model includes a product */    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/      fprintf(ficresprobmorprev," p.%-d SE",j);
         if (strcmp(strc,"age")==0) { /* Vn*age */      for(i=1; i<=nlstate;i++)
           cptcovprod--;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           cutv(strb,stre,strd,'V');    }  
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/    fprintf(ficresprobmorprev,"\n");
           cptcovage++;    fprintf(ficgp,"\n# Routine varevsij");
             Tage[cptcovage]=i;    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
             /*printf("stre=%s ", stre);*/    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
         }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
         else if (strcmp(strd,"age")==0) { /* or age*Vn */  /*   } */
           cptcovprod--;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           cutv(strb,stre,strc,'V');    pstamp(ficresvij);
           Tvar[i]=atoi(stre);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
           cptcovage++;    if(popbased==1)
           Tage[cptcovage]=i;      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
         }    else
         else {  /* Age is not in the model */      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/    fprintf(ficresvij,"# Age");
           Tvar[i]=ncovcol+k1;    for(i=1; i<=nlstate;i++)
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */      for(j=1; j<=nlstate;j++)
           Tprod[k1]=i;        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
           Tvard[k1][1]=atoi(strc); /* m*/    fprintf(ficresvij,"\n");
           Tvard[k1][2]=atoi(stre); /* n */  
           Tvar[cptcovn+k2]=Tvard[k1][1];    xp=vector(1,npar);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    dnewm=matrix(1,nlstate,1,npar);
           for (k=1; k<=lastobs;k++)    doldm=matrix(1,nlstate,1,nlstate);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           k1++;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           k2=k2+2;  
         }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       }    gpp=vector(nlstate+1,nlstate+ndeath);
       else { /* no more sum */    gmp=vector(nlstate+1,nlstate+ndeath);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        /*  scanf("%d",i);*/    
       cutv(strd,strc,strb,'V');    if(estepm < stepm){
       Tvar[i]=atoi(strc);      printf ("Problem %d lower than %d\n",estepm, stepm);
       }    }
       strcpy(modelsav,stra);      else  hstepm=estepm;   
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    /* For example we decided to compute the life expectancy with the smallest unit */
         scanf("%d",i);*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     } /* end of loop + */       nhstepm is the number of hstepm from age to agelim 
   } /* end model */       nstepm is the number of stepm from age to agelin. 
         Look at function hpijx to understand why (it is linked to memory size questions) */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   printf("cptcovprod=%d ", cptcovprod);       survival function given by stepm (the optimization length). Unfortunately it
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);       means that if the survival funtion is printed every two years of age and if
   scanf("%d ",i);*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fclose(fic);       results. So we changed our mind and took the option of the best precision.
     */
     /*  if(mle==1){*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     if (weightopt != 1) { /* Maximisation without weights*/    agelim = AGESUP;
       for(i=1;i<=n;i++) weight[i]=1.0;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     /*-calculation of age at interview from date of interview and age at death -*/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     agev=matrix(1,maxwav,1,imx);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     for (i=1; i<=imx; i++) {      gp=matrix(0,nhstepm,1,nlstate);
       for(m=2; (m<= maxwav); m++) {      gm=matrix(0,nhstepm,1,nlstate);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;  
          s[m][i]=-1;      for(theta=1; theta <=npar; theta++){
        }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
     }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        if (popbased==1) {
       for(m=1; (m<= maxwav); m++){          if(mobilav ==0){
         if(s[m][i] >0){            for(i=1; i<=nlstate;i++)
           if (s[m][i] >= nlstate+1) {              prlim[i][i]=probs[(int)age][i][ij];
             if(agedc[i]>0)          }else{ /* mobilav */ 
               if(moisdc[i]!=99 && andc[i]!=9999)            for(i=1; i<=nlstate;i++)
                 agev[m][i]=agedc[i];              prlim[i][i]=mobaverage[(int)age][i][ij];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/          }
            else {        }
               if (andc[i]!=9999){    
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        for(j=1; j<= nlstate; j++){
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);          for(h=0; h<=nhstepm; h++){
               agev[m][i]=-1;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
             }          }
           }        }
           else if(s[m][i] !=9){ /* Should no more exist */        /* This for computing probability of death (h=1 means
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);           computed over hstepm matrices product = hstepm*stepm months) 
             if(mint[m][i]==99 || anint[m][i]==9999)           as a weighted average of prlim.
               agev[m][i]=1;        */
             else if(agev[m][i] <agemin){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
               agemin=agev[m][i];          for(i=1,gpp[j]=0.; i<= nlstate; i++)
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
             }        }    
             else if(agev[m][i] >agemax){        /* end probability of death */
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
             }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             /*agev[m][i]=anint[m][i]-annais[i];*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             /*   agev[m][i] = age[i]+2*m;*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           }   
           else { /* =9 */        if (popbased==1) {
             agev[m][i]=1;          if(mobilav ==0){
             s[m][i]=-1;            for(i=1; i<=nlstate;i++)
           }              prlim[i][i]=probs[(int)age][i][ij];
         }          }else{ /* mobilav */ 
         else /*= 0 Unknown */            for(i=1; i<=nlstate;i++)
           agev[m][i]=1;              prlim[i][i]=mobaverage[(int)age][i][ij];
       }          }
            }
     }  
     for (i=1; i<=imx; i++)  {        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
       for(m=1; (m<= maxwav); m++){          for(h=0; h<=nhstepm; h++){
         if (s[m][i] > (nlstate+ndeath)) {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           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;        }
         }        /* This for computing probability of death (h=1 means
       }           computed over hstepm matrices product = hstepm*stepm months) 
     }           as a weighted average of prlim.
         */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
     free_vector(severity,1,maxwav);        }    
     free_imatrix(outcome,1,maxwav+1,1,n);        /* end probability of death */
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);        for(j=1; j<= nlstate; j++) /* vareij */
     /* free_matrix(mint,1,maxwav,1,n);          for(h=0; h<=nhstepm; h++){
        free_matrix(anint,1,maxwav,1,n);*/            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     free_vector(moisdc,1,n);          }
     free_vector(andc,1,n);  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
              gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     wav=ivector(1,imx);        }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      } /* End theta */
      
     /* Concatenates waves */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
       Tcode=ivector(1,100);          for(theta=1; theta <=npar; theta++)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            trgradg[h][j][theta]=gradg[h][theta][j];
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
              for(theta=1; theta <=npar; theta++)
    codtab=imatrix(1,100,1,10);          trgradgp[j][theta]=gradgp[theta][j];
    h=0;    
    m=pow(2,cptcoveff);  
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    for(k=1;k<=cptcoveff; k++){      for(i=1;i<=nlstate;i++)
      for(i=1; i <=(m/pow(2,k));i++){        for(j=1;j<=nlstate;j++)
        for(j=1; j <= ncodemax[k]; j++){          vareij[i][j][(int)age] =0.;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  
            h++;      for(h=0;h<=nhstepm;h++){
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        for(k=0;k<=nhstepm;k++){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
          }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
        }          for(i=1;i<=nlstate;i++)
      }            for(j=1;j<=nlstate;j++)
    }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
    /* 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++){      /* pptj */
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      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);
       printf("\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       scanf("%d",i);*/          varppt[j][i]=doldmp[j][i];
          /* end ppptj */
    /* Calculates basic frequencies. Computes observed prevalence at single age      /*  x centered again */
        and prints on file fileres'p'. */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       
          if (popbased==1) {
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if(mobilav ==0){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(i=1; i<=nlstate;i++)
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            prlim[i][i]=probs[(int)age][i][ij];
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }else{ /* mobilav */ 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          for(i=1; i<=nlstate;i++)
                  prlim[i][i]=mobaverage[(int)age][i][ij];
     /* 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) */               
       /* This for computing probability of death (h=1 means
     if(mle==1){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);         as a weighted average of prlim.
     }      */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
     /*--------- results files --------------*/        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     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);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        }    
       /* end probability of death */
    jk=1;  
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
    for(i=1,jk=1; i <=nlstate; i++){        for(i=1; i<=nlstate;i++){
      for(k=1; k <=(nlstate+ndeath); k++){          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
        if (k != i)        }
          {      } 
            printf("%d%d ",i,k);      fprintf(ficresprobmorprev,"\n");
            fprintf(ficlog,"%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);      fprintf(ficresvij,"%.0f ",age );
            for(j=1; j <=ncovmodel; j++){      for(i=1; i<=nlstate;i++)
              printf("%f ",p[jk]);        for(j=1; j<=nlstate;j++){
              fprintf(ficlog,"%f ",p[jk]);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
              fprintf(ficres,"%f ",p[jk]);        }
              jk++;      fprintf(ficresvij,"\n");
            }      free_matrix(gp,0,nhstepm,1,nlstate);
            printf("\n");      free_matrix(gm,0,nhstepm,1,nlstate);
            fprintf(ficlog,"\n");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
            fprintf(ficres,"\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
          }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      }    } /* End age */
    }    free_vector(gpp,nlstate+1,nlstate+ndeath);
    if(mle==1){    free_vector(gmp,nlstate+1,nlstate+ndeath);
      /* Computing hessian and covariance matrix */    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
      ftolhess=ftol; /* Usually correct */    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      hesscov(matcov, p, npar, delti, ftolhess, func);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
    }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
    printf("# Scales (for hessian or gradient estimation)\n");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
    for(i=1,jk=1; i <=nlstate; i++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      for(j=1; j <=nlstate+ndeath; j++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
        if (j!=i) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
          fprintf(ficres,"%1d%1d",i,j);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
          printf("%1d%1d",i,j);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
          fprintf(ficlog,"%1d%1d",i,j);    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);
          for(k=1; k<=ncovmodel;k++){    /*  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);
            printf(" %.5e",delti[jk]);  */
            fprintf(ficlog," %.5e",delti[jk]);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
            fprintf(ficres," %.5e",delti[jk]);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
            jk++;  
          }    free_vector(xp,1,npar);
          printf("\n");    free_matrix(doldm,1,nlstate,1,nlstate);
          fprintf(ficlog,"\n");    free_matrix(dnewm,1,nlstate,1,npar);
          fprintf(ficres,"\n");    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        fclose(ficresprobmorprev);
    k=1;    fflush(ficgp);
    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");    fflush(fichtm); 
    if(mle==1)  }  /* end varevsij */
      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");  /************ Variance of prevlim ******************/
    for(i=1;i<=npar;i++){  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
      /*  if (k>nlstate) k=1;  {
          i1=(i-1)/(ncovmodel*nlstate)+1;    /* Variance of prevalence limit */
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
          printf("%s%d%d",alph[k],i1,tab[i]);*/  
      fprintf(ficres,"%3d",i);    double **dnewm,**doldm;
      if(mle==1)    int i, j, nhstepm, hstepm;
        printf("%3d",i);    double *xp;
      fprintf(ficlog,"%3d",i);    double *gp, *gm;
      for(j=1; j<=i;j++){    double **gradg, **trgradg;
        fprintf(ficres," %.5e",matcov[i][j]);    double age,agelim;
        if(mle==1)    int theta;
          printf(" %.5e",matcov[i][j]);    
        fprintf(ficlog," %.5e",matcov[i][j]);    pstamp(ficresvpl);
      }    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
      fprintf(ficres,"\n");    fprintf(ficresvpl,"# Age");
      if(mle==1)    for(i=1; i<=nlstate;i++)
        printf("\n");        fprintf(ficresvpl," %1d-%1d",i,i);
      fprintf(ficlog,"\n");    fprintf(ficresvpl,"\n");
      k++;  
    }    xp=vector(1,npar);
        dnewm=matrix(1,nlstate,1,npar);
    while((c=getc(ficpar))=='#' && c!= EOF){    doldm=matrix(1,nlstate,1,nlstate);
      ungetc(c,ficpar);    
      fgets(line, MAXLINE, ficpar);    hstepm=1*YEARM; /* Every year of age */
      puts(line);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
      fputs(line,ficparo);    agelim = AGESUP;
    }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
    ungetc(c,ficpar);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    estepm=0;      if (stepm >= YEARM) hstepm=1;
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
    if (estepm==0 || estepm < stepm) estepm=stepm;      gradg=matrix(1,npar,1,nlstate);
    if (fage <= 2) {      gp=vector(1,nlstate);
      bage = ageminpar;      gm=vector(1,nlstate);
      fage = agemaxpar;  
    }      for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient */
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    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);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
            for(i=1;i<=nlstate;i++)
    while((c=getc(ficpar))=='#' && c!= EOF){          gp[i] = prlim[i][i];
      ungetc(c,ficpar);      
      fgets(line, MAXLINE, ficpar);        for(i=1; i<=npar; i++) /* Computes gradient */
      puts(line);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      fputs(line,ficparo);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    }        for(i=1;i<=nlstate;i++)
    ungetc(c,ficpar);          gm[i] = prlim[i][i];
    
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        for(i=1;i<=nlstate;i++)
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      } /* End theta */
      
    while((c=getc(ficpar))=='#' && c!= EOF){      trgradg =matrix(1,nlstate,1,npar);
      ungetc(c,ficpar);  
      fgets(line, MAXLINE, ficpar);      for(j=1; j<=nlstate;j++)
      puts(line);        for(theta=1; theta <=npar; theta++)
      fputs(line,ficparo);          trgradg[j][theta]=gradg[theta][j];
    }  
    ungetc(c,ficpar);      for(i=1;i<=nlstate;i++)
          varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
   fprintf(ficparo,"pop_based=%d\n",popbased);        fprintf(ficresvpl,"%.0f ",age );
   fprintf(ficres,"pop_based=%d\n",popbased);        for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficresvpl,"\n");
     ungetc(c,ficpar);      free_vector(gp,1,nlstate);
     fgets(line, MAXLINE, ficpar);      free_vector(gm,1,nlstate);
     puts(line);      free_matrix(gradg,1,npar,1,nlstate);
     fputs(line,ficparo);      free_matrix(trgradg,1,nlstate,1,npar);
   }    } /* End age */
   ungetc(c,ficpar);  
     free_vector(xp,1,npar);
   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);    free_matrix(doldm,1,nlstate,1,npar);
 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);    free_matrix(dnewm,1,nlstate,1,nlstate);
 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);  
   }
   
 while((c=getc(ficpar))=='#' && c!= EOF){  /************ Variance of one-step probabilities  ******************/
     ungetc(c,ficpar);  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[])
     fgets(line, MAXLINE, ficpar);  {
     puts(line);    int i, j=0,  k1, l1, tj;
     fputs(line,ficparo);    int k2, l2, j1,  z1;
   }    int k=0, l;
   ungetc(c,ficpar);    int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    double **dnewm,**doldm;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    double *xp;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    double *gp, *gm;
     double **gradg, **trgradg;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double **mu;
     double age, cov[NCOVMAX+1];
 /*------------ gnuplot -------------*/    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   strcpy(optionfilegnuplot,optionfilefiname);    int theta;
   strcat(optionfilegnuplot,".gp");    char fileresprob[FILENAMELENGTH];
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    char fileresprobcov[FILENAMELENGTH];
     printf("Problem with file %s",optionfilegnuplot);    char fileresprobcor[FILENAMELENGTH];
   }    double ***varpij;
   fclose(ficgp);  
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    strcpy(fileresprob,"prob"); 
 /*--------- index.htm --------*/    strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   strcpy(optionfilehtm,optionfile);      printf("Problem with resultfile: %s\n", fileresprob);
   strcat(optionfilehtm,".htm");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    }
     printf("Problem with %s \n",optionfilehtm), exit(0);    strcpy(fileresprobcov,"probcov"); 
   }    strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n      printf("Problem with resultfile: %s\n", fileresprobcov);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
 \n    }
 Total number of observations=%d <br>\n    strcpy(fileresprobcor,"probcor"); 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    strcat(fileresprobcor,fileres);
 <hr  size=\"2\" color=\"#EC5E5E\">    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
  <ul><li><h4>Parameter files</h4>\n      printf("Problem with resultfile: %s\n", fileresprobcor);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
  - 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);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   fclose(fichtm);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    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);
 /*------------ free_vector  -------------*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
  chdir(path);    pstamp(ficresprob);
      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
  free_ivector(wav,1,imx);    fprintf(ficresprob,"# Age");
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    pstamp(ficresprobcov);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
  free_ivector(num,1,n);    fprintf(ficresprobcov,"# Age");
  free_vector(agedc,1,n);    pstamp(ficresprobcor);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
  fclose(ficparo);    fprintf(ficresprobcor,"# Age");
  fclose(ficres);  
   
     for(i=1; i<=nlstate;i++)
   /*--------------- Prevalence limit --------------*/      for(j=1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   strcpy(filerespl,"pl");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   strcat(filerespl,fileres);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      }  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;   /* fprintf(ficresprob,"\n");
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;    fprintf(ficresprobcov,"\n");
   }    fprintf(ficresprobcor,"\n");
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);   */
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);    xp=vector(1,npar);
   fprintf(ficrespl,"#Prevalence limit\n");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   fprintf(ficrespl,"#Age ");    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   fprintf(ficrespl,"\n");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
   prlim=matrix(1,nlstate,1,nlstate);    fprintf(ficgp,"\n# Routine varprob");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(fichtm,"\n");
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   k=0;    file %s<br>\n",optionfilehtmcov);
   agebase=ageminpar;    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   agelim=agemaxpar;  and drawn. It helps understanding how is the covariance between two incidences.\
   ftolpl=1.e-10;   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   i1=cptcoveff;    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   if (cptcovn < 1){i1=1;}  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   for(cptcov=1;cptcov<=i1;cptcov++){  standard deviations wide on each axis. <br>\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
         k=k+1;   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
         fprintf(ficrespl,"\n#******");  
         printf("\n#******");    cov[1]=1;
         fprintf(ficlog,"\n#******");    /* tj=cptcoveff; */
         for(j=1;j<=cptcoveff;j++) {    tj = (int) pow(2,cptcoveff);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    j1=0;
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(j1=1; j1<=tj;j1++){
         }      /*for(i1=1; i1<=ncodemax[t];i1++){ */
         fprintf(ficrespl,"******\n");      /*j1++;*/
         printf("******\n");        if  (cptcovn>0) {
         fprintf(ficlog,"******\n");          fprintf(ficresprob, "\n#********** Variable "); 
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for (age=agebase; age<=agelim; age++){          fprintf(ficresprob, "**********\n#\n");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          fprintf(ficresprobcov, "\n#********** Variable "); 
           fprintf(ficrespl,"%.0f",age );          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for(i=1; i<=nlstate;i++)          fprintf(ficresprobcov, "**********\n#\n");
           fprintf(ficrespl," %.5f", prlim[i][i]);          
           fprintf(ficrespl,"\n");          fprintf(ficgp, "\n#********** Variable "); 
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficgp, "**********\n#\n");
     }          
   fclose(ficrespl);          
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   /*------------- h Pij x at various ages ------------*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          fprintf(ficresprobcor, "\n#********** Variable ");    
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;          fprintf(ficresprobcor, "**********\n#");    
   }        }
   printf("Computing pij: result on file '%s' \n", filerespij);        
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   stepsize=(int) (stepm+YEARM-1)/YEARM;        gp=vector(1,(nlstate)*(nlstate+ndeath));
   /*if (stepm<=24) stepsize=2;*/        gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
   agelim=AGESUP;          cov[2]=age;
   hstepm=stepsize*YEARM; /* Every year of age */          for (k=1; k<=cptcovn;k++) {
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
   /* hstepm=1;   aff par mois*/                                                           * 2  2 1 1 1
                                                            * 3  1 2 1 1
   k=0;                                                           */
   for(cptcov=1;cptcov<=i1;cptcov++){            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          }
       k=k+1;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         fprintf(ficrespij,"\n#****** ");          for (k=1; k<=cptcovprod;k++)
         for(j=1;j<=cptcoveff;j++)            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          
         fprintf(ficrespij,"******\n");      
                  for(theta=1; theta <=npar; theta++){
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            for(i=1; i<=npar; i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
           /*      nhstepm=nhstepm*YEARM; aff par mois*/            
             k=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(i=1; i<= (nlstate); i++){
           oldm=oldms;savm=savms;              for(j=1; j<=(nlstate+ndeath);j++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  k=k+1;
           fprintf(ficrespij,"# Age");                gp[k]=pmmij[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(i=1; i<=npar; i++)
            for (h=0; h<=nhstepm; h++){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      
             for(i=1; i<=nlstate;i++)            pmij(pmmij,cov,ncovmodel,xp,nlstate);
               for(j=1; j<=nlstate+ndeath;j++)            k=0;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            for(i=1; i<=(nlstate); i++){
             fprintf(ficrespij,"\n");              for(j=1; j<=(nlstate+ndeath);j++){
              }                k=k+1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                gm[k]=pmmij[i][j];
           fprintf(ficrespij,"\n");              }
         }            }
     }       
   }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          }
   
   fclose(ficrespij);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
   /*---------- Forecasting ------------------*/          
   if((stepm == 1) && (strcmp(model,".")==0)){          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
   }          pmij(pmmij,cov,ncovmodel,x,nlstate);
   else{          
     erreur=108;          k=0;
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);          for(i=1; i<=(nlstate); i++){
     fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);            for(j=1; j<=(nlstate+ndeath);j++){
   }              k=k+1;
                mu[k][(int) age]=pmmij[i][j];
             }
   /*---------- Health expectancies and variances ------------*/          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   strcpy(filerest,"t");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   strcat(filerest,fileres);              varpij[i][j][(int)age] = doldm[i][j];
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          /*printf("\n%d ",(int)age);
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   }            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   printf("Computing Total LEs with variances: file '%s' \n", filerest);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);            }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
   strcpy(filerese,"e");          fprintf(ficresprobcov,"\n%d ",(int)age);
   strcat(filerese,fileres);          fprintf(ficresprobcor,"\n%d ",(int)age);
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
   strcpy(fileresv,"v");          i=0;
   strcat(fileresv,fileres);          for (k=1; k<=(nlstate);k++){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {            for (l=1; l<=(nlstate+ndeath);l++){ 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);              i++;
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);              for (j=1; j<=i;j++){
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
   calagedate=-1;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
   k=0;            }
   for(cptcov=1;cptcov<=i1;cptcov++){          }/* end of loop for state */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        } /* end of loop for age */
       k=k+1;        free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
       fprintf(ficrest,"\n#****** ");        free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       for(j=1;j<=cptcoveff;j++)        free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       fprintf(ficrest,"******\n");        
         /* Confidence intervalle of pij  */
       fprintf(ficreseij,"\n#****** ");        /*
       for(j=1;j<=cptcoveff;j++)          fprintf(ficgp,"\nunset parametric;unset label");
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       fprintf(ficreseij,"******\n");          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(ficresvij,"\n#****** ");          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       for(j=1;j<=cptcoveff;j++)          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       fprintf(ficresvij,"******\n");        */
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       oldm=oldms;savm=savms;        first1=1;first2=2;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);          for (k2=1; k2<=(nlstate);k2++){
            for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            if(l2==k2) continue;
       oldm=oldms;savm=savms;            j=(k2-1)*(nlstate+ndeath)+l2;
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);            for (k1=1; k1<=(nlstate);k1++){
       if(popbased==1){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);                if(l1==k1) continue;
        }                i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                  for (age=bage; age<=fage; age ++){ 
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                  if ((int)age %5==0){
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       fprintf(ficrest,"\n");                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       epj=vector(1,nlstate+1);                    mu1=mu[i][(int) age]/stepm*YEARM ;
       for(age=bage; age <=fage ;age++){                    mu2=mu[j][(int) age]/stepm*YEARM;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                    c12=cv12/sqrt(v1*v2);
         if (popbased==1) {                    /* Computing eigen value of matrix of covariance */
           for(i=1; i<=nlstate;i++)                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
             prlim[i][i]=probs[(int)age][i][k];                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         }                    if ((lc2 <0) || (lc1 <0) ){
                              if(first2==1){
         fprintf(ficrest," %4.0f",age);                        first1=0;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                      printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                      }
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                      fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                      /* lc1=fabs(lc1); */ /* If we want to have them positive */
           }                      /* lc2=fabs(lc2); */
           epj[nlstate+1] +=epj[j];                    }
         }  
                     /* Eigen vectors */
         for(i=1, vepp=0.;i <=nlstate;i++)                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           for(j=1;j <=nlstate;j++)                    /*v21=sqrt(1.-v11*v11); *//* error */
             vepp += vareij[i][j][(int)age];                    v21=(lc1-v1)/cv12*v11;
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));                    v12=-v21;
         for(j=1;j <=nlstate;j++){                    v22=v11;
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                    tnalp=v21/v11;
         }                    if(first1==1){
         fprintf(ficrest,"\n");                      first1=0;
       }                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     }                    }
   }                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
 free_matrix(mint,1,maxwav,1,n);                    /*printf(fignu*/
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     free_vector(weight,1,n);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   fclose(ficreseij);                    if(first==1){
   fclose(ficresvij);                      first=0;
   fclose(ficrest);                      fprintf(ficgp,"\nset parametric;unset label");
   fclose(ficpar);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   free_vector(epj,1,nlstate+1);                      fprintf(ficgp,"\nset ter png small size 320, 240");
                        fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   /*------- Variance limit prevalence------*/     :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   strcpy(fileresvpl,"vpl");                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   strcat(fileresvpl,fileres);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     exit(0);                      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);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   k=0;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   for(cptcov=1;cptcov<=i1;cptcov++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    }else{
       k=k+1;                      first=0;
       fprintf(ficresvpl,"\n#****** ");                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
       for(j=1;j<=cptcoveff;j++)                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       fprintf(ficresvpl,"******\n");                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       oldm=oldms;savm=savms;                    }/* if first */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                  } /* age mod 5 */
     }                } /* end loop age */
  }                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
   fclose(ficresvpl);              } /*l12 */
             } /* k12 */
   /*---------- End : free ----------------*/          } /*l1 */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        }/* k1 */
          /* } /* loop covariates */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_vector(xp,1,npar);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    fclose(ficresprob);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    fclose(ficresprobcov);
      fclose(ficresprobcor);
   free_matrix(matcov,1,npar,1,npar);    fflush(ficgp);
   free_vector(delti,1,npar);    fflush(fichtmcov);
   free_matrix(agev,1,maxwav,1,imx);  }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
   
   fprintf(fichtm,"\n</body>");  /******************* Printing html file ***********/
   fclose(fichtm);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   fclose(ficgp);                    int lastpass, int stepm, int weightopt, char model[],\
                      int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
   if(erreur >0){                    double jprev1, double mprev1,double anprev1, \
     printf("End of Imach with error or warning %d\n",erreur);                    double jprev2, double mprev2,double anprev2){
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);    int jj1, k1, i1, cpt;
   }else{  
    printf("End of Imach\n");     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
    fprintf(ficlog,"End of Imach\n");     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   }  </ul>");
   printf("See log file on %s\n",filelog);     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
   fclose(ficlog);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
       fprintf(fichtm,"\
   /* 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);*/   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
   /*printf("Total time was %d uSec.\n", total_usecs);*/             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
   /*------ End -----------*/     fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
  end:     fprintf(fichtm,"\
 #ifdef windows   - (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): \
   /* chdir(pathcd);*/     <a href=\"%s\">%s</a> <br>\n",
 #endif             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
  /*system("wgnuplot graph.plt");*/     fprintf(fichtm,"\
  /*system("../gp37mgw/wgnuplot graph.plt");*/   - Population projections by age and states: \
  /*system("cd ../gp37mgw");*/     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);   m=pow(2,cptcoveff);
  system(plotcmd);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
 #ifdef windows   jj1=0;
   while (z[0] != 'q') {   for(k1=1; k1<=m;k1++){
     /* chdir(path); */     for(i1=1; i1<=ncodemax[k1];i1++){
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");       jj1++;
     scanf("%s",z);       if (cptcovn > 0) {
     if (z[0] == 'c') system("./imach");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     else if (z[0] == 'e') system(optionfilehtm);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     else if (z[0] == 'g') system(plotcmd);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     else if (z[0] == 'q') exit(0);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   }       }
 #endif       /* Pij */
 }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),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: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, 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 in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <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>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int 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 size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
   #include <gnu/libc-version.h>
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
   #endif
   
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
   #elif __unix__ // all unices, not all compilers
       // Unix
   #elif __linux__
       // linux
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   #include <stdint.h>
   #if UINTPTR_MAX == 0xffffffff
      printf("32-bit \n"); /* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
     printf("64-bit \n");/* 64-bit */
   #else
    printf("wtf-bit \n"); /* wtf */
   #endif
   
   struct utsname sysInfo;
   
      if (uname(&sysInfo) != -1) {
         puts(sysInfo.sysname);
         puts(sysInfo.nodename);
         puts(sysInfo.release);
         puts(sysInfo.version);
         puts(sysInfo.machine);
      }
      else
         perror("uname() error");
      printf("GNU C version %d\n", __GNUC_VERSION__);
     printf("GNU libc version: %s\n", gnu_get_libc_version());
   
    }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *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=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double 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]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_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.tm_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';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         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);
   
     syscompilerinfo();
   
     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.tm_sec-start_time.tm_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' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     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 guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           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);  
           /*
            */
           /* goto endfree; */
    
           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; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             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,NCOVMAX,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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       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);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     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(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  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");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or 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("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       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.1.50  
changed lines
  Added in v.1.167


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