Diff for /imach/src/imach.c between versions 1.4 and 1.128

version 1.4, 2001/05/02 17:34:41 version 1.128, 2006/06/30 13:02:05
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.128  2006/06/30 13:02:05  brouard
   individuals from different ages are interviewed on their health status    (Module): Clarifications on computing e.j
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.127  2006/04/28 18:11:50  brouard
   Health expectancies are computed from the transistions observed between    (Module): Yes the sum of survivors was wrong since
   waves and are computed for each degree of severity of disability (number    imach-114 because nhstepm was no more computed in the age
   of life states). More degrees you consider, more time is necessary to    loop. Now we define nhstepma in the age loop.
   reach the Maximum Likelihood of the parameters involved in the model.    (Module): In order to speed up (in case of numerous covariates) we
   The simplest model is the multinomial logistic model where pij is    compute health expectancies (without variances) in a first step
   the probabibility to be observed in state j at the second wave conditional    and then all the health expectancies with variances or standard
   to be observed in state i at the first wave. Therefore the model is:    deviation (needs data from the Hessian matrices) which slows the
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    computation.
   is a covariate. If you want to have a more complex model than "constant and    In the future we should be able to stop the program is only health
   age", you should modify the program where the markup    expectancies and graph are needed without standard deviations.
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
   The advantage that this computer programme claims, comes from that if the    imach-114 because nhstepm was no more computed in the age
   delay between waves is not identical for each individual, or if some    loop. Now we define nhstepma in the age loop.
   individual missed an interview, the information is not rounded or lost, but    Version 0.98h
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Revision 1.125  2006/04/04 15:20:31  lievre
   observed in state i at age x+h conditional to the observed state i at age    Errors in calculation of health expectancies. Age was not initialized.
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Forecasting file added.
   unobserved intermediate  states. This elementary transition (by month or  
   quarter trimester, semester or year) is model as a multinomial logistic.    Revision 1.124  2006/03/22 17:13:53  lievre
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Parameters are printed with %lf instead of %f (more numbers after the comma).
   and the contribution of each individual to the likelihood is simply hPijx.    The log-likelihood is printed in the log file
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.123  2006/03/20 10:52:43  brouard
   of the life expectancies. It also computes the prevalence limits.    * imach.c (Module): <title> changed, corresponds to .htm file
      name. <head> headers where missing.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    * imach.c (Module): Weights can have a decimal point as for
   This software have been partly granted by Euro-REVES, a concerted action    English (a comma might work with a correct LC_NUMERIC environment,
   from the European Union.    otherwise the weight is truncated).
   It is copyrighted identically to a GNU software product, ie programme and    Modification of warning when the covariates values are not 0 or
   software can be distributed freely for non commercial use. Latest version    1.
   can be accessed at http://euroreves.ined.fr/imach .    Version 0.98g
   **********************************************************************/  
      Revision 1.122  2006/03/20 09:45:41  brouard
 #include <math.h>    (Module): Weights can have a decimal point as for
 #include <stdio.h>    English (a comma might work with a correct LC_NUMERIC environment,
 #include <stdlib.h>    otherwise the weight is truncated).
 #include <unistd.h>    Modification of warning when the covariates values are not 0 or
     1.
 #define MAXLINE 256    Version 0.98g
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.121  2006/03/16 17:45:01  lievre
 #define windows    * imach.c (Module): Comments concerning covariates added
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    * imach.c (Module): refinements in the computation of lli if
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.120  2006/03/16 15:10:38  lievre
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): refinements in the computation of lli if
 #define NCOVMAX 8 /* Maximum number of covariates */    status=-2 in order to have more reliable computation if stepm is
 #define MAXN 20000    not 1 month. Version 0.98f
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.119  2006/03/15 17:42:26  brouard
 #define AGEBASE 40    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
   
 int nvar;    Revision 1.118  2006/03/14 18:20:07  brouard
 static int cptcov;    (Module): varevsij Comments added explaining the second
 int cptcovn;    table of variances if popbased=1 .
 int npar=NPARMAX;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int nlstate=2; /* Number of live states */    (Module): Function pstamp added
 int ndeath=1; /* Number of dead states */    (Module): Version 0.98d
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
     Revision 1.117  2006/03/14 17:16:22  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): varevsij Comments added explaining the second
 int maxwav; /* Maxim number of waves */    table of variances if popbased=1 .
 int mle, weightopt;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Function pstamp added
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): Version 0.98d
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.116  2006/03/06 10:29:27  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    (Module): Variance-covariance wrong links and
 FILE *ficgp, *fichtm;    varian-covariance of ej. is needed (Saito).
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.115  2006/02/27 12:17:45  brouard
  FILE  *ficresvij;    (Module): One freematrix added in mlikeli! 0.98c
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.114  2006/02/26 12:57:58  brouard
   char fileresvpl[FILENAMELENGTH];    (Module): Some improvements in processing parameter
     filename with strsep.
   
     Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 #define NR_END 1    datafile was not closed, some imatrix were not freed and on matrix
 #define FREE_ARG char*    allocation too.
 #define FTOL 1.0e-10  
     Revision 1.112  2006/01/30 09:55:26  brouard
 #define NRANSI    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define ITMAX 200  
     Revision 1.111  2006/01/25 20:38:18  brouard
 #define TOL 2.0e-4    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
 #define CGOLD 0.3819660    can be a simple dot '.'.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.109  2006/01/24 19:37:15  brouard
 #define TINY 1.0e-20    (Module): Comments (lines starting with a #) are allowed in data.
   
 static double maxarg1,maxarg2;    Revision 1.108  2006/01/19 18:05:42  lievre
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Gnuplot problem appeared...
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    To be fixed
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.107  2006/01/19 16:20:37  brouard
 #define rint(a) floor(a+0.5)    Test existence of gnuplot in imach path
   
 static double sqrarg;    Revision 1.106  2006/01/19 13:24:36  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Some cleaning and links added in html output
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.105  2006/01/05 20:23:19  lievre
 int imx;    *** empty log message ***
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 int m,nb;    (Module): If the status is missing at the last wave but we know
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;    that the person is alive, then we can code his/her status as -2
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (instead of missing=-1 in earlier versions) and his/her
 double **pmmij;    contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
 double *weight;    the healthy state at last known wave). Version is 0.98
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.103  2005/09/30 15:54:49  lievre
 int **nbcode, *Tcode, *Tvar, **codtab;    (Module): sump fixed, loop imx fixed, and simplifications.
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.102  2004/09/15 17:31:30  brouard
 double ftolhess; /* Tolerance for computing hessian */    Add the possibility to read data file including tab characters.
   
     Revision 1.101  2004/09/15 10:38:38  brouard
 /******************************************/    Fix on curr_time
   
 void replace(char *s, char*t)    Revision 1.100  2004/07/12 18:29:06  brouard
 {    Add version for Mac OS X. Just define UNIX in Makefile
   int i;  
   int lg=20;    Revision 1.99  2004/06/05 08:57:40  brouard
   i=0;    *** empty log message ***
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.98  2004/05/16 15:05:56  brouard
     (s[i] = t[i]);    New version 0.97 . First attempt to estimate force of mortality
     if (t[i]== '\\') s[i]='/';    directly from the data i.e. without the need of knowing the health
   }    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
     other analysis, in order to test if the mortality estimated from the
 int nbocc(char *s, char occ)    cross-longitudinal survey is different from the mortality estimated
 {    from other sources like vital statistic data.
   int i,j=0;  
   int lg=20;    The same imach parameter file can be used but the option for mle should be -3.
   i=0;  
   lg=strlen(s);    Agnès, who wrote this part of the code, tried to keep most of the
   for(i=0; i<= lg; i++) {    former routines in order to include the new code within the former code.
   if  (s[i] == occ ) j++;  
   }    The output is very simple: only an estimate of the intercept and of
   return j;    the slope with 95% confident intervals.
 }  
     Current limitations:
 void cutv(char *u,char *v, char*t, char occ)    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.
   int i,lg,j,p;    B) There is no computation of Life Expectancy nor Life Table.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.97  2004/02/20 13:25:42  lievre
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Version 0.96d. Population forecasting command line is (temporarily)
   }    suppressed.
   
   lg=strlen(t);    Revision 1.96  2003/07/15 15:38:55  brouard
   for(j=0; j<p; j++) {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     (u[j] = t[j]);    rewritten within the same printf. Workaround: many printfs.
     u[p]='\0';  
   }    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
    for(j=0; j<= lg; j++) {    (Repository): Using imachwizard code to output a more meaningful covariance
     if (j>=(p+1))(v[j-p-1] = t[j]);    matrix (cov(a12,c31) instead of numbers.
   }  
 }    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 /********************** nrerror ********************/  
     Revision 1.93  2003/06/25 16:33:55  brouard
 void nrerror(char error_text[])    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   fprintf(stderr,"ERREUR ...\n");    (Module): Version 0.96b
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Revision 1.92  2003/06/25 16:30:45  brouard
 }    (Module): On windows (cygwin) function asctime_r doesn't
 /*********************** vector *******************/    exist so I changed back to asctime which exists.
 double *vector(int nl, int nh)  
 {    Revision 1.91  2003/06/25 15:30:29  brouard
   double *v;    * imach.c (Repository): Duplicated warning errors corrected.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    (Repository): Elapsed time after each iteration is now output. It
   if (!v) nrerror("allocation failure in vector");    helps to forecast when convergence will be reached. Elapsed time
   return v-nl+NR_END;    is stamped in powell.  We created a new html file for the graphs
 }    concerning matrix of covariance. It has extension -cov.htm.
   
 /************************ free vector ******************/    Revision 1.90  2003/06/24 12:34:15  brouard
 void free_vector(double*v, int nl, int nh)    (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)(v+nl-NR_END));    of the covariance matrix to be input.
 }  
     Revision 1.89  2003/06/24 12:30:52  brouard
 /************************ivector *******************************/    (Module): Some bugs corrected for windows. Also, when
 int *ivector(long nl,long nh)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Revision 1.88  2003/06/23 17:54:56  brouard
   if (!v) nrerror("allocation failure in ivector");    * 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.
   return v-nl+NR_END;  
 }    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Revision 1.86  2003/06/17 20:04:08  brouard
 {    (Module): Change position of html and gnuplot routines and added
   free((FREE_ARG)(v+nl-NR_END));    routine fileappend.
 }  
     Revision 1.85  2003/06/17 13:12:43  brouard
 /******************* imatrix *******************************/    * imach.c (Repository): Check when date of death was earlier that
 int **imatrix(long nrl, long nrh, long ncl, long nch)    current date of interview. It may happen when the death was just
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    prior to the death. In this case, dh was negative and likelihood
 {    was wrong (infinity). We still send an "Error" but patch by
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    assuming that the date of death was just one stepm after the
   int **m;    interview.
      (Repository): Because some people have very long ID (first column)
   /* allocate pointers to rows */    we changed int to long in num[] and we added a new lvector for
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    memory allocation. But we also truncated to 8 characters (left
   if (!m) nrerror("allocation failure 1 in matrix()");    truncation)
   m += NR_END;    (Repository): No more line truncation errors.
   m -= nrl;  
      Revision 1.84  2003/06/13 21:44:43  brouard
      * imach.c (Repository): Replace "freqsummary" at a correct
   /* allocate rows and set pointers to them */    place. It differs from routine "prevalence" which may be called
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    many times. Probs is memory consuming and must be used with
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    parcimony.
   m[nrl] += NR_END;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   m[nrl] -= ncl;  
      Revision 1.83  2003/06/10 13:39:11  lievre
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    *** empty log message ***
    
   /* return pointer to array of pointers to rows */    Revision 1.82  2003/06/05 15:57:20  brouard
   return m;    Add log in  imach.c and  fullversion number is now printed.
 }  
   */
 /****************** free_imatrix *************************/  /*
 void free_imatrix(m,nrl,nrh,ncl,nch)     Interpolated Markov Chain
       int **m;  
       long nch,ncl,nrh,nrl;    Short summary of the programme:
      /* free an int matrix allocated by imatrix() */    
 {    This program computes Healthy Life Expectancies from
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   free((FREE_ARG) (m+nrl-NR_END));    first survey ("cross") where individuals from different ages are
 }    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
 /******************* matrix *******************************/    second wave of interviews ("longitudinal") which measure each change
 double **matrix(long nrl, long nrh, long ncl, long nch)    (if any) in individual health status.  Health expectancies are
 {    computed from the time spent in each health state according to a
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    model. More health states you consider, more time is necessary to reach the
   double **m;    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    probability to be observed in state j at the second wave
   if (!m) nrerror("allocation failure 1 in matrix()");    conditional to be observed in state i at the first wave. Therefore
   m += NR_END;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   m -= nrl;    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    where the markup *Covariates have to be included here again* invites
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    you to do it.  More covariates you add, slower the
   m[nrl] += NR_END;    convergence.
   m[nrl] -= ncl;  
     The advantage of this computer programme, compared to a simple
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    multinomial logistic model, is clear when the delay between waves is not
   return m;    identical for each individual. Also, if a individual missed an
 }    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    hPijx is the probability to be observed in state i at age x+h
 {    conditional to the observed state i at age x. The delay 'h' can be
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    split into an exact number (nh*stepm) of unobserved intermediate
   free((FREE_ARG)(m+nrl-NR_END));    states. This elementary transition (by month, quarter,
 }    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 /******************* ma3x *******************************/    and the contribution of each individual to the likelihood is simply
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    hPijx.
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Also this programme outputs the covariance matrix of the parameters but also
   double ***m;    of the life expectancies. It also computes the period (stable) prevalence. 
     
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   if (!m) nrerror("allocation failure 1 in matrix()");             Institut national d'études démographiques, Paris.
   m += NR_END;    This software have been partly granted by Euro-REVES, a concerted action
   m -= nrl;    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    software can be distributed freely for non commercial use. Latest version
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    can be accessed at http://euroreves.ined.fr/imach .
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    
     **********************************************************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  /*
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    main
   m[nrl][ncl] += NR_END;    read parameterfile
   m[nrl][ncl] -= nll;    read datafile
   for (j=ncl+1; j<=nch; j++)    concatwav
     m[nrl][j]=m[nrl][j-1]+nlay;    freqsummary
      if (mle >= 1)
   for (i=nrl+1; i<=nrh; i++) {      mlikeli
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    print results files
     for (j=ncl+1; j<=nch; j++)    if mle==1 
       m[i][j]=m[i][j-1]+nlay;       computes hessian
   }    read end of parameter file: agemin, agemax, bage, fage, estepm
   return m;        begin-prev-date,...
 }    open gnuplot file
     open html file
 /*************************free ma3x ************************/    period (stable) prevalence
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)     for age prevalim()
 {    h Pij x
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    variance of p varprob
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    forecasting if prevfcast==1 prevforecast call prevalence()
   free((FREE_ARG)(m+nrl-NR_END));    health expectancies
 }    Variance-covariance of DFLE
     prevalence()
 /***************** f1dim *************************/     movingaverage()
 extern int ncom;    varevsij() 
 extern double *pcom,*xicom;    if popbased==1 varevsij(,popbased)
 extern double (*nrfunc)(double []);    total life expectancies
      Variance of period (stable) prevalence
 double f1dim(double x)   end
 {  */
   int j;  
   double f;  
   double *xt;  
     
   xt=vector(1,ncom);  #include <math.h>
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #include <stdio.h>
   f=(*nrfunc)(xt);  #include <stdlib.h>
   free_vector(xt,1,ncom);  #include <string.h>
   return f;  #include <unistd.h>
 }  
   #include <limits.h>
 /*****************brent *************************/  #include <sys/types.h>
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #include <sys/stat.h>
 {  #include <errno.h>
   int iter;  extern int errno;
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  /* #include <sys/time.h> */
   double ftemp;  #include <time.h>
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #include "timeval.h"
   double e=0.0;  
    /* #include <libintl.h> */
   a=(ax < cx ? ax : cx);  /* #define _(String) gettext (String) */
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  #define MAXLINE 256
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  #define GNUPLOTPROGRAM "gnuplot"
     xm=0.5*(a+b);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #define FILENAMELENGTH 132
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #ifdef DEBUG  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #endif  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  #define NINTERVMAX 8
       return fx;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
     }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
     ftemp=fu;  #define NCOVMAX 8 /* Maximum number of covariates */
     if (fabs(e) > tol1) {  #define MAXN 20000
       r=(x-w)*(fx-fv);  #define YEARM 12. /* Number of months per year */
       q=(x-v)*(fx-fw);  #define AGESUP 130
       p=(x-v)*q-(x-w)*r;  #define AGEBASE 40
       q=2.0*(q-r);  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
       if (q > 0.0) p = -p;  #ifdef UNIX
       q=fabs(q);  #define DIRSEPARATOR '/'
       etemp=e;  #define CHARSEPARATOR "/"
       e=d;  #define ODIRSEPARATOR '\\'
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #else
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define DIRSEPARATOR '\\'
       else {  #define CHARSEPARATOR "\\"
         d=p/q;  #define ODIRSEPARATOR '/'
         u=x+d;  #endif
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  /* $Id$ */
       }  /* $State$ */
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
     }  char fullversion[]="$Revision$ $Date$"; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  char strstart[80];
     fu=(*f)(u);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
     if (fu <= fx) {  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       if (u >= x) a=x; else b=x;  int nvar;
       SHFT(v,w,x,u)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
         SHFT(fv,fw,fx,fu)  int npar=NPARMAX;
         } else {  int nlstate=2; /* Number of live states */
           if (u < x) a=u; else b=u;  int ndeath=1; /* Number of dead states */
           if (fu <= fw || w == x) {  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
             v=w;  int popbased=0;
             w=u;  
             fv=fw;  int *wav; /* Number of waves for this individuual 0 is possible */
             fw=fu;  int maxwav; /* Maxim number of waves */
           } else if (fu <= fv || v == x || v == w) {  int jmin, jmax; /* min, max spacing between 2 waves */
             v=u;  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
             fv=fu;  int gipmx, gsw; /* Global variables on the number of contributions 
           }                     to the likelihood and the sum of weights (done by funcone)*/
         }  int mle, weightopt;
   }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   nrerror("Too many iterations in brent");  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   *xmin=x;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   return fx;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 }  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 /****************** mnbrak ***********************/  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  FILE *ficlog, *ficrespow;
             double (*func)(double))  int globpr; /* Global variable for printing or not */
 {  double fretone; /* Only one call to likelihood */
   double ulim,u,r,q, dum;  long ipmx; /* Number of contributions */
   double fu;  double sw; /* Sum of weights */
    char filerespow[FILENAMELENGTH];
   *fa=(*func)(*ax);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   *fb=(*func)(*bx);  FILE *ficresilk;
   if (*fb > *fa) {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     SHFT(dum,*ax,*bx,dum)  FILE *ficresprobmorprev;
       SHFT(dum,*fb,*fa,dum)  FILE *fichtm, *fichtmcov; /* Html File */
       }  FILE *ficreseij;
   *cx=(*bx)+GOLD*(*bx-*ax);  char filerese[FILENAMELENGTH];
   *fc=(*func)(*cx);  FILE *ficresstdeij;
   while (*fb > *fc) {  char fileresstde[FILENAMELENGTH];
     r=(*bx-*ax)*(*fb-*fc);  FILE *ficrescveij;
     q=(*bx-*cx)*(*fb-*fa);  char filerescve[FILENAMELENGTH];
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  FILE  *ficresvij;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  char fileresv[FILENAMELENGTH];
     ulim=(*bx)+GLIMIT*(*cx-*bx);  FILE  *ficresvpl;
     if ((*bx-u)*(u-*cx) > 0.0) {  char fileresvpl[FILENAMELENGTH];
       fu=(*func)(u);  char title[MAXLINE];
     } else if ((*cx-u)*(u-ulim) > 0.0) {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       fu=(*func)(u);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       if (fu < *fc) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  char command[FILENAMELENGTH];
           SHFT(*fb,*fc,fu,(*func)(u))  int  outcmd=0;
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       u=ulim;  
       fu=(*func)(u);  char filelog[FILENAMELENGTH]; /* Log file */
     } else {  char filerest[FILENAMELENGTH];
       u=(*cx)+GOLD*(*cx-*bx);  char fileregp[FILENAMELENGTH];
       fu=(*func)(u);  char popfile[FILENAMELENGTH];
     }  
     SHFT(*ax,*bx,*cx,u)  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       SHFT(*fa,*fb,*fc,fu)  
       }  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 }  struct timezone tzp;
   extern int gettimeofday();
 /*************** linmin ************************/  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
 int ncom;  extern long time();
 double *pcom,*xicom;  char strcurr[80], strfor[80];
 double (*nrfunc)(double []);  
    char *endptr;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  long lval;
 {  double dval;
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  #define NR_END 1
   double f1dim(double x);  #define FREE_ARG char*
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  #define FTOL 1.0e-10
               double *fc, double (*func)(double));  
   int j;  #define NRANSI 
   double xx,xmin,bx,ax;  #define ITMAX 200 
   double fx,fb,fa;  
    #define TOL 2.0e-4 
   ncom=n;  
   pcom=vector(1,n);  #define CGOLD 0.3819660 
   xicom=vector(1,n);  #define ZEPS 1.0e-10 
   nrfunc=func;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  #define GOLD 1.618034 
     xicom[j]=xi[j];  #define GLIMIT 100.0 
   }  #define TINY 1.0e-20 
   ax=0.0;  
   xx=1.0;  static double maxarg1,maxarg2;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 #ifdef DEBUG    
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #endif  #define rint(a) floor(a+0.5)
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  static double sqrarg;
     p[j] += xi[j];  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   free_vector(xicom,1,n);  int agegomp= AGEGOMP;
   free_vector(pcom,1,n);  
 }  int imx; 
   int stepm=1;
 /*************** powell ************************/  /* Stepm, step in month: minimum step interpolation*/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  int estepm;
 {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));  int m,nb;
   int i,ibig,j;  long *num;
   double del,t,*pt,*ptt,*xit;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double fp,fptt;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double *xits;  double **pmmij, ***probs;
   pt=vector(1,n);  double *ageexmed,*agecens;
   ptt=vector(1,n);  double dateintmean=0;
   xit=vector(1,n);  
   xits=vector(1,n);  double *weight;
   *fret=(*func)(p);  int **s; /* Status */
   for (j=1;j<=n;j++) pt[j]=p[j];  double *agedc, **covar, idx;
   for (*iter=1;;++(*iter)) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     fp=(*fret);  double *lsurv, *lpop, *tpop;
     ibig=0;  
     del=0.0;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  double ftolhess; /* Tolerance for computing hessian */
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  /**************** split *************************/
     printf("\n");  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     for (i=1;i<=n;i++) {  {
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       fptt=(*fret);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 #ifdef DEBUG    */ 
       printf("fret=%lf \n",*fret);    char  *ss;                            /* pointer */
 #endif    int   l1, l2;                         /* length counters */
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);    l1 = strlen(path );                   /* length of path */
       if (fabs(fptt-(*fret)) > del) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         del=fabs(fptt-(*fret));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
         ibig=i;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       }      strcpy( name, path );               /* we got the fullname name because no directory */
 #ifdef DEBUG      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       printf("%d %.12e",i,(*fret));        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       for (j=1;j<=n;j++) {      /* get current working directory */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      /*    extern  char* getcwd ( char *buf , int len);*/
         printf(" x(%d)=%.12e",j,xit[j]);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       }        return( GLOCK_ERROR_GETCWD );
       for(j=1;j<=n;j++)      }
         printf(" p=%.12e",p[j]);      /* got dirc from getcwd*/
       printf("\n");      printf(" DIRC = %s \n",dirc);
 #endif    } else {                              /* strip direcotry from path */
     }      ss++;                               /* after this, the filename */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      l2 = strlen( ss );                  /* length of filename */
 #ifdef DEBUG      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       int k[2],l;      strcpy( name, ss );         /* save file name */
       k[0]=1;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       k[1]=-1;      dirc[l1-l2] = 0;                    /* add zero */
       printf("Max: %.12e",(*func)(p));      printf(" DIRC2 = %s \n",dirc);
       for (j=1;j<=n;j++)    }
         printf(" %.12e",p[j]);    /* We add a separator at the end of dirc if not exists */
       printf("\n");    l1 = strlen( dirc );                  /* length of directory */
       for(l=0;l<=1;l++) {    if( dirc[l1-1] != DIRSEPARATOR ){
         for (j=1;j<=n;j++) {      dirc[l1] =  DIRSEPARATOR;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      dirc[l1+1] = 0; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      printf(" DIRC3 = %s \n",dirc);
         }    }
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    ss = strrchr( name, '.' );            /* find last / */
       }    if (ss >0){
 #endif      ss++;
       strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
       free_vector(xit,1,n);      l2= strlen(ss)+1;
       free_vector(xits,1,n);      strncpy( finame, name, l1-l2);
       free_vector(ptt,1,n);      finame[l1-l2]= 0;
       free_vector(pt,1,n);    }
       return;  
     }    return( 0 );                          /* we're done */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  }
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  /******************************************/
       pt[j]=p[j];  
     }  void replace_back_to_slash(char *s, char*t)
     fptt=(*func)(ptt);  {
     if (fptt < fp) {    int i;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    int lg=0;
       if (t < 0.0) {    i=0;
         linmin(p,xit,n,fret,func);    lg=strlen(t);
         for (j=1;j<=n;j++) {    for(i=0; i<= lg; i++) {
           xi[j][ibig]=xi[j][n];      (s[i] = t[i]);
           xi[j][n]=xit[j];      if (t[i]== '\\') s[i]='/';
         }    }
 #ifdef DEBUG  }
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)  int nbocc(char *s, char occ)
           printf(" %.12e",xit[j]);  {
         printf("\n");    int i,j=0;
 #endif    int lg=20;
       }    i=0;
     }    lg=strlen(s);
   }    for(i=0; i<= lg; i++) {
 }    if  (s[i] == occ ) j++;
     }
 /**** Prevalence limit ****************/    return j;
   }
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {  void cutv(char *u,char *v, char*t, char occ)
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  {
      matrix by transitions matrix until convergence is reached */    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
        and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   int i, ii,j,k;       gives u="abcedf" and v="ghi2j" */
   double min, max, maxmin, maxmax,sumnew=0.;    int i,lg,j,p=0;
   double **matprod2();    i=0;
   double **out, cov[NCOVMAX], **pmij();    for(j=0; j<=strlen(t)-1; j++) {
   double **newm;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   double agefin, delaymax=50 ; /* Max number of years to converge */    }
   
   for (ii=1;ii<=nlstate+ndeath;ii++)    lg=strlen(t);
     for (j=1;j<=nlstate+ndeath;j++){    for(j=0; j<p; j++) {
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      (u[j] = t[j]);
     }    }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */       u[p]='\0';
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;     for(j=0; j<= lg; j++) {
     /* Covariates have to be included here again */      if (j>=(p+1))(v[j-p-1] = t[j]);
     cov[1]=1.;    }
     cov[2]=agefin;  }
     if (cptcovn>0){  
       for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}  /********************** nrerror ********************/
     }  
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  void nrerror(char error_text[])
   {
     savm=oldm;    fprintf(stderr,"ERREUR ...\n");
     oldm=newm;    fprintf(stderr,"%s\n",error_text);
     maxmax=0.;    exit(EXIT_FAILURE);
     for(j=1;j<=nlstate;j++){  }
       min=1.;  /*********************** vector *******************/
       max=0.;  double *vector(int nl, int nh)
       for(i=1; i<=nlstate; i++) {  {
         sumnew=0;    double *v;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
         prlim[i][j]= newm[i][j]/(1-sumnew);    if (!v) nrerror("allocation failure in vector");
         max=FMAX(max,prlim[i][j]);    return v-nl+NR_END;
         min=FMIN(min,prlim[i][j]);  }
       }  
       maxmin=max-min;  /************************ free vector ******************/
       maxmax=FMAX(maxmax,maxmin);  void free_vector(double*v, int nl, int nh)
     }  {
     if(maxmax < ftolpl){    free((FREE_ARG)(v+nl-NR_END));
       return prlim;  }
     }  
   }  /************************ivector *******************************/
 }  int *ivector(long nl,long nh)
   {
 /*************** transition probabilities **********/    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    if (!v) nrerror("allocation failure in ivector");
 {    return v-nl+NR_END;
   double s1, s2;  }
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
     for(i=1; i<= nlstate; i++){  {
     for(j=1; j<i;j++){    free((FREE_ARG)(v+nl-NR_END));
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  }
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /************************lvector *******************************/
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  long *lvector(long nl,long nh)
       }  {
       ps[i][j]=s2;    long *v;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     }    if (!v) nrerror("allocation failure in ivector");
     for(j=i+1; j<=nlstate+ndeath;j++){    return v-nl+NR_END;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  /******************free lvector **************************/
       }  void free_lvector(long *v, long nl, long nh)
       ps[i][j]=s2;  {
     }    free((FREE_ARG)(v+nl-NR_END));
   }  }
   for(i=1; i<= nlstate; i++){  
      s1=0;  /******************* imatrix *******************************/
     for(j=1; j<i; j++)  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       s1+=exp(ps[i][j]);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     for(j=i+1; j<=nlstate+ndeath; j++)  { 
       s1+=exp(ps[i][j]);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     ps[i][i]=1./(s1+1.);    int **m; 
     for(j=1; j<i; j++)    
       ps[i][j]= exp(ps[i][j])*ps[i][i];    /* allocate pointers to rows */ 
     for(j=i+1; j<=nlstate+ndeath; j++)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    if (!m) nrerror("allocation failure 1 in matrix()"); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    m += NR_END; 
   } /* end i */    m -= nrl; 
     
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    
     for(jj=1; jj<= nlstate+ndeath; jj++){    /* allocate rows and set pointers to them */ 
       ps[ii][jj]=0;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       ps[ii][ii]=1;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     }    m[nrl] += NR_END; 
   }    m[nrl] -= ncl; 
     
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    
      printf("%lf ",ps[ii][jj]);    /* return pointer to array of pointers to rows */ 
    }    return m; 
     printf("\n ");  } 
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  /****************** free_imatrix *************************/
 /*  void free_imatrix(m,nrl,nrh,ncl,nch)
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        int **m;
   goto end;*/        long nch,ncl,nrh,nrl; 
     return ps;       /* free an int matrix allocated by imatrix() */ 
 }  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 /**************** Product of 2 matrices ******************/    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  
 {  /******************* matrix *******************************/
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  double **matrix(long nrl, long nrh, long ncl, long nch)
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  {
   /* in, b, out are matrice of pointers which should have been initialized    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
      before: only the contents of out is modified. The function returns    double **m;
      a pointer to pointers identical to out */  
   long i, j, k;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for(i=nrl; i<= nrh; i++)    if (!m) nrerror("allocation failure 1 in matrix()");
     for(k=ncolol; k<=ncoloh; k++)    m += NR_END;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    m -= nrl;
         out[i][k] +=in[i][j]*b[j][k];  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   return out;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
   
 /************* Higher Matrix Product ***************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 {     */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  }
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  /*************************free matrix ************************/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
      (typically every 2 years instead of every month which is too big).  {
      Model is determined by parameters x and covariates have to be    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      included manually here.    free((FREE_ARG)(m+nrl-NR_END));
   }
      */  
   /******************* ma3x *******************************/
   int i, j, d, h, k;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   double **out, cov[NCOVMAX];  {
   double **newm;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for (j=1;j<=nlstate+ndeath;j++){    if (!m) nrerror("allocation failure 1 in matrix()");
       oldm[i][j]=(i==j ? 1.0 : 0.0);    m += NR_END;
       po[i][j][0]=(i==j ? 1.0 : 0.0);    m -= nrl;
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for(h=1; h <=nhstepm; h++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for(d=1; d <=hstepm; d++){    m[nrl] += NR_END;
       newm=savm;    m[nrl] -= ncl;
       /* Covariates have to be included here again */  
       cov[1]=1.;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       if (cptcovn>0){    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     }    m[nrl][ncl] += NR_END;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    m[nrl][ncl] -= nll;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    for (j=ncl+1; j<=nch; j++) 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      m[nrl][j]=m[nrl][j-1]+nlay;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    
       savm=oldm;    for (i=nrl+1; i<=nrh; i++) {
       oldm=newm;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     }      for (j=ncl+1; j<=nch; j++) 
     for(i=1; i<=nlstate+ndeath; i++)        m[i][j]=m[i][j-1]+nlay;
       for(j=1;j<=nlstate+ndeath;j++) {    }
         po[i][j][h]=newm[i][j];    return m; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
          */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       }    */
   } /* end h */  }
   return po;  
 }  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
 /*************** log-likelihood *************/    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 double func( double *x)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   int i, ii, j, k, mi, d;  }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;  /*************** function subdirf ***********/
   double sw; /* Sum of weights */  char *subdirf(char fileres[])
   double lli; /* Individual log likelihood */  {
   long ipmx;    /* Caution optionfilefiname is hidden */
   /*extern weight */    strcpy(tmpout,optionfilefiname);
   /* We are differentiating ll according to initial status */    strcat(tmpout,"/"); /* Add to the right */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    strcat(tmpout,fileres);
   /*for(i=1;i<imx;i++)    return tmpout;
 printf(" %d\n",s[4][i]);  }
   */  
   /*************** function subdirf2 ***********/
   for(k=1; k<=nlstate; k++) ll[k]=0.;  char *subdirf2(char fileres[], char *preop)
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  {
        for(mi=1; mi<= wav[i]-1; mi++){    
       for (ii=1;ii<=nlstate+ndeath;ii++)    /* Caution optionfilefiname is hidden */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    strcpy(tmpout,optionfilefiname);
             for(d=0; d<dh[mi][i]; d++){    strcat(tmpout,"/");
         newm=savm;    strcat(tmpout,preop);
           cov[1]=1.;    strcat(tmpout,fileres);
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return tmpout;
           if (cptcovn>0){  }
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];  
             }  /*************** function subdirf3 ***********/
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  char *subdirf3(char fileres[], char *preop, char *preop2)
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  {
           savm=oldm;    
           oldm=newm;    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
       } /* end mult */    strcat(tmpout,preop);
        strcat(tmpout,preop2);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    strcat(tmpout,fileres);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    return tmpout;
       ipmx +=1;  }
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  /***************** f1dim *************************/
     } /* end of wave */  extern int ncom; 
   } /* end of individual */  extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];   
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  double f1dim(double x) 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  { 
   return -l;    int j; 
 }    double f;
     double *xt; 
    
 /*********** Maximum Likelihood Estimation ***************/    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    f=(*nrfunc)(xt); 
 {    free_vector(xt,1,ncom); 
   int i,j, iter;    return f; 
   double **xi,*delti;  } 
   double fret;  
   xi=matrix(1,npar,1,npar);  /*****************brent *************************/
   for (i=1;i<=npar;i++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     for (j=1;j<=npar;j++)  { 
       xi[i][j]=(i==j ? 1.0 : 0.0);    int iter; 
   printf("Powell\n");    double a,b,d,etemp;
   powell(p,xi,npar,ftol,&iter,&fret,func);    double fu,fv,fw,fx;
     double ftemp;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    double e=0.0; 
    
 }    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
 /**** Computes Hessian and covariance matrix ***/    x=w=v=bx; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    fw=fv=fx=(*f)(x); 
 {    for (iter=1;iter<=ITMAX;iter++) { 
   double  **a,**y,*x,pd;      xm=0.5*(a+b); 
   double **hess;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   int i, j,jk;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   int *indx;      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
   double hessii(double p[], double delta, int theta, double delti[]);  #ifdef DEBUG
   double hessij(double p[], double delti[], int i, int 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);
   void lubksb(double **a, int npar, int *indx, double b[]) ;      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);
   void ludcmp(double **a, int npar, int *indx, double *d) ;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   hess=matrix(1,npar,1,npar);        *xmin=x; 
         return fx; 
   printf("\nCalculation of the hessian matrix. Wait...\n");      } 
   for (i=1;i<=npar;i++){      ftemp=fu;
     printf("%d",i);fflush(stdout);      if (fabs(e) > tol1) { 
     hess[i][i]=hessii(p,ftolhess,i,delti);        r=(x-w)*(fx-fv); 
     /*printf(" %f ",p[i]);*/        q=(x-v)*(fx-fw); 
   }        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
   for (i=1;i<=npar;i++) {        if (q > 0.0) p = -p; 
     for (j=1;j<=npar;j++)  {        q=fabs(q); 
       if (j>i) {        etemp=e; 
         printf(".%d%d",i,j);fflush(stdout);        e=d; 
         hess[i][j]=hessij(p,delti,i,j);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         hess[j][i]=hess[i][j];          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }        else { 
     }          d=p/q; 
   }          u=x+d; 
   printf("\n");          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        } 
        } else { 
   a=matrix(1,npar,1,npar);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   y=matrix(1,npar,1,npar);      } 
   x=vector(1,npar);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   indx=ivector(1,npar);      fu=(*f)(u); 
   for (i=1;i<=npar;i++)      if (fu <= fx) { 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        if (u >= x) a=x; else b=x; 
   ludcmp(a,npar,indx,&pd);        SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
   for (j=1;j<=npar;j++) {          } else { 
     for (i=1;i<=npar;i++) x[i]=0;            if (u < x) a=u; else b=u; 
     x[j]=1;            if (fu <= fw || w == x) { 
     lubksb(a,npar,indx,x);              v=w; 
     for (i=1;i<=npar;i++){              w=u; 
       matcov[i][j]=x[i];              fv=fw; 
     }              fw=fu; 
   }            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
   printf("\n#Hessian matrix#\n");              fv=fu; 
   for (i=1;i<=npar;i++) {            } 
     for (j=1;j<=npar;j++) {          } 
       printf("%.3e ",hess[i][j]);    } 
     }    nrerror("Too many iterations in brent"); 
     printf("\n");    *xmin=x; 
   }    return fx; 
   } 
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  /****************** mnbrak ***********************/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
   /*  printf("\n#Hessian matrix recomputed#\n");  { 
     double ulim,u,r,q, dum;
   for (j=1;j<=npar;j++) {    double fu; 
     for (i=1;i<=npar;i++) x[i]=0;   
     x[j]=1;    *fa=(*func)(*ax); 
     lubksb(a,npar,indx,x);    *fb=(*func)(*bx); 
     for (i=1;i<=npar;i++){    if (*fb > *fa) { 
       y[i][j]=x[i];      SHFT(dum,*ax,*bx,dum) 
       printf("%.3e ",y[i][j]);        SHFT(dum,*fb,*fa,dum) 
     }        } 
     printf("\n");    *cx=(*bx)+GOLD*(*bx-*ax); 
   }    *fc=(*func)(*cx); 
   */    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
   free_matrix(a,1,npar,1,npar);      q=(*bx-*cx)*(*fb-*fa); 
   free_matrix(y,1,npar,1,npar);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   free_vector(x,1,npar);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   free_ivector(indx,1,npar);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   free_matrix(hess,1,npar,1,npar);      if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
 }        fu=(*func)(u); 
         if (fu < *fc) { 
 /*************** hessian matrix ****************/          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 double hessii( double x[], double delta, int theta, double delti[])            SHFT(*fb,*fc,fu,(*func)(u)) 
 {            } 
   int i;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   int l=1, lmax=20;        u=ulim; 
   double k1,k2;        fu=(*func)(u); 
   double p2[NPARMAX+1];      } else { 
   double res;        u=(*cx)+GOLD*(*cx-*bx); 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        fu=(*func)(u); 
   double fx;      } 
   int k=0,kmax=10;      SHFT(*ax,*bx,*cx,u) 
   double l1;        SHFT(*fa,*fb,*fc,fu) 
         } 
   fx=func(x);  } 
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){  /*************** linmin ************************/
     l1=pow(10,l);  
     delts=delt;  int ncom; 
     for(k=1 ; k <kmax; k=k+1){  double *pcom,*xicom;
       delt = delta*(l1*k);  double (*nrfunc)(double []); 
       p2[theta]=x[theta] +delt;   
       k1=func(p2)-fx;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       p2[theta]=x[theta]-delt;  { 
       k2=func(p2)-fx;    double brent(double ax, double bx, double cx, 
       /*res= (k1-2.0*fx+k2)/delt/delt; */                 double (*f)(double), double tol, double *xmin); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    double f1dim(double x); 
          void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 #ifdef DEBUG                double *fc, double (*func)(double)); 
       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);    int j; 
 #endif    double xx,xmin,bx,ax; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    double fx,fb,fa;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){   
         k=kmax;    ncom=n; 
       }    pcom=vector(1,n); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    xicom=vector(1,n); 
         k=kmax; l=lmax*10.;    nrfunc=func; 
       }    for (j=1;j<=n;j++) { 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      pcom[j]=p[j]; 
         delts=delt;      xicom[j]=xi[j]; 
       }    } 
     }    ax=0.0; 
   }    xx=1.0; 
   delti[theta]=delts;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   return res;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
    #ifdef DEBUG
 }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 double hessij( double x[], double delti[], int thetai,int thetaj)  #endif
 {    for (j=1;j<=n;j++) { 
   int i;      xi[j] *= xmin; 
   int l=1, l1, lmax=20;      p[j] += xi[j]; 
   double k1,k2,k3,k4,res,fx;    } 
   double p2[NPARMAX+1];    free_vector(xicom,1,n); 
   int k;    free_vector(pcom,1,n); 
   } 
   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,"%d day(s) %d hour(s) %d minute(s) %d 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;  
    /*************** powell ************************/
     p2[thetai]=x[thetai]-delti[thetai]/k;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;              double (*func)(double [])) 
     k4=func(p2)-fx;  { 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    void linmin(double p[], double xi[], int n, double *fret, 
 #ifdef DEBUG                double (*func)(double [])); 
     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);    int i,ibig,j; 
 #endif    double del,t,*pt,*ptt,*xit;
   }    double fp,fptt;
   return res;    double *xits;
 }    int niterf, itmp;
   
 /************** Inverse of matrix **************/    pt=vector(1,n); 
 void ludcmp(double **a, int n, int *indx, double *d)    ptt=vector(1,n); 
 {    xit=vector(1,n); 
   int i,imax,j,k;    xits=vector(1,n); 
   double big,dum,sum,temp;    *fret=(*func)(p); 
   double *vv;    for (j=1;j<=n;j++) pt[j]=p[j]; 
      for (*iter=1;;++(*iter)) { 
   vv=vector(1,n);      fp=(*fret); 
   *d=1.0;      ibig=0; 
   for (i=1;i<=n;i++) {      del=0.0; 
     big=0.0;      last_time=curr_time;
     for (j=1;j<=n;j++)      (void) gettimeofday(&curr_time,&tzp);
       if ((temp=fabs(a[i][j])) > big) big=temp;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
     vv[i]=1.0/big;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
   }     for (i=1;i<=n;i++) {
   for (j=1;j<=n;j++) {        printf(" %d %.12f",i, p[i]);
     for (i=1;i<j;i++) {        fprintf(ficlog," %d %.12lf",i, p[i]);
       sum=a[i][j];        fprintf(ficrespow," %.12lf", p[i]);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      }
       a[i][j]=sum;      printf("\n");
     }      fprintf(ficlog,"\n");
     big=0.0;      fprintf(ficrespow,"\n");fflush(ficrespow);
     for (i=j;i<=n;i++) {      if(*iter <=3){
       sum=a[i][j];        tm = *localtime(&curr_time.tv_sec);
       for (k=1;k<j;k++)        strcpy(strcurr,asctime(&tm));
         sum -= a[i][k]*a[k][j];  /*       asctime_r(&tm,strcurr); */
       a[i][j]=sum;        forecast_time=curr_time; 
       if ( (dum=vv[i]*fabs(sum)) >= big) {        itmp = strlen(strcurr);
         big=dum;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         imax=i;          strcurr[itmp-1]='\0';
       }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     if (j != imax) {        for(niterf=10;niterf<=30;niterf+=10){
       for (k=1;k<=n;k++) {          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
         dum=a[imax][k];          tmf = *localtime(&forecast_time.tv_sec);
         a[imax][k]=a[j][k];  /*      asctime_r(&tmf,strfor); */
         a[j][k]=dum;          strcpy(strfor,asctime(&tmf));
       }          itmp = strlen(strfor);
       *d = -(*d);          if(strfor[itmp-1]=='\n')
       vv[imax]=vv[j];          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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     indx[j]=imax;          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     if (a[j][j] == 0.0) a[j][j]=TINY;        }
     if (j != n) {      }
       dum=1.0/(a[j][j]);      for (i=1;i<=n;i++) { 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     }        fptt=(*fret); 
   }  #ifdef DEBUG
   free_vector(vv,1,n);  /* Doesn't work */        printf("fret=%lf \n",*fret);
 ;        fprintf(ficlog,"fret=%lf \n",*fret);
 }  #endif
         printf("%d",i);fflush(stdout);
 void lubksb(double **a, int n, int *indx, double b[])        fprintf(ficlog,"%d",i);fflush(ficlog);
 {        linmin(p,xit,n,fret,func); 
   int i,ii=0,ip,j;        if (fabs(fptt-(*fret)) > del) { 
   double sum;          del=fabs(fptt-(*fret)); 
            ibig=i; 
   for (i=1;i<=n;i++) {        } 
     ip=indx[i];  #ifdef DEBUG
     sum=b[ip];        printf("%d %.12e",i,(*fret));
     b[ip]=b[i];        fprintf(ficlog,"%d %.12e",i,(*fret));
     if (ii)        for (j=1;j<=n;j++) {
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     else if (sum) ii=i;          printf(" x(%d)=%.12e",j,xit[j]);
     b[i]=sum;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   }        }
   for (i=n;i>=1;i--) {        for(j=1;j<=n;j++) {
     sum=b[i];          printf(" p=%.12e",p[j]);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          fprintf(ficlog," p=%.12e",p[j]);
     b[i]=sum/a[i][i];        }
   }        printf("\n");
 }        fprintf(ficlog,"\n");
   #endif
 /************ Frequencies ********************/      } 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 {  /* Some frequencies */  #ifdef DEBUG
          int k[2],l;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        k[0]=1;
   double ***freq; /* Frequencies */        k[1]=-1;
   double *pp;        printf("Max: %.12e",(*func)(p));
   double pos;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   FILE *ficresp;        for (j=1;j<=n;j++) {
   char fileresp[FILENAMELENGTH];          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
   pp=vector(1,nlstate);        }
         printf("\n");
   strcpy(fileresp,"p");        fprintf(ficlog,"\n");
   strcat(fileresp,fileres);        for(l=0;l<=1;l++) {
   if((ficresp=fopen(fileresp,"w"))==NULL) {          for (j=1;j<=n;j++) {
     printf("Problem with prevalence resultfile: %s\n", fileresp);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     exit(0);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          }
   j1=0;          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)));
   j=cptcovn;        }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  #endif
   
   for(k1=1; k1<=j;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){        free_vector(xit,1,n); 
        j1++;        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
         for (i=-1; i<=nlstate+ndeath; i++)          free_vector(pt,1,n); 
          for (jk=-1; jk<=nlstate+ndeath; jk++)          return; 
            for(m=agemin; m <= agemax+3; m++)      } 
              freq[i][jk][m]=0;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
              for (j=1;j<=n;j++) { 
        for (i=1; i<=imx; i++) {        ptt[j]=2.0*p[j]-pt[j]; 
          bool=1;        xit[j]=p[j]-pt[j]; 
          if  (cptcovn>0) {        pt[j]=p[j]; 
            for (z1=1; z1<=cptcovn; z1++)      } 
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;      fptt=(*func)(ptt); 
          }      if (fptt < fp) { 
           if (bool==1) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
            for(m=firstpass; m<=lastpass-1; m++){        if (t < 0.0) { 
              if(agev[m][i]==0) agev[m][i]=agemax+1;          linmin(p,xit,n,fret,func); 
              if(agev[m][i]==1) agev[m][i]=agemax+2;          for (j=1;j<=n;j++) { 
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            xi[j][ibig]=xi[j][n]; 
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            xi[j][n]=xit[j]; 
            }          }
          }  #ifdef DEBUG
        }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         if  (cptcovn>0) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
          fprintf(ficresp, "\n#Variable");          for(j=1;j<=n;j++){
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);            printf(" %.12e",xit[j]);
        }            fprintf(ficlog," %.12e",xit[j]);
        fprintf(ficresp, "\n#");          }
        for(i=1; i<=nlstate;i++)          printf("\n");
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          fprintf(ficlog,"\n");
        fprintf(ficresp, "\n");  #endif
                }
   for(i=(int)agemin; i <= (int)agemax+3; i++){      } 
     if(i==(int)agemax+3)    } 
       printf("Total");  } 
     else  
       printf("Age %d", i);  /**** Prevalence limit (stable or period prevalence)  ****************/
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         pp[jk] += freq[jk][m][i];  {
     }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     for(jk=1; jk <=nlstate ; jk++){       matrix by transitions matrix until convergence is reached */
       for(m=-1, pos=0; m <=0 ; m++)  
         pos += freq[jk][m][i];    int i, ii,j,k;
       if(pp[jk]>=1.e-10)    double min, max, maxmin, maxmax,sumnew=0.;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    double **matprod2();
       else    double **out, cov[NCOVMAX], **pmij();
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    double **newm;
     }    double agefin, delaymax=50 ; /* Max number of years to converge */
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)    for (ii=1;ii<=nlstate+ndeath;ii++)
         pp[jk] += freq[jk][m][i];      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(jk=1,pos=0; jk <=nlstate ; jk++)      }
       pos += pp[jk];  
     for(jk=1; jk <=nlstate ; jk++){     cov[1]=1.;
       if(pos>=1.e-5)   
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       else    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      newm=savm;
       if( i <= (int) agemax){      /* Covariates have to be included here again */
         if(pos>=1.e-5)       cov[2]=agefin;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    
       else        for (k=1; k<=cptcovn;k++) {
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       }          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     }        }
     for(jk=-1; jk <=nlstate+ndeath; jk++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for(m=-1; m <=nlstate+ndeath; m++)        for (k=1; k<=cptcovprod;k++)
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     printf("\n");        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
  }  
        savm=oldm;
   fclose(ficresp);      oldm=newm;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      maxmax=0.;
   free_vector(pp,1,nlstate);      for(j=1;j<=nlstate;j++){
         min=1.;
 }  /* End of Freq */        max=0.;
         for(i=1; i<=nlstate; i++) {
 /************* Waves Concatenation ***************/          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          prlim[i][j]= newm[i][j]/(1-sumnew);
 {          max=FMAX(max,prlim[i][j]);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          min=FMIN(min,prlim[i][j]);
      Death is a valid wave (if date is known).        }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        maxmin=max-min;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        maxmax=FMAX(maxmax,maxmin);
      and mw[mi+1][i]. dh depends on stepm.      }
      */      if(maxmax < ftolpl){
         return prlim;
   int i, mi, m;      }
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    }
 float sum=0.;  }
   
   for(i=1; i<=imx; i++){  /*************** transition probabilities ***************/ 
     mi=0;  
     m=firstpass;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     while(s[m][i] <= nlstate){  {
       if(s[m][i]>=1)    double s1, s2;
         mw[++mi][i]=m;    /*double t34;*/
       if(m >=lastpass)    int i,j,j1, nc, ii, jj;
         break;  
       else      for(i=1; i<= nlstate; i++){
         m++;        for(j=1; j<i;j++){
     }/* end while */          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     if (s[m][i] > nlstate){            /*s2 += param[i][j][nc]*cov[nc];*/
       mi++;     /* Death is another wave */            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       /* if(mi==0)  never been interviewed correctly before death */  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
          /* Only death is a correct wave */          }
       mw[mi][i]=m;          ps[i][j]=s2;
     }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         }
     wav[i]=mi;        for(j=i+1; j<=nlstate+ndeath;j++){
     if(mi==0)          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   }  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
           }
   for(i=1; i<=imx; i++){          ps[i][j]=s2;
     for(mi=1; mi<wav[i];mi++){        }
       if (stepm <=0)      }
         dh[mi][i]=1;      /*ps[3][2]=1;*/
       else{      
         if (s[mw[mi+1][i]][i] > nlstate) {      for(i=1; i<= nlstate; i++){
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        s1=0;
           if(j=0) j=1;  /* Survives at least one month after exam */        for(j=1; j<i; j++)
         }          s1+=exp(ps[i][j]);
         else{        for(j=i+1; j<=nlstate+ndeath; j++)
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          s1+=exp(ps[i][j]);
           k=k+1;        ps[i][i]=1./(s1+1.);
           if (j >= jmax) jmax=j;        for(j=1; j<i; j++)
           else if (j <= jmin)jmin=j;          ps[i][j]= exp(ps[i][j])*ps[i][i];
           sum=sum+j;        for(j=i+1; j<=nlstate+ndeath; j++)
         }          ps[i][j]= exp(ps[i][j])*ps[i][i];
         jk= j/stepm;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         jl= j -jk*stepm;      } /* end i */
         ju= j -(jk+1)*stepm;      
         if(jl <= -ju)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
           dh[mi][i]=jk;        for(jj=1; jj<= nlstate+ndeath; jj++){
         else          ps[ii][jj]=0;
           dh[mi][i]=jk+1;          ps[ii][ii]=1;
         if(dh[mi][i]==0)        }
           dh[mi][i]=1; /* At least one step */      }
       }      
     }  
   }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
 }  /*         printf("ddd %lf ",ps[ii][jj]); */
 /*********** Tricode ****************************/  /*       } */
 void tricode(int *Tvar, int **nbcode, int imx)  /*       printf("\n "); */
 {  /*        } */
   int Ndum[80],ij, k, j, i;  /*        printf("\n ");printf("%lf ",cov[2]); */
   int cptcode=0;         /*
   for (k=0; k<79; k++) Ndum[k]=0;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for (k=1; k<=7; k++) ncodemax[k]=0;        goto end;*/
        return ps;
   for (j=1; j<=cptcovn; j++) {  }
     for (i=1; i<=imx; i++) {  
       ij=(int)(covar[Tvar[j]][i]);  /**************** Product of 2 matrices ******************/
       Ndum[ij]++;  
       if (ij > cptcode) cptcode=ij;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     }  {
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     for (i=0; i<=cptcode; i++) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       if(Ndum[i]!=0) ncodemax[j]++;    /* in, b, out are matrice of pointers which should have been initialized 
     }       before: only the contents of out is modified. The function returns
         a pointer to pointers identical to out */
     ij=1;    long i, j, k;
     for (i=1; i<=ncodemax[j]; i++) {    for(i=nrl; i<= nrh; i++)
       for (k=0; k<=79; k++) {      for(k=ncolol; k<=ncoloh; k++)
         if (Ndum[k] != 0) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           nbcode[Tvar[j]][ij]=k;          out[i][k] +=in[i][j]*b[j][k];
           ij++;  
         }    return out;
         if (ij > ncodemax[j]) break;  }
       }    
     }  
   }    /************* Higher Matrix Product ***************/
   
   }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
 /*********** Health Expectancies ****************/    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 {       nhstepm*hstepm matrices. 
   /* Health expectancies */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   int i, j, nhstepm, hstepm, h;       (typically every 2 years instead of every month which is too big 
   double age, agelim,hf;       for the memory).
   double ***p3mat;       Model is determined by parameters x and covariates have to be 
         included manually here. 
   fprintf(ficreseij,"# Health expectancies\n");  
   fprintf(ficreseij,"# Age");       */
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)    int i, j, d, h, k;
       fprintf(ficreseij," %1d-%1d",i,j);    double **out, cov[NCOVMAX];
   fprintf(ficreseij,"\n");    double **newm;
   
   hstepm=1*YEARM; /*  Every j years of age (in month) */    /* Hstepm could be zero and should return the unit matrix */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   agelim=AGESUP;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        po[i][j][0]=(i==j ? 1.0 : 0.0);
     /* nhstepm age range expressed in number of stepm */      }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* Typically if 20 years = 20*12/6=40 stepm */    for(h=1; h <=nhstepm; h++){
     if (stepm >= YEARM) hstepm=1;      for(d=1; d <=hstepm; d++){
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        newm=savm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* Covariates have to be included here again */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        cov[1]=1.;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovprod;k++)
       for(j=1; j<=nlstate;j++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){  
           eij[i][j][(int)age] +=p3mat[i][j][h];  
         }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
            /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     hf=1;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     if (stepm >= YEARM) hf=stepm/YEARM;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     fprintf(ficreseij,"%.0f",age );        savm=oldm;
     for(i=1; i<=nlstate;i++)        oldm=newm;
       for(j=1; j<=nlstate;j++){      }
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);      for(i=1; i<=nlstate+ndeath; i++)
       }        for(j=1;j<=nlstate+ndeath;j++) {
     fprintf(ficreseij,"\n");          po[i][j][h]=newm[i][j];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   }        }
 }      /*printf("h=%d ",h);*/
     } /* end h */
 /************ Variance ******************/  /*     printf("\n H=%d \n",h); */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    return po;
 {  }
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;  /*************** log-likelihood *************/
   double **dnewm,**doldm;  double func( double *x)
   int i, j, nhstepm, hstepm, h;  {
   int k, cptcode;    int i, ii, j, k, mi, d, kk;
    double *xp;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double **gp, **gm;    double **out;
   double ***gradg, ***trgradg;    double sw; /* Sum of weights */
   double ***p3mat;    double lli; /* Individual log likelihood */
   double age,agelim;    int s1, s2;
   int theta;    double bbh, survp;
     long ipmx;
    fprintf(ficresvij,"# Covariances of life expectancies\n");    /*extern weight */
   fprintf(ficresvij,"# Age");    /* We are differentiating ll according to initial status */
   for(i=1; i<=nlstate;i++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(j=1; j<=nlstate;j++)    /*for(i=1;i<imx;i++) 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      printf(" %d\n",s[4][i]);
   fprintf(ficresvij,"\n");    */
     cov[1]=1.;
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   doldm=matrix(1,nlstate,1,nlstate);  
      if(mle==1){
   hstepm=1*YEARM; /* Every year of age */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 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++)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            for (j=1;j<=nlstate+ndeath;j++){
     if (stepm >= YEARM) hstepm=1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
     gp=matrix(0,nhstepm,1,nlstate);            newm=savm;
     gm=matrix(0,nhstepm,1,nlstate);            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;
       for(j=1; j<= nlstate; j++){          } /* end mult */
         for(h=0; h<=nhstepm; h++){        
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          /* But now since version 0.9 we anticipate for bias at large stepm.
         }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       }           * (in months) between two waves is not a multiple of stepm, we rounded to 
               * the nearest (and in case of equal distance, to the lowest) interval but now
       for(i=1; i<=npar; i++) /* Computes gradient */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         xp[i] = x[i] - (i==theta ?delti[theta]:0);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             * probability in order to take into account the bias as a fraction of the way
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       for(j=1; j<= nlstate; j++){           * -stepm/2 to stepm/2 .
         for(h=0; h<=nhstepm; h++){           * For stepm=1 the results are the same as for previous versions of Imach.
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)           * For stepm > 1 the results are less biased than in previous versions. 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];           */
         }          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
       for(j=1; j<= nlstate; j++)          bbh=(double)bh[mi][i]/(double)stepm; 
         for(h=0; h<=nhstepm; h++){          /* bias bh is positive if real duration
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];           * is higher than the multiple of stepm and negative otherwise.
         }           */
     } /* End theta */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            /* i.e. if s2 is a death state and if the date of death is known 
                then the contribution to the likelihood is the probability to 
     for(h=0; h<=nhstepm; h++)               die between last step unit time and current  step unit time, 
       for(j=1; j<=nlstate;j++)               which is also equal to probability to die before dh 
         for(theta=1; theta <=npar; theta++)               minus probability to die before dh-stepm . 
           trgradg[h][j][theta]=gradg[h][theta][j];               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
     for(i=1;i<=nlstate;i++)          health state: the date of the interview describes the actual state
       for(j=1;j<=nlstate;j++)          and not the date of a change in health state. The former idea was
         vareij[i][j][(int)age] =0.;          to consider that at each interview the state was recorded
     for(h=0;h<=nhstepm;h++){          (healthy, disable or death) and IMaCh was corrected; but when we
       for(k=0;k<=nhstepm;k++){          introduced the exact date of death then we should have modified
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          the contribution of an exact death to the likelihood. This new
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          contribution is smaller and very dependent of the step unit
         for(i=1;i<=nlstate;i++)          stepm. It is no more the probability to die between last interview
           for(j=1;j<=nlstate;j++)          and month of death but the probability to survive from last
             vareij[i][j][(int)age] += doldm[i][j];          interview up to one month before death multiplied by the
       }          probability to die within a month. Thanks to Chris
     }          Jackson for correcting this bug.  Former versions increased
     h=1;          mortality artificially. The bad side is that we add another loop
     if (stepm >= YEARM) h=stepm/YEARM;          which slows down the processing. The difference can be up to 10%
     fprintf(ficresvij,"%.0f ",age );          lower mortality.
     for(i=1; i<=nlstate;i++)            */
       for(j=1; j<=nlstate;j++){            lli=log(out[s1][s2] - savm[s1][s2]);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  
       }  
     fprintf(ficresvij,"\n");          } else if  (s2==-2) {
     free_matrix(gp,0,nhstepm,1,nlstate);            for (j=1,survp=0. ; j<=nlstate; j++) 
     free_matrix(gm,0,nhstepm,1,nlstate);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            /*survp += out[s1][j]; */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            lli= log(survp);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
   } /* End age */          
            else if  (s2==-4) { 
   free_vector(xp,1,npar);            for (j=3,survp=0. ; j<=nlstate; j++)  
   free_matrix(doldm,1,nlstate,1,npar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   free_matrix(dnewm,1,nlstate,1,nlstate);            lli= log(survp); 
           } 
 }  
           else if  (s2==-5) { 
 /************ Variance of prevlim ******************/            for (j=1,survp=0. ; j<=2; j++)  
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 {            lli= log(survp); 
   /* Variance of prevalence limit */          } 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          
   double **newm;          else{
   double **dnewm,**doldm;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   int i, j, nhstepm, hstepm;            /*  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 */
   int k, cptcode;          } 
   double *xp;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double *gp, *gm;          /*if(lli ==000.0)*/
   double **gradg, **trgradg;          /*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); */
   double age,agelim;          ipmx +=1;
   int theta;          sw += weight[i];
              ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        } /* end of wave */
   fprintf(ficresvpl,"# Age");      } /* end of individual */
   for(i=1; i<=nlstate;i++)    }  else if(mle==2){
       fprintf(ficresvpl," %1d-%1d",i,i);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficresvpl,"\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   xp=vector(1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   dnewm=matrix(1,nlstate,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   doldm=matrix(1,nlstate,1,nlstate);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=1*YEARM; /* Every year of age */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          for(d=0; d<=dh[mi][i]; d++){
   agelim = AGESUP;            newm=savm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            for (kk=1; kk<=cptcovage;kk++) {
     if (stepm >= YEARM) hstepm=1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            }
     gradg=matrix(1,npar,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gp=vector(1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     gm=vector(1,nlstate);            savm=oldm;
             oldm=newm;
     for(theta=1; theta <=npar; theta++){          } /* end mult */
       for(i=1; i<=npar; i++){ /* Computes gradient */        
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          bbh=(double)bh[mi][i]/(double)stepm; 
       for(i=1;i<=nlstate;i++)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         gp[i] = prlim[i][i];          ipmx +=1;
              sw += weight[i];
       for(i=1; i<=npar; i++) /* Computes gradient */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        } /* end of wave */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } /* end of individual */
       for(i=1;i<=nlstate;i++)    }  else if(mle==3){  /* exponential inter-extrapolation */
         gm[i] = prlim[i][i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         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++){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          for (ii=1;ii<=nlstate+ndeath;ii++)
     } /* End theta */            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     trgradg =matrix(1,nlstate,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     for(j=1; j<=nlstate;j++)          for(d=0; d<dh[mi][i]; d++){
       for(theta=1; theta <=npar; theta++)            newm=savm;
         trgradg[j][theta]=gradg[theta][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for(i=1;i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       varpl[i][(int)age] =0.;            }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1;i<=nlstate;i++)            savm=oldm;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            oldm=newm;
           } /* end mult */
     fprintf(ficresvpl,"%.0f ",age );        
     for(i=1; i<=nlstate;i++)          s1=s[mw[mi][i]][i];
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          s2=s[mw[mi+1][i]][i];
     fprintf(ficresvpl,"\n");          bbh=(double)bh[mi][i]/(double)stepm; 
     free_vector(gp,1,nlstate);          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 */
     free_vector(gm,1,nlstate);          ipmx +=1;
     free_matrix(gradg,1,npar,1,nlstate);          sw += weight[i];
     free_matrix(trgradg,1,nlstate,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   } /* End age */        } /* end of wave */
       } /* end of individual */
   free_vector(xp,1,npar);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   free_matrix(doldm,1,nlstate,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_matrix(dnewm,1,nlstate,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /***********************************************/            }
 /**************** Main Program *****************/          for(d=0; d<dh[mi][i]; d++){
 /***********************************************/            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 /*int main(int argc, char *argv[])*/            for (kk=1; kk<=cptcovage;kk++) {
 int main()              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {            }
           
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double agedeb, agefin,hf;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double agemin=1.e20, agemax=-1.e20;            savm=oldm;
             oldm=newm;
   double fret;          } /* end mult */
   double **xi,tmp,delta;        
           s1=s[mw[mi][i]][i];
   double dum; /* Dummy variable */          s2=s[mw[mi+1][i]][i];
   double ***p3mat;          if( s2 > nlstate){ 
   int *indx;            lli=log(out[s1][s2] - savm[s1][s2]);
   char line[MAXLINE], linepar[MAXLINE];          }else{
   char title[MAXLINE];            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];          ipmx +=1;
   char filerest[FILENAMELENGTH];          sw += weight[i];
   char fileregp[FILENAMELENGTH];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  /*      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]); */
   int firstobs=1, lastobs=10;        } /* end of wave */
   int sdeb, sfin; /* Status at beginning and end */      } /* end of individual */
   int c,  h , cpt,l;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   int ju,jl, mi;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i1,j1, k1,jk,aa,bb, stepsize;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   int hstepm, nhstepm;            for (j=1;j<=nlstate+ndeath;j++){
   double bage, fage, age, agelim, agebase;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ftolpl=FTOL;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **prlim;            }
   double *severity;          for(d=0; d<dh[mi][i]; d++){
   double ***param; /* Matrix of parameters */            newm=savm;
   double  *p;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **matcov; /* Matrix of covariance */            for (kk=1; kk<=cptcovage;kk++) {
   double ***delti3; /* Scale */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *delti; /* Scale */            }
   double ***eij, ***vareij;          
   double **varpl; /* Variances of prevalence limits by age */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double *epj, vepp;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   char version[80]="Imach version 0.64, May 2000, INED-EUROREVES ";            savm=oldm;
   char *alph[]={"a","a","b","c","d","e"}, str[4];            oldm=newm;
   char z[1]="c", occ;          } /* end mult */
 #include <sys/time.h>        
 #include <time.h>          s1=s[mw[mi][i]][i];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          s2=s[mw[mi+1][i]][i];
   /* long total_usecs;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   struct timeval start_time, end_time;          ipmx +=1;
            sw += weight[i];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
   printf("\nIMACH, Version 0.64a");      } /* end of individual */
   printf("\nEnter the parameter file name: ");    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 #ifdef windows    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   scanf("%s",pathtot);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   cygwin_split_path(pathtot,path,optionfile);    return -l;
      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);  }
      chdir(path);  
    /*************** log-likelihood *************/
   /*size=30;  double funcone( double *x)
   getcwd(pathcd, size);    {
   printf("pathcd=%s, path=%s, optionfile=%s\n",pathcd,path,optionfile);    /* Same as likeli but slower because of a lot of printf and if */
   cutv(path,optionfile,pathtot,'\\');    int i, ii, j, k, mi, d, kk;
   chdir(path);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   replace(pathc,path);    double **out;
   printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);    double lli; /* Individual log likelihood */
   */    double llt;
 #endif    int s1, s2;
 #ifdef unix    double bbh, survp;
   scanf("%s",optionfile);    /*extern weight */
 #endif    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 /*-------- arguments in the command line --------*/    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   strcpy(fileres,"r");    */
   strcat(fileres, optionfile);    cov[1]=1.;
   
   /*---------arguments file --------*/    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     printf("Problem with optionfile %s\n",optionfile);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     goto end;      for(mi=1; mi<= wav[i]-1; mi++){
   }        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
   strcpy(filereso,"o");            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcat(filereso,fileres);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((ficparo=fopen(filereso,"w"))==NULL) {          }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        for(d=0; d<dh[mi][i]; d++){
   }          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* Reads comments: lines beginning with '#' */          for (kk=1; kk<=cptcovage;kk++) {
   while((c=getc(ficpar))=='#' && c!= EOF){            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     puts(line);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     fputs(line,ficparo);          savm=oldm;
   }          oldm=newm;
   ungetc(c,ficpar);        } /* end mult */
         
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        s1=s[mw[mi][i]][i];
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        s2=s[mw[mi+1][i]][i];
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
   covar=matrix(1,NCOVMAX,1,n);             * is higher than the multiple of stepm and negative otherwise.
   if (strlen(model)<=1) cptcovn=0;         */
   else {        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     j=0;          lli=log(out[s1][s2] - savm[s1][s2]);
     j=nbocc(model,'+');        } else if  (s2==-2) {
     cptcovn=j+1;          for (j=1,survp=0. ; j<=nlstate; j++) 
   }            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
   ncovmodel=2+cptcovn;        }else if (mle==1){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          } else if(mle==2){
   /* Read guess parameters */          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 */
   /* Reads comments: lines beginning with '#' */        } else if(mle==3){  /* exponential inter-extrapolation */
   while((c=getc(ficpar))=='#' && c!= EOF){          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 */
     ungetc(c,ficpar);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     fgets(line, MAXLINE, ficpar);          lli=log(out[s1][s2]); /* Original formula */
     puts(line);        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     fputs(line,ficparo);          lli=log(out[s1][s2]); /* Original formula */
   }        } /* End of if */
   ungetc(c,ficpar);        ipmx +=1;
          sw += weight[i];
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i=1; i <=nlstate; i++)  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     for(j=1; j <=nlstate+ndeath-1; j++){        if(globpr){
       fscanf(ficpar,"%1d%1d",&i1,&j1);          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       fprintf(ficparo,"%1d%1d",i1,j1);   %11.6f %11.6f %11.6f ", \
       printf("%1d%1d",i,j);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       for(k=1; k<=ncovmodel;k++){                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         fscanf(ficpar," %lf",&param[i][j][k]);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         printf(" %lf",param[i][j][k]);            llt +=ll[k]*gipmx/gsw;
         fprintf(ficparo," %lf",param[i][j][k]);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       }          }
       fscanf(ficpar,"\n");          fprintf(ficresilk," %10.6f\n", -llt);
       printf("\n");        }
       fprintf(ficparo,"\n");      } /* end of wave */
     }    } /* end of individual */
      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   p=param[1][1];    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 */
   /* Reads comments: lines beginning with '#' */      gipmx=ipmx;
   while((c=getc(ficpar))=='#' && c!= EOF){      gsw=sw;
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    return -l;
     puts(line);  }
     fputs(line,ficparo);  
   }  
   ungetc(c,ficpar);  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  {
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    /* This routine should help understanding what is done with 
   for(i=1; i <=nlstate; i++){       the selection of individuals/waves and
     for(j=1; j <=nlstate+ndeath-1; j++){       to check the exact contribution to the likelihood.
       fscanf(ficpar,"%1d%1d",&i1,&j1);       Plotting could be done.
       printf("%1d%1d",i,j);     */
       fprintf(ficparo,"%1d%1d",i1,j1);    int k;
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);    if(*globpri !=0){ /* Just counts and sums, no printings */
         printf(" %le",delti3[i][j][k]);      strcpy(fileresilk,"ilk"); 
         fprintf(ficparo," %le",delti3[i][j][k]);      strcat(fileresilk,fileres);
       }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       fscanf(ficpar,"\n");        printf("Problem with resultfile: %s\n", fileresilk);
       printf("\n");        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       fprintf(ficparo,"\n");      }
     }      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
   }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   delti=delti3[1][1];      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
        for(k=1; k<=nlstate; k++) 
   /* Reads comments: lines beginning with '#' */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);  
     puts(line);    *fretone=(*funcone)(p);
     fputs(line,ficparo);    if(*globpri !=0){
   }      fclose(ficresilk);
   ungetc(c,ficpar);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
        fflush(fichtm); 
   matcov=matrix(1,npar,1,npar);    } 
   for(i=1; i <=npar; i++){    return;
     fscanf(ficpar,"%s",&str);  }
     printf("%s",str);  
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){  /*********** Maximum Likelihood Estimation ***************/
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       fprintf(ficparo," %.5le",matcov[i][j]);  {
     }    int i,j, iter;
     fscanf(ficpar,"\n");    double **xi;
     printf("\n");    double fret;
     fprintf(ficparo,"\n");    double fretone; /* Only one call to likelihood */
   }    /*  char filerespow[FILENAMELENGTH];*/
   for(i=1; i <=npar; i++)    xi=matrix(1,npar,1,npar);
     for(j=i+1;j<=npar;j++)    for (i=1;i<=npar;i++)
       matcov[i][j]=matcov[j][i];      for (j=1;j<=npar;j++)
            xi[i][j]=(i==j ? 1.0 : 0.0);
   printf("\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
    if(mle==1){    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     /*-------- data file ----------*/      printf("Problem with resultfile: %s\n", filerespow);
     if((ficres =fopen(fileres,"w"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       printf("Problem with resultfile: %s\n", fileres);goto end;    }
     }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     fprintf(ficres,"#%s\n",version);    for (i=1;i<=nlstate;i++)
          for(j=1;j<=nlstate+ndeath;j++)
     if((fic=fopen(datafile,"r"))==NULL)    {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       printf("Problem with datafile: %s\n", datafile);goto end;    fprintf(ficrespow,"\n");
     }  
     powell(p,xi,npar,ftol,&iter,&fret,func);
     n= lastobs;  
     severity = vector(1,maxwav);    free_matrix(xi,1,npar,1,npar);
     outcome=imatrix(1,maxwav+1,1,n);    fclose(ficrespow);
     num=ivector(1,n);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     moisnais=vector(1,n);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     annais=vector(1,n);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     moisdc=vector(1,n);  
     andc=vector(1,n);  }
     agedc=vector(1,n);  
     cod=ivector(1,n);  /**** Computes Hessian and covariance matrix ***/
     weight=vector(1,n);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  {
     mint=matrix(1,maxwav,1,n);    double  **a,**y,*x,pd;
     anint=matrix(1,maxwav,1,n);    double **hess;
     s=imatrix(1,maxwav+1,1,n);    int i, j,jk;
     adl=imatrix(1,maxwav+1,1,n);        int *indx;
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     i=1;    void lubksb(double **a, int npar, int *indx, double b[]) ;
     while (fgets(line, MAXLINE, fic) != NULL)    {    void ludcmp(double **a, int npar, int *indx, double *d) ;
       if ((i >= firstobs) && (i <=lastobs)) {    double gompertz(double p[]);
            hess=matrix(1,npar,1,npar);
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    printf("\nCalculation of the hessian matrix. Wait...\n");
           strcpy(line,stra);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for (i=1;i<=npar;i++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      printf("%d",i);fflush(stdout);
         }      fprintf(ficlog,"%d",i);fflush(ficlog);
             
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      
       /*  printf(" %f ",p[i]);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    }
     
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    for (i=1;i<=npar;i++) {
         for (j=ncov;j>=1;j--){      for (j=1;j<=npar;j++)  {
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        if (j>i) { 
         }          printf(".%d%d",i,j);fflush(stdout);
         num[i]=atol(stra);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j,func,npar);
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.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]),  (mint[5][i]), (anint[5][i]), (s[5][i]),  (mint[6][i]), (anint[6][i]), (s[6][i]));*/          
           hess[j][i]=hess[i][j];    
         i=i+1;          /*printf(" %lf ",hess[i][j]);*/
       }        }
     }      }
     }
     /*scanf("%d",i);*/    printf("\n");
   imx=i-1; /* Number of individuals */    fprintf(ficlog,"\n");
   
   /* Calculation of the number of parameter from char model*/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   Tvar=ivector(1,8);        fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
        
   if (strlen(model) >1){    a=matrix(1,npar,1,npar);
     j=0;    y=matrix(1,npar,1,npar);
     j=nbocc(model,'+');    x=vector(1,npar);
     cptcovn=j+1;    indx=ivector(1,npar);
        for (i=1;i<=npar;i++)
     strcpy(modelsav,model);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     if (j==0) {    ludcmp(a,npar,indx,&pd);
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);  
     }    for (j=1;j<=npar;j++) {
     else {      for (i=1;i<=npar;i++) x[i]=0;
       for(i=j; i>=1;i--){      x[j]=1;
         cutv(stra,strb,modelsav,'+');      lubksb(a,npar,indx,x);
         if (strchr(strb,'*')) {      for (i=1;i<=npar;i++){ 
           cutv(strd,strc,strb,'*');        matcov[i][j]=x[i];
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;      }
           cutv(strb,strc,strd,'V');    }
           for (k=1; k<=lastobs;k++)  
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    printf("\n#Hessian matrix#\n");
         }    fprintf(ficlog,"\n#Hessian matrix#\n");
         else {cutv(strd,strc,strb,'V');    for (i=1;i<=npar;i++) { 
         Tvar[i+1]=atoi(strc);      for (j=1;j<=npar;j++) { 
         }        printf("%.3e ",hess[i][j]);
         strcpy(modelsav,stra);          fprintf(ficlog,"%.3e ",hess[i][j]);
       }      }
       cutv(strd,strc,stra,'V');      printf("\n");
       Tvar[1]=atoi(strc);      fprintf(ficlog,"\n");
     }    }
   }  
   /*printf("tvar=%d ",Tvar[1]);    /* Recompute Inverse */
   scanf("%d ",i);*/    for (i=1;i<=npar;i++)
     fclose(fic);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;    /*  printf("\n#Hessian matrix recomputed#\n");
     }  
     /*-calculation of age at interview from date of interview and age at death -*/    for (j=1;j<=npar;j++) {
     agev=matrix(1,maxwav,1,imx);      for (i=1;i<=npar;i++) x[i]=0;
          x[j]=1;
     for (i=1; i<=imx; i++)  {      lubksb(a,npar,indx,x);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      for (i=1;i<=npar;i++){ 
       for(m=1; (m<= maxwav); m++){        y[i][j]=x[i];
         if(s[m][i] >0){        printf("%.3e ",y[i][j]);
           if (s[m][i] == nlstate+1) {        fprintf(ficlog,"%.3e ",y[i][j]);
             if(agedc[i]>0)      }
               if(moisdc[i]!=99 && andc[i]!=9999)      printf("\n");
               agev[m][i]=agedc[i];      fprintf(ficlog,"\n");
             else{    }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    */
               agev[m][i]=-1;  
             }    free_matrix(a,1,npar,1,npar);
           }    free_matrix(y,1,npar,1,npar);
           else if(s[m][i] !=9){ /* Should no more exist */    free_vector(x,1,npar);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    free_ivector(indx,1,npar);
             if(mint[m][i]==99 || anint[m][i]==9999)    free_matrix(hess,1,npar,1,npar);
               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);*/  
             }  /*************** hessian matrix ****************/
             else if(agev[m][i] >agemax){  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
               agemax=agev[m][i];  {
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    int i;
             }    int l=1, lmax=20;
             /*agev[m][i]=anint[m][i]-annais[i];*/    double k1,k2;
             /*   agev[m][i] = age[i]+2*m;*/    double p2[NPARMAX+1];
           }    double res;
           else { /* =9 */    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
             agev[m][i]=1;    double fx;
             s[m][i]=-1;    int k=0,kmax=10;
           }    double l1;
         }  
         else /*= 0 Unknown */    fx=func(x);
           agev[m][i]=1;    for (i=1;i<=npar;i++) p2[i]=x[i];
       }    for(l=0 ; l <=lmax; l++){
          l1=pow(10,l);
     }      delts=delt;
     for (i=1; i<=imx; i++)  {      for(k=1 ; k <kmax; k=k+1){
       for(m=1; (m<= maxwav); m++){        delt = delta*(l1*k);
         if (s[m][i] > (nlstate+ndeath)) {        p2[theta]=x[theta] +delt;
           printf("Error: Wrong value in nlstate or ndeath\n");          k1=func(p2)-fx;
           goto end;        p2[theta]=x[theta]-delt;
         }        k2=func(p2)-fx;
       }        /*res= (k1-2.0*fx+k2)/delt/delt; */
     }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  #ifdef DEBUG
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     free_vector(severity,1,maxwav);        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);
     free_imatrix(outcome,1,maxwav+1,1,n);  #endif
     free_vector(moisnais,1,n);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     free_vector(annais,1,n);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     free_matrix(mint,1,maxwav,1,n);          k=kmax;
     free_matrix(anint,1,maxwav,1,n);        }
     free_vector(moisdc,1,n);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     free_vector(andc,1,n);          k=kmax; l=lmax*10.;
         }
            else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     wav=ivector(1,imx);          delts=delt;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      }
        }
     /* Concatenates waves */    delti[theta]=delts;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    return res; 
     
   }
 Tcode=ivector(1,100);  
    nbcode=imatrix(1,nvar,1,8);    double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
    ncodemax[1]=1;  {
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);    int i;
      int l=1, l1, lmax=20;
    codtab=imatrix(1,100,1,10);    double k1,k2,k3,k4,res,fx;
    h=0;    double p2[NPARMAX+1];
    m=pow(2,cptcovn);    int k;
    
    for(k=1;k<=cptcovn; k++){    fx=func(x);
      for(i=1; i <=(m/pow(2,k));i++){    for (k=1; k<=2; k++) {
        for(j=1; j <= ncodemax[k]; j++){      for (i=1;i<=npar;i++) p2[i]=x[i];
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){      p2[thetai]=x[thetai]+delti[thetai]/k;
            h++;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
            if (h>m) h=1;codtab[h][k]=j;      k1=func(p2)-fx;
          }    
        }      p2[thetai]=x[thetai]+delti[thetai]/k;
      }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
    }      k2=func(p2)-fx;
     
    /*for(i=1; i <=m ;i++){      p2[thetai]=x[thetai]-delti[thetai]/k;
      for(k=1; k <=cptcovn; k++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);      k3=func(p2)-fx;
      }    
      printf("\n");      p2[thetai]=x[thetai]-delti[thetai]/k;
    }*/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
    /*scanf("%d",i);*/      k4=func(p2)-fx;
          res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    /* Calculates basic frequencies. Computes observed prevalence at single age  #ifdef DEBUG
        and prints on file fileres'p'. */      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);
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);      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);
   #endif
     }
   /*scanf("%d ",i);*/    return res;
   }
   
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /************** Inverse of matrix **************/
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  void ludcmp(double **a, int n, int *indx, double *d) 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  { 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int i,imax,j,k; 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double big,dum,sum,temp; 
        double *vv; 
     /* 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] */    vv=vector(1,n); 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    *d=1.0; 
        for (i=1;i<=n;i++) { 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      big=0.0; 
       for (j=1;j<=n;j++) 
            if ((temp=fabs(a[i][j])) > big) big=temp; 
     /*--------- results files --------------*/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);      vv[i]=1.0/big; 
        } 
    jk=1;    for (j=1;j<=n;j++) { 
    fprintf(ficres,"# Parameters\n");      for (i=1;i<j;i++) { 
    printf("# Parameters\n");        sum=a[i][j]; 
    for(i=1,jk=1; i <=nlstate; i++){        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
      for(k=1; k <=(nlstate+ndeath); k++){        a[i][j]=sum; 
        if (k != i)      } 
          {      big=0.0; 
            printf("%d%d ",i,k);      for (i=j;i<=n;i++) { 
            fprintf(ficres,"%1d%1d ",i,k);        sum=a[i][j]; 
            for(j=1; j <=ncovmodel; j++){        for (k=1;k<j;k++) 
              printf("%f ",p[jk]);          sum -= a[i][k]*a[k][j]; 
              fprintf(ficres,"%f ",p[jk]);        a[i][j]=sum; 
              jk++;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
            }          big=dum; 
            printf("\n");          imax=i; 
            fprintf(ficres,"\n");        } 
          }      } 
      }      if (j != imax) { 
    }        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
     /* Computing hessian and covariance matrix */          a[imax][k]=a[j][k]; 
     ftolhess=ftol; /* Usually correct */          a[j][k]=dum; 
     hesscov(matcov, p, npar, delti, ftolhess, func);        } 
     fprintf(ficres,"# Scales\n");        *d = -(*d); 
     printf("# Scales\n");        vv[imax]=vv[j]; 
      for(i=1,jk=1; i <=nlstate; i++){      } 
       for(j=1; j <=nlstate+ndeath; j++){      indx[j]=imax; 
         if (j!=i) {      if (a[j][j] == 0.0) a[j][j]=TINY; 
           fprintf(ficres,"%1d%1d",i,j);      if (j != n) { 
           printf("%1d%1d",i,j);        dum=1.0/(a[j][j]); 
           for(k=1; k<=ncovmodel;k++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
             printf(" %.5e",delti[jk]);      } 
             fprintf(ficres," %.5e",delti[jk]);    } 
             jk++;    free_vector(vv,1,n);  /* Doesn't work */
           }  ;
           printf("\n");  } 
           fprintf(ficres,"\n");  
         }  void lubksb(double **a, int n, int *indx, double b[]) 
       }  { 
       }    int i,ii=0,ip,j; 
        double sum; 
     k=1;   
     fprintf(ficres,"# Covariance\n");    for (i=1;i<=n;i++) { 
     printf("# Covariance\n");      ip=indx[i]; 
     for(i=1;i<=npar;i++){      sum=b[ip]; 
       /*  if (k>nlstate) k=1;      b[ip]=b[i]; 
       i1=(i-1)/(ncovmodel*nlstate)+1;      if (ii) 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       printf("%s%d%d",alph[k],i1,tab[i]);*/      else if (sum) ii=i; 
       fprintf(ficres,"%3d",i);      b[i]=sum; 
       printf("%3d",i);    } 
       for(j=1; j<=i;j++){    for (i=n;i>=1;i--) { 
         fprintf(ficres," %.5e",matcov[i][j]);      sum=b[i]; 
         printf(" %.5e",matcov[i][j]);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       }      b[i]=sum/a[i][i]; 
       fprintf(ficres,"\n");    } 
       printf("\n");  } 
       k++;  
     }  void pstamp(FILE *fichier)
      {
     while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       ungetc(c,ficpar);  }
       fgets(line, MAXLINE, ficpar);  
       puts(line);  /************ Frequencies ********************/
       fputs(line,ficparo);  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[])
     }  {  /* Some frequencies */
     ungetc(c,ficpar);    
      int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    int first;
        double ***freq; /* Frequencies */
     if (fage <= 2) {    double *pp, **prop;
       bage = agemin;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       fage = agemax;    char fileresp[FILENAMELENGTH];
     }    
     pp=vector(1,nlstate);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    prop=matrix(1,nlstate,iagemin,iagemax+3);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    strcpy(fileresp,"p");
 /*------------ gnuplot -------------*/    strcat(fileresp,fileres);
 chdir(pathcd);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   if((ficgp=fopen("graph.plt","w"))==NULL) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
     printf("Problem with file graph.plt");goto end;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   }      exit(0);
 #ifdef windows    }
   fprintf(ficgp,"cd \"%s\" \n",pathc);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 #endif    j1=0;
 m=pow(2,cptcovn);    
      j=cptcoveff;
  /* 1eme*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {    first=1;
   
 #ifdef windows    for(k1=1; k1<=j;k1++){
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);      for(i1=1; i1<=ncodemax[k1];i1++){
 #endif        j1++;
 #ifdef unix        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          scanf("%d", i);*/
 #endif        for (i=-5; i<=nlstate+ndeath; i++)  
           for (jk=-5; jk<=nlstate+ndeath; jk++)  
 for (i=1; i<= nlstate ; i ++) {            for(m=iagemin; m <= iagemax+3; m++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              freq[i][jk][m]=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      for (i=1; i<=nlstate; 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);        for(m=iagemin; m <= iagemax+3; m++)
     for (i=1; i<= nlstate ; i ++) {          prop[i][m]=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        
   else fprintf(ficgp," \%%*lf (\%%*lf)");        dateintsum=0;
 }        k2cpt=0;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        for (i=1; i<=imx; i++) {
      for (i=1; i<= nlstate ; i ++) {          bool=1;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          if  (cptcovn>0) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for (z1=1; z1<=cptcoveff; z1++) 
 }                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                bool=0;
 #ifdef unix          }
 fprintf(ficgp,"\nset ter gif small size 400,300");          if (bool==1){
 #endif            for(m=firstpass; m<=lastpass; m++){
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              k2=anint[m][i]+(mint[m][i]/12.);
    }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   /*2 eme*/                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];
   for (k1=1; k1<= m ; k1 ++) {                if (m<lastpass) {
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                      freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     for (i=1; i<= nlstate+1 ; i ++) {                }
       k=2*i;                
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       for (j=1; j<= nlstate+1 ; j ++) {                  dateintsum=dateintsum+k2;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                  k2cpt++;
   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,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {         
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");        pstamp(ficresp);
 }          if  (cptcovn>0) {
       fprintf(ficgp,"\" t\"\" w l 0,");          fprintf(ficresp, "\n#********** Variable "); 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for (j=1; j<= nlstate+1 ; j ++) {          fprintf(ficresp, "**********\n#");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=1; i<=nlstate;i++) 
 }            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        fprintf(ficresp, "\n");
       else fprintf(ficgp,"\" t\"\" w l 0,");        
     }        for(i=iagemin; i <= iagemax+3; i++){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          if(i==iagemax+3){
   }            fprintf(ficlog,"Total");
            }else{
   /*3eme*/            if(first==1){
               first=0;
    for (k1=1; k1<= m ; k1 ++) {              printf("See log file for details...\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {            }
       k=2+nlstate*(cpt-1);            fprintf(ficlog,"Age %d", i);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          }
       for (i=1; i< nlstate ; i ++) {          for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       }              pp[jk] += freq[jk][m][i]; 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          }
     }          for(jk=1; jk <=nlstate ; jk++){
    }            for(m=-1, pos=0; m <=0 ; m++)
                pos += freq[jk][m][i];
   /* CV preval stat */            if(pp[jk]>=1.e-10){
     for (k1=1; k1<= m ; k1 ++) {              if(first==1){
     for (cpt=1; cpt<nlstate ; cpt ++) {              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       k=3;              }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for (i=1; i< nlstate ; i ++)            }else{
         fprintf(ficgp,"+$%d",k+i+1);              if(first==1)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                    fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       l=3+(nlstate+ndeath)*cpt;            }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          }
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;          for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficgp,"+$%d",l+i+1);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       }              pp[jk] += freq[jk][m][i];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            }       
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     }            pos += pp[jk];
   }            posprop += prop[jk][i];
            }
   /* proba elementaires */          for(jk=1; jk <=nlstate ; jk++){
   for(i=1,jk=1; i <=nlstate; i++){            if(pos>=1.e-5){
     for(k=1; k <=(nlstate+ndeath); k++){              if(first==1)
       if (k != i) {                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         /*  fprintf(ficgp,"%1d%1d ",i,k);*/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         for(j=1; j <=ncovmodel; j++){            }else{
           fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);              if(first==1)
           jk++;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           fprintf(ficgp,"\n");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         }            }
       }            if( i <= iagemax){
     }              if(pos>=1.e-5){
   }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   for(jk=1; jk <=m; jk++) {                /*probs[i][jk][j1]= pp[jk]/pos;*/
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   for(i=1; i <=nlstate; i++) {              }
     for(k=1; k <=(nlstate+ndeath); k++){              else
       if (k != i) {                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);            }
         for(j=3; j <=ncovmodel; j++)          }
           fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          
         fprintf(ficgp,")/(1");          for(jk=-1; jk <=nlstate+ndeath; jk++)
         for(k1=1; k1 <=(nlstate+ndeath); k1++)            for(m=-1; m <=nlstate+ndeath; m++)
           if (k1 != i) {              if(freq[jk][m][i] !=0 ) {
             fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);              if(first==1)
             for(j=3; j <=ncovmodel; j++)                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
               fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
             fprintf(ficgp,")");              }
           }          if(i <= iagemax)
         fprintf(ficgp,") t \"p%d%d\" ", i,k);            fprintf(ficresp,"\n");
       if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          if(first==1)
       }            printf("Others in log...\n");
     }          fprintf(ficlog,"\n");
   }        }
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        }
   }    }
      dateintmean=dateintsum/k2cpt; 
  fclose(ficgp);   
     fclose(ficresp);
     chdir(path);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_matrix(agev,1,maxwav,1,imx);    free_vector(pp,1,nlstate);
     free_ivector(wav,1,imx);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    /* End of Freq */
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);  }
      
     free_imatrix(s,1,maxwav+1,1,n);  /************ Prevalence ********************/
      void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
      {  
     free_ivector(num,1,n);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     free_vector(agedc,1,n);       in each health status at the date of interview (if between dateprev1 and dateprev2).
     free_vector(weight,1,n);       We still use firstpass and lastpass as another selection.
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    */
     fclose(ficparo);   
     fclose(ficres);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
    }    double ***freq; /* Frequencies */
        double *pp, **prop;
    /*________fin mle=1_________*/    double pos,posprop; 
        double  y2; /* in fractional years */
     int iagemin, iagemax;
    
     /* No more information from the sample is required now */    iagemin= (int) agemin;
   /* Reads comments: lines beginning with '#' */    iagemax= (int) agemax;
   while((c=getc(ficpar))=='#' && c!= EOF){    /*pp=vector(1,nlstate);*/
     ungetc(c,ficpar);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     fgets(line, MAXLINE, ficpar);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     puts(line);    j1=0;
     fputs(line,ficparo);    
   }    j=cptcoveff;
   ungetc(c,ficpar);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
     for(k1=1; k1<=j;k1++){
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      for(i1=1; i1<=ncodemax[k1];i1++){
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        j1++;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        
 /*--------- index.htm --------*/        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
   if((fichtm=fopen("index.htm","w"))==NULL)    {            prop[i][m]=0.0;
     printf("Problem with index.htm \n");goto end;       
   }        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
  fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n          if  (cptcovn>0) {
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            for (z1=1; z1<=cptcoveff; z1++) 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>                bool=0;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>          } 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          if (bool==1) { 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
  fprintf(fichtm," <li>Graphs</li>\n<p>");                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) { 
  m=cptcovn;                  /*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]]);*/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
  j1=0;                } 
  for(k1=1; k1<=m;k1++){              }
    for(i1=1; i1<=ncodemax[k1];i1++){            } /* end selection of waves */
        j1++;          }
        if (cptcovn > 0) {        }
          fprintf(fichtm,"<hr>************ Results for covariates");        for(i=iagemin; i <= iagemax+3; i++){  
          for (cpt=1; cpt<=cptcovn;cpt++)          
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
          fprintf(fichtm," ************\n<hr>");            posprop += prop[jk][i]; 
        }          } 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              for(jk=1; jk <=nlstate ; jk++){     
        for(cpt=1; cpt<nlstate;cpt++){            if( i <=  iagemax){ 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              if(posprop>=1.e-5){ 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                probs[i][jk][j1]= prop[jk][i]/posprop;
        }              } else
     for(cpt=1; cpt<=nlstate;cpt++) {                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            } 
 interval) in state (%d): v%s%d%d.gif <br>          }/* end jk */ 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          }/* end i */ 
      }      } /* end i1 */
      for(cpt=1; cpt<=nlstate;cpt++) {    } /* end k1 */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    
 <img src=\"ex%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      }    /*free_vector(pp,1,nlstate);*/
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 health expectancies in states (1) and (2): e%s%d.gif<br>  }  /* End of prevalence */
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);  
 fprintf(fichtm,"\n</body>");  /************* Waves Concatenation ***************/
    }  
  }  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)
 fclose(fichtm);  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   /*--------------- Prevalence limit --------------*/       Death is a valid wave (if date is known).
         mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   strcpy(filerespl,"pl");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   strcat(filerespl,fileres);       and mw[mi+1][i]. dh depends on stepm.
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }    int i, mi, m;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   fprintf(ficrespl,"#Prevalence limit\n");       double sum=0., jmean=0.;*/
   fprintf(ficrespl,"#Age ");    int first;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    int j, k=0,jk, ju, jl;
   fprintf(ficrespl,"\n");    double sum=0.;
      first=0;
   prlim=matrix(1,nlstate,1,nlstate);    jmin=1e+5;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    jmax=-1;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    jmean=0.;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for(i=1; i<=imx; i++){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      mi=0;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      m=firstpass;
   k=0;      while(s[m][i] <= nlstate){
   agebase=agemin;        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   agelim=agemax;          mw[++mi][i]=m;
   ftolpl=1.e-10;        if(m >=lastpass)
   i1=cptcovn;          break;
   if (cptcovn < 1){i1=1;}        else
           m++;
   for(cptcov=1;cptcov<=i1;cptcov++){      }/* end while */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      if (s[m][i] > nlstate){
         k=k+1;        mi++;     /* Death is another wave */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        /* if(mi==0)  never been interviewed correctly before death */
         fprintf(ficrespl,"\n#****** ");           /* Only death is a correct wave */
         for(j=1;j<=cptcovn;j++)        mw[mi][i]=m;
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);      }
         fprintf(ficrespl,"******\n");  
              wav[i]=mi;
         for (age=agebase; age<=agelim; age++){      if(mi==0){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        nbwarn++;
           fprintf(ficrespl,"%.0f",age );        if(first==0){
           for(i=1; i<=nlstate;i++)          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           fprintf(ficrespl," %.5f", prlim[i][i]);          first=1;
           fprintf(ficrespl,"\n");        }
         }        if(first==1){
       }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     }        }
   fclose(ficrespl);      } /* end mi==0 */
   /*------------- h Pij x at various ages ------------*/    } /* End individuals */
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    for(i=1; i<=imx; i++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      for(mi=1; mi<wav[i];mi++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        if (stepm <=0)
   }          dh[mi][i]=1;
   printf("Computing pij: result on file '%s' \n", filerespij);        else{
            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   stepsize=(int) (stepm+YEARM-1)/YEARM;            if (agedc[i] < 2*AGESUP) {
   if (stepm<=24) stepsize=2;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
   agelim=AGESUP;              else if(j<0){
   hstepm=stepsize*YEARM; /* Every year of age */                nberr++;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                  j=1; /* Temporary Dangerous patch */
   k=0;                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   for(cptcov=1;cptcov<=i1;cptcov++){                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                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);
       k=k+1;              }
         fprintf(ficrespij,"\n#****** ");              k=k+1;
         for(j=1;j<=cptcovn;j++)              if (j >= jmax){
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);                jmax=j;
         fprintf(ficrespij,"******\n");                ijmax=i;
                      }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */              if (j <= jmin){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                jmin=j;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                ijmin=i;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              }
           oldm=oldms;savm=savms;              sum=sum+j;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                /*if (j<0) printf("j=%d num=%d \n",j,i);*/
           fprintf(ficrespij,"# Age");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           for(i=1; i<=nlstate;i++)            }
             for(j=1; j<=nlstate+ndeath;j++)          }
               fprintf(ficrespij," %1d-%1d",i,j);          else{
           fprintf(ficrespij,"\n");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           for (h=0; h<=nhstepm; h++){  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)            k=k+1;
               for(j=1; j<=nlstate+ndeath;j++)            if (j >= jmax) {
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              jmax=j;
             fprintf(ficrespij,"\n");              ijmax=i;
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            else if (j <= jmin){
           fprintf(ficrespij,"\n");              jmin=j;
         }              ijmin=i;
     }            }
   }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*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]);*/
   fclose(ficrespij);            if(j<0){
               nberr++;
   /*---------- Health expectancies and variances ------------*/              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]);
   strcpy(filerest,"t");            }
   strcat(filerest,fileres);            sum=sum+j;
   if((ficrest=fopen(filerest,"w"))==NULL) {          }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          jk= j/stepm;
   }          jl= j -jk*stepm;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
   strcpy(filerese,"e");              dh[mi][i]=jk;
   strcat(filerese,fileres);              bh[mi][i]=0;
   if((ficreseij=fopen(filerese,"w"))==NULL) {            }else{ /* We want a negative bias in order to only have interpolation ie
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                    * at the price of an extra matrix product in likelihood */
   }              dh[mi][i]=jk+1;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);              bh[mi][i]=ju;
             }
  strcpy(fileresv,"v");          }else{
   strcat(fileresv,fileres);            if(jl <= -ju){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {              dh[mi][i]=jk;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);              bh[mi][i]=jl;       /* bias is positive if real duration
   }                                   * is higher than the multiple of stepm and negative otherwise.
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                                   */
             }
   k=0;            else{
   for(cptcov=1;cptcov<=i1;cptcov++){              dh[mi][i]=jk+1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              bh[mi][i]=ju;
       k=k+1;            }
       fprintf(ficrest,"\n#****** ");            if(dh[mi][i]==0){
       for(j=1;j<=cptcovn;j++)              dh[mi][i]=1; /* At least one step */
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);              bh[mi][i]=ju; /* At least one step */
       fprintf(ficrest,"******\n");              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
       fprintf(ficreseij,"\n#****** ");          } /* end if mle */
       for(j=1;j<=cptcovn;j++)        }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      } /* end wave */
       fprintf(ficreseij,"******\n");    }
     jmean=sum/k;
       fprintf(ficresvij,"\n#****** ");    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);
       for(j=1;j<=cptcovn;j++)    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   }
       fprintf(ficresvij,"******\n");  
   /*********** Tricode ****************************/
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  void tricode(int *Tvar, int **nbcode, int imx)
       oldm=oldms;savm=savms;  {
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    int Ndum[20],ij=1, k, j, i, maxncov=19;
       oldm=oldms;savm=savms;    int cptcode=0;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    cptcoveff=0; 
         
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    for (k=0; k<maxncov; k++) Ndum[k]=0;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    for (k=1; k<=7; k++) ncodemax[k]=0;
       fprintf(ficrest,"\n");  
            for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       hf=1;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       if (stepm >= YEARM) hf=stepm/YEARM;                                 modality*/ 
       epj=vector(1,nlstate+1);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       for(age=bage; age <=fage ;age++){        Ndum[ij]++; /*store the modality */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         fprintf(ficrest," %.0f",age);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                                         Tvar[j]. If V=sex and male is 0 and 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                                         female is 1, then  cptcode=1.*/
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      }
           }  
           epj[nlstate+1] +=epj[j];      for (i=0; i<=cptcode; i++) {
         }        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
         for(i=1, vepp=0.;i <=nlstate;i++)      }
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];      ij=1; 
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));      for (i=1; i<=ncodemax[j]; i++) {
         for(j=1;j <=nlstate;j++){        for (k=0; k<= maxncov; k++) {
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));          if (Ndum[k] != 0) {
         }            nbcode[Tvar[j]][ij]=k; 
         fprintf(ficrest,"\n");            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       }            
     }            ij++;
   }          }
                  if (ij > ncodemax[j]) break; 
  fclose(ficreseij);        }  
  fclose(ficresvij);      } 
   fclose(ficrest);    }  
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   /*scanf("%d ",i); */  
    for (i=1; i<=ncovmodel-2; i++) { 
   /*------- Variance limit prevalence------*/       /* 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];
 strcpy(fileresvpl,"vpl");     Ndum[ij]++;
   strcat(fileresvpl,fileres);   }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);   ij=1;
     exit(0);   for (i=1; i<= maxncov; i++) {
   }     if((Ndum[i]!=0) && (i<=ncovcol)){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);       Tvaraff[ij]=i; /*For printing */
        ij++;
  k=0;     }
  for(cptcov=1;cptcov<=i1;cptcov++){   }
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   
      k=k+1;   cptcoveff=ij-1; /*Number of simple covariates*/
      fprintf(ficresvpl,"\n#****** ");  }
      for(j=1;j<=cptcovn;j++)  
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);  /*********** Health Expectancies ****************/
      fprintf(ficresvpl,"******\n");  
        void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
      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);    /* Health expectancies, no variances */
    }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
  }    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
   fclose(ficresvpl);    double ***p3mat;
     double eip;
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    pstamp(ficreseij);
      fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficreseij,"# Age");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    for(i=1; i<=nlstate;i++){
        for(j=1; j<=nlstate;j++){
          fprintf(ficreseij," e%1d%1d ",i,j);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      }
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficreseij," e%1d. ",i);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficreseij,"\n");
    
   free_matrix(matcov,1,npar,1,npar);    
   free_vector(delti,1,npar);    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    }
     else  hstepm=estepm;   
   printf("End of Imach\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */     * This is mainly to measure the difference between two models: for example
       * if stepm=24 months pijx are given only every 2 years and by summing them
   /* 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);*/     * we are calculating an estimate of the Life Expectancy assuming a linear 
   /*printf("Total time was %d uSec.\n", total_usecs);*/     * progression in between and thus overestimating or underestimating according
   /*------ End -----------*/     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
  end:     * to compare the new estimate of Life expectancy with the same linear 
 #ifdef windows     * hypothesis. A more precise result, taking into account a more precise
  chdir(pathcd);     * curvature will be obtained if estepm is as small as stepm. */
 #endif  
  system("wgnuplot graph.plt");    /* 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. 
 #ifdef windows       nhstepm is the number of hstepm from age to agelim 
   while (z[0] != 'q') {       nstepm is the number of stepm from age to agelin. 
     chdir(pathcd);       Look at hpijx to understand the reason of that which relies in memory size
     printf("\nType e to edit output files, c to start again, and q for exiting: ");       and note for a fixed period like estepm months */
     scanf("%s",z);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     if (z[0] == 'c') system("./imach");       survival function given by stepm (the optimization length). Unfortunately it
     else if (z[0] == 'e') {       means that if the survival funtion is printed only each two years of age and if
       chdir(path);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       system("index.htm");       results. So we changed our mind and took the option of the best precision.
     }    */
     else if (z[0] == 'q') exit(0);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
 #endif    agelim=AGESUP;
 }    /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* 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 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
       
     }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
     
   }
   
   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   
   {
     /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
     */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
     double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   
     double eip, vip;
   
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * 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 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* 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 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* 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 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ 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[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     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);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     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);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* 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. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           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);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;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;
         }
       }
     
       /* pptj */
       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);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       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);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  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%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       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);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     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);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   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 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\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");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           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];
           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]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(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",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* 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;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     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(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.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%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,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=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 m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         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 '%d' at line number %d %s 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);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         exit(1);
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           exit(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 */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         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 */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.4  
changed lines
  Added in v.1.128


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