Diff for /imach/src/imach.c between versions 1.4 and 1.198

version 1.4, 2001/05/02 17:34:41 version 1.198, 2015/09/03 07:14:39
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 1.198  2015/09/03 07:14:39  brouard
   individuals from different ages are interviewed on their health status    Summary: 0.98q5 Flavia
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.197  2015/09/01 18:24:39  brouard
   Health expectancies are computed from the transistions observed between    *** empty log message ***
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.196  2015/08/18 23:17:52  brouard
   reach the Maximum Likelihood of the parameters involved in the model.    Summary: 0.98q5
   The simplest model is the multinomial logistic model where pij is  
   the probabibility to be observed in state j at the second wave conditional    Revision 1.195  2015/08/18 16:28:39  brouard
   to be observed in state i at the first wave. Therefore the model is:    Summary: Adding a hack for testing purpose
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'  
   is a covariate. If you want to have a more complex model than "constant and    After reading the title, ftol and model lines, if the comment line has
   age", you should modify the program where the markup    a q, starting with #q, the answer at the end of the run is quit. It
     *Covariates have to be included here again* invites you to do it.    permits to run test files in batch with ctest. The former workaround was
   More covariates you add, less is the speed of the convergence.    $ echo q | imach foo.imach
   
   The advantage that this computer programme claims, comes from that if the    Revision 1.194  2015/08/18 13:32:00  brouard
   delay between waves is not identical for each individual, or if some    Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.193  2015/08/04 07:17:42  brouard
   hPijx is the probability to be    Summary: 0.98q4
   observed in state i at age x+h conditional to the observed state i at age  
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Revision 1.192  2015/07/16 16:49:02  brouard
   unobserved intermediate  states. This elementary transition (by month or    Summary: Fixing some outputs
   quarter trimester, semester or year) is model as a multinomial logistic.  
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.191  2015/07/14 10:00:33  brouard
   and the contribution of each individual to the likelihood is simply hPijx.    Summary: Some fixes
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.190  2015/05/05 08:51:13  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: Adding digits in output parameters (7 digits instead of 6)
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Fix 1+age+.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.189  2015/04/30 14:45:16  brouard
   from the European Union.    Summary: 0.98q2
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.188  2015/04/30 08:27:53  brouard
   can be accessed at http://euroreves.ined.fr/imach .    *** empty log message ***
   **********************************************************************/  
      Revision 1.187  2015/04/29 09:11:15  brouard
 #include <math.h>    *** empty log message ***
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.186  2015/04/23 12:01:52  brouard
 #include <unistd.h>    Summary: V1*age is working now, version 0.98q1
   
 #define MAXLINE 256    Some codes had been disabled in order to simplify and Vn*age was
 #define FILENAMELENGTH 80    working in the optimization phase, ie, giving correct MLE parameters,
 /*#define DEBUG*/    but, as usual, outputs were not correct and program core dumped.
 #define windows  
     Revision 1.185  2015/03/11 13:26:42  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: Inclusion of compile and links command line for Intel Compiler
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.184  2015/03/11 11:52:39  brouard
 #define NINTERVMAX 8    Summary: Back from Windows 8. Intel Compiler
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.183  2015/03/10 20:34:32  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: 0.98q0, trying with directest, mnbrak fixed
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    We use directest instead of original Powell test; probably no
 #define AGESUP 130    incidence on the results, but better justifications;
 #define AGEBASE 40    We fixed Numerical Recipes mnbrak routine which was wrong and gave
     wrong results.
   
 int nvar;    Revision 1.182  2015/02/12 08:19:57  brouard
 static int cptcov;    Summary: Trying to keep directest which seems simpler and more general
 int cptcovn;    Author: Nicolas Brouard
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.181  2015/02/11 23:22:24  brouard
 int ndeath=1; /* Number of dead states */    Summary: Comments on Powell added
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
     Author:
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.180  2015/02/11 17:33:45  brouard
 int mle, weightopt;    Summary: Finishing move from main to function (hpijx and prevalence_limit)
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.179  2015/01/04 09:57:06  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Summary: back to OS/X
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    Revision 1.178  2015/01/04 09:35:48  brouard
 FILE *ficgp, *fichtm;    *** empty log message ***
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.177  2015/01/03 18:40:56  brouard
  FILE  *ficresvij;    Summary: Still testing ilc32 on OSX
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.176  2015/01/03 16:45:04  brouard
   char fileresvpl[FILENAMELENGTH];    *** empty log message ***
   
     Revision 1.175  2015/01/03 16:33:42  brouard
     *** empty log message ***
   
 #define NR_END 1    Revision 1.174  2015/01/03 16:15:49  brouard
 #define FREE_ARG char*    Summary: Still in cross-compilation
 #define FTOL 1.0e-10  
     Revision 1.173  2015/01/03 12:06:26  brouard
 #define NRANSI    Summary: trying to detect cross-compilation
 #define ITMAX 200  
     Revision 1.172  2014/12/27 12:07:47  brouard
 #define TOL 2.0e-4    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   
 #define CGOLD 0.3819660    Revision 1.171  2014/12/23 13:26:59  brouard
 #define ZEPS 1.0e-10    Summary: Back from Visual C
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Still problem with utsname.h on Windows
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.170  2014/12/23 11:17:12  brouard
 #define TINY 1.0e-20    Summary: Cleaning some \%% back to %%
   
 static double maxarg1,maxarg2;    The escape was mandatory for a specific compiler (which one?), but too many warnings.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.169  2014/12/22 23:08:31  brouard
      Summary: 0.98p
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   
 static double sqrarg;    Revision 1.168  2014/12/22 15:17:42  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Summary: update
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.167  2014/12/22 13:50:56  brouard
 int imx;    Summary: Testing uname and compiler version and if compiled 32 or 64
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Testing on Linux 64
   
 int m,nb;    Revision 1.166  2014/12/22 11:40:47  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;    *** empty log message ***
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij;    Revision 1.165  2014/12/16 11:20:36  brouard
     Summary: After compiling on Visual C
 double *weight;  
 int **s; /* Status */    * imach.c (Module): Merging 1.61 to 1.162
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab;    Revision 1.164  2014/12/16 10:52:11  brouard
     Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.163  2014/12/16 10:30:11  brouard
 /******************************************/    * imach.c (Module): Merging 1.61 to 1.162
   
 void replace(char *s, char*t)    Revision 1.162  2014/09/25 11:43:39  brouard
 {    Summary: temporary backup 0.99!
   int i;  
   int lg=20;    Revision 1.1  2014/09/16 11:06:58  brouard
   i=0;    Summary: With some code (wrong) for nlopt
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Author:
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.161  2014/09/15 20:41:41  brouard
   }    Summary: Problem with macro SQR on Intel compiler
 }  
     Revision 1.160  2014/09/02 09:24:05  brouard
 int nbocc(char *s, char occ)    *** empty log message ***
 {  
   int i,j=0;    Revision 1.159  2014/09/01 10:34:10  brouard
   int lg=20;    Summary: WIN32
   i=0;    Author: Brouard
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.158  2014/08/27 17:11:51  brouard
   if  (s[i] == occ ) j++;    *** empty log message ***
   }  
   return j;    Revision 1.157  2014/08/27 16:26:55  brouard
 }    Summary: Preparing windows Visual studio version
     Author: Brouard
 void cutv(char *u,char *v, char*t, char occ)  
 {    In order to compile on Visual studio, time.h is now correct and time_t
   int i,lg,j,p;    and tm struct should be used. difftime should be used but sometimes I
   i=0;    just make the differences in raw time format (time(&now).
   for(j=0; j<=strlen(t)-1; j++) {    Trying to suppress #ifdef LINUX
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Add xdg-open for __linux in order to open default browser.
   }  
     Revision 1.156  2014/08/25 20:10:10  brouard
   lg=strlen(t);    *** empty log message ***
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Revision 1.155  2014/08/25 18:32:34  brouard
     u[p]='\0';    Summary: New compile, minor changes
   }    Author: Brouard
   
    for(j=0; j<= lg; j++) {    Revision 1.154  2014/06/20 17:32:08  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    Summary: Outputs now all graphs of convergence to period prevalence
   }  
 }    Revision 1.153  2014/06/20 16:45:46  brouard
     Summary: If 3 live state, convergence to period prevalence on same graph
 /********************** nrerror ********************/    Author: Brouard
   
 void nrerror(char error_text[])    Revision 1.152  2014/06/18 17:54:09  brouard
 {    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.151  2014/06/18 16:43:30  brouard
   exit(1);    *** empty log message ***
 }  
 /*********************** vector *******************/    Revision 1.150  2014/06/18 16:42:35  brouard
 double *vector(int nl, int nh)    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 {    Author: brouard
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.149  2014/06/18 15:51:14  brouard
   if (!v) nrerror("allocation failure in vector");    Summary: Some fixes in parameter files errors
   return v-nl+NR_END;    Author: Nicolas Brouard
 }  
     Revision 1.148  2014/06/17 17:38:48  brouard
 /************************ free vector ******************/    Summary: Nothing new
 void free_vector(double*v, int nl, int nh)    Author: Brouard
 {  
   free((FREE_ARG)(v+nl-NR_END));    Just a new packaging for OS/X version 0.98nS
 }  
     Revision 1.147  2014/06/16 10:33:11  brouard
 /************************ivector *******************************/    *** empty log message ***
 int *ivector(long nl,long nh)  
 {    Revision 1.146  2014/06/16 10:20:28  brouard
   int *v;    Summary: Merge
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Author: Brouard
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    Merge, before building revised version.
 }  
     Revision 1.145  2014/06/10 21:23:15  brouard
 /******************free ivector **************************/    Summary: Debugging with valgrind
 void free_ivector(int *v, long nl, long nh)    Author: Nicolas Brouard
 {  
   free((FREE_ARG)(v+nl-NR_END));    Lot of changes in order to output the results with some covariates
 }    After the Edimburgh REVES conference 2014, it seems mandatory to
     improve the code.
 /******************* imatrix *******************************/    No more memory valgrind error but a lot has to be done in order to
 int **imatrix(long nrl, long nrh, long ncl, long nch)    continue the work of splitting the code into subroutines.
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Also, decodemodel has been improved. Tricode is still not
 {    optimal. nbcode should be improved. Documentation has been added in
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    the source code.
   int **m;  
      Revision 1.143  2014/01/26 09:45:38  brouard
   /* allocate pointers to rows */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   m += NR_END;    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   m -= nrl;  
      Revision 1.142  2014/01/26 03:57:36  brouard
      Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.141  2014/01/26 02:42:01  brouard
   m[nrl] -= ncl;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Revision 1.140  2011/09/02 10:37:54  brouard
      Summary: times.h is ok with mingw32 now.
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.139  2010/06/14 07:50:17  brouard
 }    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
     I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.138  2010/04/30 18:19:40  brouard
       int **m;    *** empty log message ***
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.137  2010/04/29 18:11:38  brouard
 {    (Module): Checking covariates for more complex models
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    than V1+V2. A lot of change to be done. Unstable.
   free((FREE_ARG) (m+nrl-NR_END));  
 }    Revision 1.136  2010/04/26 20:30:53  brouard
     (Module): merging some libgsl code. Fixing computation
 /******************* matrix *******************************/    of likelione (using inter/intrapolation if mle = 0) in order to
 double **matrix(long nrl, long nrh, long ncl, long nch)    get same likelihood as if mle=1.
 {    Some cleaning of code and comments added.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.135  2009/10/29 15:33:14  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.134  2009/10/29 13:18:53  brouard
   m += NR_END;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   m -= nrl;  
     Revision 1.133  2009/07/06 10:21:25  brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    just nforces
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.132  2009/07/06 08:22:05  brouard
   m[nrl] -= ncl;    Many tings
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.131  2009/06/20 16:22:47  brouard
   return m;    Some dimensions resccaled
 }  
     Revision 1.130  2009/05/26 06:44:34  brouard
 /*************************free matrix ************************/    (Module): Max Covariate is now set to 20 instead of 8. A
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    lot of cleaning with variables initialized to 0. Trying to make
 {    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.129  2007/08/31 13:49:27  lievre
 }    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   
 /******************* ma3x *******************************/    Revision 1.128  2006/06/30 13:02:05  brouard
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    (Module): Clarifications on computing e.j
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.127  2006/04/28 18:11:50  brouard
   double ***m;    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    loop. Now we define nhstepma in the age loop.
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): In order to speed up (in case of numerous covariates) we
   m += NR_END;    compute health expectancies (without variances) in a first step
   m -= nrl;    and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    computation.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    In the future we should be able to stop the program is only health
   m[nrl] += NR_END;    expectancies and graph are needed without standard deviations.
   m[nrl] -= ncl;  
     Revision 1.126  2006/04/28 17:23:28  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    loop. Now we define nhstepma in the age loop.
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Version 0.98h
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    Revision 1.125  2006/04/04 15:20:31  lievre
   for (j=ncl+1; j<=nch; j++)    Errors in calculation of health expectancies. Age was not initialized.
     m[nrl][j]=m[nrl][j-1]+nlay;    Forecasting file added.
    
   for (i=nrl+1; i<=nrh; i++) {    Revision 1.124  2006/03/22 17:13:53  lievre
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Parameters are printed with %lf instead of %f (more numbers after the comma).
     for (j=ncl+1; j<=nch; j++)    The log-likelihood is printed in the log file
       m[i][j]=m[i][j-1]+nlay;  
   }    Revision 1.123  2006/03/20 10:52:43  brouard
   return m;    * imach.c (Module): <title> changed, corresponds to .htm file
 }    name. <head> headers where missing.
   
 /*************************free ma3x ************************/    * imach.c (Module): Weights can have a decimal point as for
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    English (a comma might work with a correct LC_NUMERIC environment,
 {    otherwise the weight is truncated).
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Modification of warning when the covariates values are not 0 or
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    1.
   free((FREE_ARG)(m+nrl-NR_END));    Version 0.98g
 }  
     Revision 1.122  2006/03/20 09:45:41  brouard
 /***************** f1dim *************************/    (Module): Weights can have a decimal point as for
 extern int ncom;    English (a comma might work with a correct LC_NUMERIC environment,
 extern double *pcom,*xicom;    otherwise the weight is truncated).
 extern double (*nrfunc)(double []);    Modification of warning when the covariates values are not 0 or
      1.
 double f1dim(double x)    Version 0.98g
 {  
   int j;    Revision 1.121  2006/03/16 17:45:01  lievre
   double f;    * imach.c (Module): Comments concerning covariates added
   double *xt;  
      * imach.c (Module): refinements in the computation of lli if
   xt=vector(1,ncom);    status=-2 in order to have more reliable computation if stepm is
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    not 1 month. Version 0.98f
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);    Revision 1.120  2006/03/16 15:10:38  lievre
   return f;    (Module): refinements in the computation of lli if
 }    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Revision 1.119  2006/03/15 17:42:26  brouard
 {    (Module): Bug if status = -2, the loglikelihood was
   int iter;    computed as likelihood omitting the logarithm. Version O.98e
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    Revision 1.118  2006/03/14 18:20:07  brouard
   double ftemp;    (Module): varevsij Comments added explaining the second
   double p,q,r,tol1,tol2,u,v,w,x,xm;    table of variances if popbased=1 .
   double e=0.0;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
      (Module): Function pstamp added
   a=(ax < cx ? ax : cx);    (Module): Version 0.98d
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    Revision 1.117  2006/03/14 17:16:22  brouard
   fw=fv=fx=(*f)(x);    (Module): varevsij Comments added explaining the second
   for (iter=1;iter<=ITMAX;iter++) {    table of variances if popbased=1 .
     xm=0.5*(a+b);    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    (Module): Function pstamp added
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    (Module): Version 0.98d
     printf(".");fflush(stdout);  
 #ifdef DEBUG    Revision 1.116  2006/03/06 10:29:27  brouard
     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);    (Module): Variance-covariance wrong links and
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    varian-covariance of ej. is needed (Saito).
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    Revision 1.115  2006/02/27 12:17:45  brouard
       *xmin=x;    (Module): One freematrix added in mlikeli! 0.98c
       return fx;  
     }    Revision 1.114  2006/02/26 12:57:58  brouard
     ftemp=fu;    (Module): Some improvements in processing parameter
     if (fabs(e) > tol1) {    filename with strsep.
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    Revision 1.113  2006/02/24 14:20:24  brouard
       p=(x-v)*q-(x-w)*r;    (Module): Memory leaks checks with valgrind and:
       q=2.0*(q-r);    datafile was not closed, some imatrix were not freed and on matrix
       if (q > 0.0) p = -p;    allocation too.
       q=fabs(q);  
       etemp=e;    Revision 1.112  2006/01/30 09:55:26  brouard
       e=d;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    Revision 1.111  2006/01/25 20:38:18  brouard
       else {    (Module): Lots of cleaning and bugs added (Gompertz)
         d=p/q;    (Module): Comments can be added in data file. Missing date values
         u=x+d;    can be a simple dot '.'.
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    Revision 1.110  2006/01/25 00:51:50  brouard
       }    (Module): Lots of cleaning and bugs added (Gompertz)
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    Revision 1.109  2006/01/24 19:37:15  brouard
     }    (Module): Comments (lines starting with a #) are allowed in data.
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);    Revision 1.108  2006/01/19 18:05:42  lievre
     if (fu <= fx) {    Gnuplot problem appeared...
       if (u >= x) a=x; else b=x;    To be fixed
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)    Revision 1.107  2006/01/19 16:20:37  brouard
         } else {    Test existence of gnuplot in imach path
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {    Revision 1.106  2006/01/19 13:24:36  brouard
             v=w;    Some cleaning and links added in html output
             w=u;  
             fv=fw;    Revision 1.105  2006/01/05 20:23:19  lievre
             fw=fu;    *** empty log message ***
           } else if (fu <= fv || v == x || v == w) {  
             v=u;    Revision 1.104  2005/09/30 16:11:43  lievre
             fv=fu;    (Module): sump fixed, loop imx fixed, and simplifications.
           }    (Module): If the status is missing at the last wave but we know
         }    that the person is alive, then we can code his/her status as -2
   }    (instead of missing=-1 in earlier versions) and his/her
   nrerror("Too many iterations in brent");    contributions to the likelihood is 1 - Prob of dying from last
   *xmin=x;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   return fx;    the healthy state at last known wave). Version is 0.98
 }  
     Revision 1.103  2005/09/30 15:54:49  lievre
 /****************** mnbrak ***********************/    (Module): sump fixed, loop imx fixed, and simplifications.
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    Revision 1.102  2004/09/15 17:31:30  brouard
             double (*func)(double))    Add the possibility to read data file including tab characters.
 {  
   double ulim,u,r,q, dum;    Revision 1.101  2004/09/15 10:38:38  brouard
   double fu;    Fix on curr_time
    
   *fa=(*func)(*ax);    Revision 1.100  2004/07/12 18:29:06  brouard
   *fb=(*func)(*bx);    Add version for Mac OS X. Just define UNIX in Makefile
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)    Revision 1.99  2004/06/05 08:57:40  brouard
       SHFT(dum,*fb,*fa,dum)    *** empty log message ***
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);    Revision 1.98  2004/05/16 15:05:56  brouard
   *fc=(*func)(*cx);    New version 0.97 . First attempt to estimate force of mortality
   while (*fb > *fc) {    directly from the data i.e. without the need of knowing the health
     r=(*bx-*ax)*(*fb-*fc);    state at each age, but using a Gompertz model: log u =a + b*age .
     q=(*bx-*cx)*(*fb-*fa);    This is the basic analysis of mortality and should be done before any
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    other analysis, in order to test if the mortality estimated from the
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    cross-longitudinal survey is different from the mortality estimated
     ulim=(*bx)+GLIMIT*(*cx-*bx);    from other sources like vital statistic data.
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);    The same imach parameter file can be used but the option for mle should be -3.
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);    Agnès, who wrote this part of the code, tried to keep most of the
       if (fu < *fc) {    former routines in order to include the new code within the former code.
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))    The output is very simple: only an estimate of the intercept and of
           }    the slope with 95% confident intervals.
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;    Current limitations:
       fu=(*func)(u);    A) Even if you enter covariates, i.e. with the
     } else {    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
       u=(*cx)+GOLD*(*cx-*bx);    B) There is no computation of Life Expectancy nor Life Table.
       fu=(*func)(u);  
     }    Revision 1.97  2004/02/20 13:25:42  lievre
     SHFT(*ax,*bx,*cx,u)    Version 0.96d. Population forecasting command line is (temporarily)
       SHFT(*fa,*fb,*fc,fu)    suppressed.
       }  
 }    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 /*************** linmin ************************/    rewritten within the same printf. Workaround: many printfs.
   
 int ncom;    Revision 1.95  2003/07/08 07:54:34  brouard
 double *pcom,*xicom;    * imach.c (Repository):
 double (*nrfunc)(double []);    (Repository): Using imachwizard code to output a more meaningful covariance
      matrix (cov(a12,c31) instead of numbers.
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {    Revision 1.94  2003/06/27 13:00:02  brouard
   double brent(double ax, double bx, double cx,    Just cleaning
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);    Revision 1.93  2003/06/25 16:33:55  brouard
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    (Module): On windows (cygwin) function asctime_r doesn't
               double *fc, double (*func)(double));    exist so I changed back to asctime which exists.
   int j;    (Module): Version 0.96b
   double xx,xmin,bx,ax;  
   double fx,fb,fa;    Revision 1.92  2003/06/25 16:30:45  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
   ncom=n;    exist so I changed back to asctime which exists.
   pcom=vector(1,n);  
   xicom=vector(1,n);    Revision 1.91  2003/06/25 15:30:29  brouard
   nrfunc=func;    * imach.c (Repository): Duplicated warning errors corrected.
   for (j=1;j<=n;j++) {    (Repository): Elapsed time after each iteration is now output. It
     pcom[j]=p[j];    helps to forecast when convergence will be reached. Elapsed time
     xicom[j]=xi[j];    is stamped in powell.  We created a new html file for the graphs
   }    concerning matrix of covariance. It has extension -cov.htm.
   ax=0.0;  
   xx=1.0;    Revision 1.90  2003/06/24 12:34:15  brouard
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    (Module): Some bugs corrected for windows. Also, when
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    mle=-1 a template is output in file "or"mypar.txt with the design
 #ifdef DEBUG    of the covariance matrix to be input.
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif    Revision 1.89  2003/06/24 12:30:52  brouard
   for (j=1;j<=n;j++) {    (Module): Some bugs corrected for windows. Also, when
     xi[j] *= xmin;    mle=-1 a template is output in file "or"mypar.txt with the design
     p[j] += xi[j];    of the covariance matrix to be input.
   }  
   free_vector(xicom,1,n);    Revision 1.88  2003/06/23 17:54:56  brouard
   free_vector(pcom,1,n);    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 }  
     Revision 1.87  2003/06/18 12:26:01  brouard
 /*************** powell ************************/    Version 0.96
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))    Revision 1.86  2003/06/17 20:04:08  brouard
 {    (Module): Change position of html and gnuplot routines and added
   void linmin(double p[], double xi[], int n, double *fret,    routine fileappend.
               double (*func)(double []));  
   int i,ibig,j;    Revision 1.85  2003/06/17 13:12:43  brouard
   double del,t,*pt,*ptt,*xit;    * imach.c (Repository): Check when date of death was earlier that
   double fp,fptt;    current date of interview. It may happen when the death was just
   double *xits;    prior to the death. In this case, dh was negative and likelihood
   pt=vector(1,n);    was wrong (infinity). We still send an "Error" but patch by
   ptt=vector(1,n);    assuming that the date of death was just one stepm after the
   xit=vector(1,n);    interview.
   xits=vector(1,n);    (Repository): Because some people have very long ID (first column)
   *fret=(*func)(p);    we changed int to long in num[] and we added a new lvector for
   for (j=1;j<=n;j++) pt[j]=p[j];    memory allocation. But we also truncated to 8 characters (left
   for (*iter=1;;++(*iter)) {    truncation)
     fp=(*fret);    (Repository): No more line truncation errors.
     ibig=0;  
     del=0.0;    Revision 1.84  2003/06/13 21:44:43  brouard
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    * imach.c (Repository): Replace "freqsummary" at a correct
     for (i=1;i<=n;i++)    place. It differs from routine "prevalence" which may be called
       printf(" %d %.12f",i, p[i]);    many times. Probs is memory consuming and must be used with
     printf("\n");    parcimony.
     for (i=1;i<=n;i++) {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);    Revision 1.83  2003/06/10 13:39:11  lievre
 #ifdef DEBUG    *** empty log message ***
       printf("fret=%lf \n",*fret);  
 #endif    Revision 1.82  2003/06/05 15:57:20  brouard
       printf("%d",i);fflush(stdout);    Add log in  imach.c and  fullversion number is now printed.
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  */
         del=fabs(fptt-(*fret));  /*
         ibig=i;     Interpolated Markov Chain
       }  
 #ifdef DEBUG    Short summary of the programme:
       printf("%d %.12e",i,(*fret));    
       for (j=1;j<=n;j++) {    This program computes Healthy Life Expectancies from
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
         printf(" x(%d)=%.12e",j,xit[j]);    first survey ("cross") where individuals from different ages are
       }    interviewed on their health status or degree of disability (in the
       for(j=1;j<=n;j++)    case of a health survey which is our main interest) -2- at least a
         printf(" p=%.12e",p[j]);    second wave of interviews ("longitudinal") which measure each change
       printf("\n");    (if any) in individual health status.  Health expectancies are
 #endif    computed from the time spent in each health state according to a
     }    model. More health states you consider, more time is necessary to reach the
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    Maximum Likelihood of the parameters involved in the model.  The
 #ifdef DEBUG    simplest model is the multinomial logistic model where pij is the
       int k[2],l;    probability to be observed in state j at the second wave
       k[0]=1;    conditional to be observed in state i at the first wave. Therefore
       k[1]=-1;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
       printf("Max: %.12e",(*func)(p));    'age' is age and 'sex' is a covariate. If you want to have a more
       for (j=1;j<=n;j++)    complex model than "constant and age", you should modify the program
         printf(" %.12e",p[j]);    where the markup *Covariates have to be included here again* invites
       printf("\n");    you to do it.  More covariates you add, slower the
       for(l=0;l<=1;l++) {    convergence.
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    The advantage of this computer programme, compared to a simple
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    multinomial logistic model, is clear when the delay between waves is not
         }    identical for each individual. Also, if a individual missed an
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    intermediate interview, the information is lost, but taken into
       }    account using an interpolation or extrapolation.  
 #endif  
     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_vector(xit,1,n);    split into an exact number (nh*stepm) of unobserved intermediate
       free_vector(xits,1,n);    states. This elementary transition (by month, quarter,
       free_vector(ptt,1,n);    semester or year) is modelled as a multinomial logistic.  The hPx
       free_vector(pt,1,n);    matrix is simply the matrix product of nh*stepm elementary matrices
       return;    and the contribution of each individual to the likelihood is simply
     }    hPijx.
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {    Also this programme outputs the covariance matrix of the parameters but also
       ptt[j]=2.0*p[j]-pt[j];    of the life expectancies. It also computes the period (stable) prevalence. 
       xit[j]=p[j]-pt[j];    
       pt[j]=p[j];    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
     }             Institut national d'études démographiques, Paris.
     fptt=(*func)(ptt);    This software have been partly granted by Euro-REVES, a concerted action
     if (fptt < fp) {    from the European Union.
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    It is copyrighted identically to a GNU software product, ie programme and
       if (t < 0.0) {    software can be distributed freely for non commercial use. Latest version
         linmin(p,xit,n,fret,func);    can be accessed at http://euroreves.ined.fr/imach .
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
           xi[j][n]=xit[j];    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
         }    
 #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++)    main
           printf(" %.12e",xit[j]);    read parameterfile
         printf("\n");    read datafile
 #endif    concatwav
       }    freqsummary
     }    if (mle >= 1)
   }      mlikeli
 }    print results files
     if mle==1 
 /**** Prevalence limit ****************/       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        begin-prev-date,...
 {    open gnuplot file
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    open html file
      matrix by transitions matrix until convergence is reached */    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
      for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   int i, ii,j,k;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   double min, max, maxmin, maxmax,sumnew=0.;      freexexit2 possible for memory heap.
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();    h Pij x                         | pij_nom  ficrestpij
   double **newm;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   double agefin, delaymax=50 ; /* Max number of years to converge */         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
          1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
     }    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
     newm=savm;  
     /* Covariates have to be included here again */    forecasting if prevfcast==1 prevforecast call prevalence()
     cov[1]=1.;    health expectancies
     cov[2]=agefin;    Variance-covariance of DFLE
     if (cptcovn>0){    prevalence()
       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]]);*/}     movingaverage()
     }    varevsij() 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    if popbased==1 varevsij(,popbased)
     total life expectancies
     savm=oldm;    Variance of period (stable) prevalence
     oldm=newm;   end
     maxmax=0.;  */
     for(j=1;j<=nlstate;j++){  
       min=1.;  /* #define DEBUG */
       max=0.;  /* #define DEBUGBRENT */
       for(i=1; i<=nlstate; i++) {  #define POWELL /* Instead of NLOPT */
         sumnew=0;  #define POWELLF1F3 /* Skip test */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
         prlim[i][j]= newm[i][j]/(1-sumnew);  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);  #include <math.h>
       }  #include <stdio.h>
       maxmin=max-min;  #include <stdlib.h>
       maxmax=FMAX(maxmax,maxmin);  #include <string.h>
     }  
     if(maxmax < ftolpl){  #ifdef _WIN32
       return prlim;  #include <io.h>
     }  #include <windows.h>
   }  #include <tchar.h>
 }  #else
   #include <unistd.h>
 /*************** transition probabilities **********/  #endif
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #include <limits.h>
 {  #include <sys/types.h>
   double s1, s2;  
   /*double t34;*/  #if defined(__GNUC__)
   int i,j,j1, nc, ii, jj;  #include <sys/utsname.h> /* Doesn't work on Windows */
   #endif
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){  #include <sys/stat.h>
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #include <errno.h>
         /*s2 += param[i][j][nc]*cov[nc];*/  /* extern int errno; */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /* #ifdef LINUX */
       }  /* #include <time.h> */
       ps[i][j]=s2;  /* #include "timeval.h" */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /* #else */
     }  /* #include <sys/time.h> */
     for(j=i+1; j<=nlstate+ndeath;j++){  /* #endif */
       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];  #include <time.h>
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }  #ifdef GSL
       ps[i][j]=s2;  #include <gsl/gsl_errno.h>
     }  #include <gsl/gsl_multimin.h>
   }  #endif
   for(i=1; i<= nlstate; i++){  
      s1=0;  
     for(j=1; j<i; j++)  #ifdef NLOPT
       s1+=exp(ps[i][j]);  #include <nlopt.h>
     for(j=i+1; j<=nlstate+ndeath; j++)  typedef struct {
       s1+=exp(ps[i][j]);    double (* function)(double [] );
     ps[i][i]=1./(s1+1.);  } myfunc_data ;
     for(j=1; j<i; j++)  #endif
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  /* #include <libintl.h> */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /* #define _(String) gettext (String) */
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #define GNUPLOTPROGRAM "gnuplot"
     for(jj=1; jj<= nlstate+ndeath; jj++){  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       ps[ii][jj]=0;  #define FILENAMELENGTH 132
       ps[ii][ii]=1;  
     }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
     for(jj=1; jj<= nlstate+ndeath; jj++){  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
      printf("%lf ",ps[ii][jj]);  
    }  #define NINTERVMAX 8
     printf("\n ");  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
     }  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     printf("\n ");printf("%lf ",cov[2]);*/  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
 /*  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  #define MAXN 20000
   goto end;*/  #define YEARM 12. /**< Number of months per year */
     return ps;  #define AGESUP 130
 }  #define AGEBASE 40
   #define AGEOVERFLOW 1.e20
 /**************** Product of 2 matrices ******************/  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
   #ifdef _WIN32
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  #define DIRSEPARATOR '\\'
 {  #define CHARSEPARATOR "\\"
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  #define ODIRSEPARATOR '/'
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  #else
   /* in, b, out are matrice of pointers which should have been initialized  #define DIRSEPARATOR '/'
      before: only the contents of out is modified. The function returns  #define CHARSEPARATOR "/"
      a pointer to pointers identical to out */  #define ODIRSEPARATOR '\\'
   long i, j, k;  #endif
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)  /* $Id$ */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /* $State$ */
         out[i][k] +=in[i][j]*b[j][k];  #include "version.h"
   char version[]=__IMACH_VERSION__;
   return out;  char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
 }  char fullversion[]="$Revision$ $Date$"; 
   char strstart[80];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 /************* Higher Matrix Product ***************/  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
 {  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
      duration (i.e. until  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  int cptcovprodnoage=0; /**< Number of covariate products without age */   
      (typically every 2 years instead of every month which is too big).  int cptcoveff=0; /* Total number of covariates to vary for printing results */
      Model is determined by parameters x and covariates have to be  int cptcov=0; /* Working variable */
      included manually here.  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
      */  int ndeath=1; /* Number of dead states */
   int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int i, j, d, h, k;  int popbased=0;
   double **out, cov[NCOVMAX];  
   double **newm;  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav=0; /* Maxim number of waves */
   /* Hstepm could be zero and should return the unit matrix */  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   for (i=1;i<=nlstate+ndeath;i++)  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     for (j=1;j<=nlstate+ndeath;j++){  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       oldm[i][j]=(i==j ? 1.0 : 0.0);                     to the likelihood and the sum of weights (done by funcone)*/
       po[i][j][0]=(i==j ? 1.0 : 0.0);  int mle=1, weightopt=0;
     }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   for(h=1; h <=nhstepm; h++){  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     for(d=1; d <=hstepm; d++){             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       newm=savm;  int countcallfunc=0;  /* Count the number of calls to func */
       /* Covariates have to be included here again */  double jmean=1; /* Mean space between 2 waves */
       cov[1]=1.;  double **matprod2(); /* test */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  double **oldm, **newm, **savm; /* Working pointers to matrices */
       if (cptcovn>0){  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];  /*FILE *fic ; */ /* Used in readdata only */
     }  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  FILE *ficlog, *ficrespow;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  int globpr=0; /* Global variable for printing or not */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  double fretone; /* Only one call to likelihood */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  long ipmx=0; /* Number of contributions */
       savm=oldm;  double sw; /* Sum of weights */
       oldm=newm;  char filerespow[FILENAMELENGTH];
     }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     for(i=1; i<=nlstate+ndeath; i++)  FILE *ficresilk;
       for(j=1;j<=nlstate+ndeath;j++) {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
         po[i][j][h]=newm[i][j];  FILE *ficresprobmorprev;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  FILE *fichtm, *fichtmcov; /* Html File */
          */  FILE *ficreseij;
       }  char filerese[FILENAMELENGTH];
   } /* end h */  FILE *ficresstdeij;
   return po;  char fileresstde[FILENAMELENGTH];
 }  FILE *ficrescveij;
   char filerescve[FILENAMELENGTH];
   FILE  *ficresvij;
 /*************** log-likelihood *************/  char fileresv[FILENAMELENGTH];
 double func( double *x)  FILE  *ficresvpl;
 {  char fileresvpl[FILENAMELENGTH];
   int i, ii, j, k, mi, d;  char title[MAXLINE];
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   double **out;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   double sw; /* Sum of weights */  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   double lli; /* Individual log likelihood */  char command[FILENAMELENGTH];
   long ipmx;  int  outcmd=0;
   /*extern weight */  
   /* We are differentiating ll according to initial status */  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  char filelog[FILENAMELENGTH]; /* Log file */
 printf(" %d\n",s[4][i]);  char filerest[FILENAMELENGTH];
   */  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
        for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /* struct timezone tzp; */
             for(d=0; d<dh[mi][i]; d++){  /* extern int gettimeofday(); */
         newm=savm;  struct tm tml, *gmtime(), *localtime();
           cov[1]=1.;  
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  extern time_t time();
           if (cptcovn>0){  
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];  struct tm start_time, end_time, curr_time, last_time, forecast_time;
             }  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  struct tm tm;
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
           savm=oldm;  char strcurr[80], strfor[80];
           oldm=newm;  
   char *endptr;
   long lval;
       } /* end mult */  double dval;
      
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  #define NR_END 1
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  #define FREE_ARG char*
       ipmx +=1;  #define FTOL 1.0e-10
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  #define NRANSI 
     } /* end of wave */  #define ITMAX 200 
   } /* end of individual */  
   #define TOL 2.0e-4 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  #define CGOLD 0.3819660 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  #define ZEPS 1.0e-10 
   return -l;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
   #define GLIMIT 100.0 
 /*********** Maximum Likelihood Estimation ***************/  #define TINY 1.0e-20 
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  static double maxarg1,maxarg2;
 {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   int i,j, iter;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   double **xi,*delti;    
   double fret;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   xi=matrix(1,npar,1,npar);  #define rint(a) floor(a+0.5)
   for (i=1;i<=npar;i++)  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
     for (j=1;j<=npar;j++)  #define mytinydouble 1.0e-16
       xi[i][j]=(i==j ? 1.0 : 0.0);  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
   printf("Powell\n");  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   powell(p,xi,npar,ftol,&iter,&fret,func);  /* static double dsqrarg; */
   /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  static double sqrarg;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 }  int agegomp= AGEGOMP;
   
 /**** Computes Hessian and covariance matrix ***/  int imx; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  int stepm=1;
 {  /* Stepm, step in month: minimum step interpolation*/
   double  **a,**y,*x,pd;  
   double **hess;  int estepm;
   int i, j,jk;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   int *indx;  
   int m,nb;
   double hessii(double p[], double delta, int theta, double delti[]);  long *num;
   double hessij(double p[], double delti[], int i, int j);  int firstpass=0, lastpass=4,*cod, *cens;
   void lubksb(double **a, int npar, int *indx, double b[]) ;  int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
   void ludcmp(double **a, int npar, int *indx, double *d) ;                     covariate for which somebody answered excluding 
                      undefined. Usually 2: 0 and 1. */
   int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
   hess=matrix(1,npar,1,npar);                               covariate for which somebody answered including 
                                undefined. Usually 3: -1, 0 and 1. */
   printf("\nCalculation of the hessian matrix. Wait...\n");  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   for (i=1;i<=npar;i++){  double **pmmij, ***probs;
     printf("%d",i);fflush(stdout);  double *ageexmed,*agecens;
     hess[i][i]=hessii(p,ftolhess,i,delti);  double dateintmean=0;
     /*printf(" %f ",p[i]);*/  
   }  double *weight;
   int **s; /* Status */
   for (i=1;i<=npar;i++) {  double *agedc;
     for (j=1;j<=npar;j++)  {  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       if (j>i) {                    * covar=matrix(0,NCOVMAX,1,n); 
         printf(".%d%d",i,j);fflush(stdout);                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
         hess[i][j]=hessij(p,delti,i,j);  double  idx; 
         hess[j][i]=hess[i][j];  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       }  int *Tage;
     }  int *Ndum; /** Freq of modality (tricode */
   }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   printf("\n");  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double *lsurv, *lpop, *tpop;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
    double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   a=matrix(1,npar,1,npar);  double ftolhess; /**< Tolerance for computing hessian */
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);  /**************** split *************************/
   indx=ivector(1,npar);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   ludcmp(a,npar,indx,&pd);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
   for (j=1;j<=npar;j++) {    char  *ss;                            /* pointer */
     for (i=1;i<=npar;i++) x[i]=0;    int   l1=0, l2=0;                             /* length counters */
     x[j]=1;  
     lubksb(a,npar,indx,x);    l1 = strlen(path );                   /* length of path */
     for (i=1;i<=npar;i++){    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       matcov[i][j]=x[i];    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     }    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   }      strcpy( name, path );               /* we got the fullname name because no directory */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   printf("\n#Hessian matrix#\n");        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for (i=1;i<=npar;i++) {      /* get current working directory */
     for (j=1;j<=npar;j++) {      /*    extern  char* getcwd ( char *buf , int len);*/
       printf("%.3e ",hess[i][j]);  #ifdef WIN32
     }      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
     printf("\n");  #else
   }          if (getcwd(dirc, FILENAME_MAX) == NULL) {
   #endif
   /* Recompute Inverse */        return( GLOCK_ERROR_GETCWD );
   for (i=1;i<=npar;i++)      }
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      /* got dirc from getcwd*/
   ludcmp(a,npar,indx,&pd);      printf(" DIRC = %s \n",dirc);
     } else {                              /* strip direcotry from path */
   /*  printf("\n#Hessian matrix recomputed#\n");      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
   for (j=1;j<=npar;j++) {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     for (i=1;i<=npar;i++) x[i]=0;      strcpy( name, ss );         /* save file name */
     x[j]=1;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     lubksb(a,npar,indx,x);      dirc[l1-l2] = '\0';                 /* add zero */
     for (i=1;i<=npar;i++){      printf(" DIRC2 = %s \n",dirc);
       y[i][j]=x[i];    }
       printf("%.3e ",y[i][j]);    /* We add a separator at the end of dirc if not exists */
     }    l1 = strlen( dirc );                  /* length of directory */
     printf("\n");    if( dirc[l1-1] != DIRSEPARATOR ){
   }      dirc[l1] =  DIRSEPARATOR;
   */      dirc[l1+1] = 0; 
       printf(" DIRC3 = %s \n",dirc);
   free_matrix(a,1,npar,1,npar);    }
   free_matrix(y,1,npar,1,npar);    ss = strrchr( name, '.' );            /* find last / */
   free_vector(x,1,npar);    if (ss >0){
   free_ivector(indx,1,npar);      ss++;
   free_matrix(hess,1,npar,1,npar);      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
       l2= strlen(ss)+1;
 }      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
 /*************** hessian matrix ****************/    }
 double hessii( double x[], double delta, int theta, double delti[])  
 {    return( 0 );                          /* we're done */
   int i;  }
   int l=1, lmax=20;  
   double k1,k2;  
   double p2[NPARMAX+1];  /******************************************/
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  void replace_back_to_slash(char *s, char*t)
   double fx;  {
   int k=0,kmax=10;    int i;
   double l1;    int lg=0;
     i=0;
   fx=func(x);    lg=strlen(t);
   for (i=1;i<=npar;i++) p2[i]=x[i];    for(i=0; i<= lg; i++) {
   for(l=0 ; l <=lmax; l++){      (s[i] = t[i]);
     l1=pow(10,l);      if (t[i]== '\\') s[i]='/';
     delts=delt;    }
     for(k=1 ; k <kmax; k=k+1){  }
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;  char *trimbb(char *out, char *in)
       k1=func(p2)-fx;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       p2[theta]=x[theta]-delt;    char *s;
       k2=func(p2)-fx;    s=out;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    while (*in != '\0'){
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
              in++;
 #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);      *out++ = *in++;
 #endif    }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    *out='\0';
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    return s;
         k=kmax;  }
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  /* char *substrchaine(char *out, char *in, char *chain) */
         k=kmax; l=lmax*10.;  /* { */
       }  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  /*   char *s, *t; */
         delts=delt;  /*   t=in;s=out; */
       }  /*   while ((*in != *chain) && (*in != '\0')){ */
     }  /*     *out++ = *in++; */
   }  /*   } */
   delti[theta]=delts;  
   return res;  /*   /\* *in matches *chain *\/ */
    /*   while ((*in++ == *chain++) && (*in != '\0')){ */
 }  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   /*   } */
 double hessij( double x[], double delti[], int thetai,int thetaj)  /*   in--; chain--; */
 {  /*   while ( (*in != '\0')){ */
   int i;  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   int l=1, l1, lmax=20;  /*     *out++ = *in++; */
   double k1,k2,k3,k4,res,fx;  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   double p2[NPARMAX+1];  /*   } */
   int k;  /*   *out='\0'; */
   /*   out=s; */
   fx=func(x);  /*   return out; */
   for (k=1; k<=2; k++) {  /* } */
     for (i=1;i<=npar;i++) p2[i]=x[i];  char *substrchaine(char *out, char *in, char *chain)
     p2[thetai]=x[thetai]+delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    /* Substract chain 'chain' from 'in', return and output 'out' */
     k1=func(p2)-fx;    /* in="V1+V1*age+age*age+V2", chain="age*age" */
    
     p2[thetai]=x[thetai]+delti[thetai]/k;    char *strloc;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;    strcpy (out, in); 
      strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
     p2[thetai]=x[thetai]-delti[thetai]/k;    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    if(strloc != NULL){ 
     k3=func(p2)-fx;      /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
        memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
     p2[thetai]=x[thetai]-delti[thetai]/k;      /* strcpy (strloc, strloc +strlen(chain));*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    }
     k4=func(p2)-fx;    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    return out;
 #ifdef DEBUG  }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif  
   }  char *cutl(char *blocc, char *alocc, char *in, char occ)
   return res;  {
 }    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
        and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
 /************** Inverse of matrix **************/       gives blocc="abcdef" and alocc="ghi2j".
 void ludcmp(double **a, int n, int *indx, double *d)       If occ is not found blocc is null and alocc is equal to in. Returns blocc
 {    */
   int i,imax,j,k;    char *s, *t;
   double big,dum,sum,temp;    t=in;s=in;
   double *vv;    while ((*in != occ) && (*in != '\0')){
        *alocc++ = *in++;
   vv=vector(1,n);    }
   *d=1.0;    if( *in == occ){
   for (i=1;i<=n;i++) {      *(alocc)='\0';
     big=0.0;      s=++in;
     for (j=1;j<=n;j++)    }
       if ((temp=fabs(a[i][j])) > big) big=temp;   
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    if (s == t) {/* occ not found */
     vv[i]=1.0/big;      *(alocc-(in-s))='\0';
   }      in=s;
   for (j=1;j<=n;j++) {    }
     for (i=1;i<j;i++) {    while ( *in != '\0'){
       sum=a[i][j];      *blocc++ = *in++;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    }
       a[i][j]=sum;  
     }    *blocc='\0';
     big=0.0;    return t;
     for (i=j;i<=n;i++) {  }
       sum=a[i][j];  char *cutv(char *blocc, char *alocc, char *in, char occ)
       for (k=1;k<j;k++)  {
         sum -= a[i][k]*a[k][j];    /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
       a[i][j]=sum;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       if ( (dum=vv[i]*fabs(sum)) >= big) {       gives blocc="abcdef2ghi" and alocc="j".
         big=dum;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
         imax=i;    */
       }    char *s, *t;
     }    t=in;s=in;
     if (j != imax) {    while (*in != '\0'){
       for (k=1;k<=n;k++) {      while( *in == occ){
         dum=a[imax][k];        *blocc++ = *in++;
         a[imax][k]=a[j][k];        s=in;
         a[j][k]=dum;      }
       }      *blocc++ = *in++;
       *d = -(*d);    }
       vv[imax]=vv[j];    if (s == t) /* occ not found */
     }      *(blocc-(in-s))='\0';
     indx[j]=imax;    else
     if (a[j][j] == 0.0) a[j][j]=TINY;      *(blocc-(in-s)-1)='\0';
     if (j != n) {    in=s;
       dum=1.0/(a[j][j]);    while ( *in != '\0'){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      *alocc++ = *in++;
     }    }
   }  
   free_vector(vv,1,n);  /* Doesn't work */    *alocc='\0';
 ;    return s;
 }  }
   
 void lubksb(double **a, int n, int *indx, double b[])  int nbocc(char *s, char occ)
 {  {
   int i,ii=0,ip,j;    int i,j=0;
   double sum;    int lg=20;
      i=0;
   for (i=1;i<=n;i++) {    lg=strlen(s);
     ip=indx[i];    for(i=0; i<= lg; i++) {
     sum=b[ip];    if  (s[i] == occ ) j++;
     b[ip]=b[i];    }
     if (ii)    return j;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  }
     else if (sum) ii=i;  
     b[i]=sum;  /* void cutv(char *u,char *v, char*t, char occ) */
   }  /* { */
   for (i=n;i>=1;i--) {  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     sum=b[i];  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /*      gives u="abcdef2ghi" and v="j" *\/ */
     b[i]=sum/a[i][i];  /*   int i,lg,j,p=0; */
   }  /*   i=0; */
 }  /*   lg=strlen(t); */
   /*   for(j=0; j<=lg-1; j++) { */
 /************ Frequencies ********************/  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  /*   } */
 {  /* Some frequencies */  
    /*   for(j=0; j<p; j++) { */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  /*     (u[j] = t[j]); */
   double ***freq; /* Frequencies */  /*   } */
   double *pp;  /*      u[p]='\0'; */
   double pos;  
   FILE *ficresp;  /*    for(j=0; j<= lg; j++) { */
   char fileresp[FILENAMELENGTH];  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   pp=vector(1,nlstate);  /* } */
   
   strcpy(fileresp,"p");  #ifdef _WIN32
   strcat(fileresp,fileres);  char * strsep(char **pp, const char *delim)
   if((ficresp=fopen(fileresp,"w"))==NULL) {  {
     printf("Problem with prevalence resultfile: %s\n", fileresp);    char *p, *q;
     exit(0);           
   }    if ((p = *pp) == NULL)
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      return 0;
   j1=0;    if ((q = strpbrk (p, delim)) != NULL)
     {
   j=cptcovn;      *pp = q + 1;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      *q = '\0';
     }
   for(k1=1; k1<=j;k1++){    else
    for(i1=1; i1<=ncodemax[k1];i1++){      *pp = 0;
        j1++;    return p;
   }
         for (i=-1; i<=nlstate+ndeath; i++)    #endif
          for (jk=-1; jk<=nlstate+ndeath; jk++)    
            for(m=agemin; m <= agemax+3; m++)  /********************** nrerror ********************/
              freq[i][jk][m]=0;  
          void nrerror(char error_text[])
        for (i=1; i<=imx; i++) {  {
          bool=1;    fprintf(stderr,"ERREUR ...\n");
          if  (cptcovn>0) {    fprintf(stderr,"%s\n",error_text);
            for (z1=1; z1<=cptcovn; z1++)    exit(EXIT_FAILURE);
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;  }
          }  /*********************** vector *******************/
           if (bool==1) {  double *vector(int nl, int nh)
            for(m=firstpass; m<=lastpass-1; m++){  {
              if(agev[m][i]==0) agev[m][i]=agemax+1;    double *v;
              if(agev[m][i]==1) agev[m][i]=agemax+2;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    if (!v) nrerror("allocation failure in vector");
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    return v-nl+NR_END;
            }  }
          }  
        }  /************************ free vector ******************/
         if  (cptcovn>0) {  void free_vector(double*v, int nl, int nh)
          fprintf(ficresp, "\n#Variable");  {
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);    free((FREE_ARG)(v+nl-NR_END));
        }  }
        fprintf(ficresp, "\n#");  
        for(i=1; i<=nlstate;i++)  /************************ivector *******************************/
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  int *ivector(long nl,long nh)
        fprintf(ficresp, "\n");  {
            int *v;
   for(i=(int)agemin; i <= (int)agemax+3; i++){    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if(i==(int)agemax+3)    if (!v) nrerror("allocation failure in ivector");
       printf("Total");    return v-nl+NR_END;
     else  }
       printf("Age %d", i);  
     for(jk=1; jk <=nlstate ; jk++){  /******************free ivector **************************/
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  void free_ivector(int *v, long nl, long nh)
         pp[jk] += freq[jk][m][i];  {
     }    free((FREE_ARG)(v+nl-NR_END));
     for(jk=1; jk <=nlstate ; jk++){  }
       for(m=-1, pos=0; m <=0 ; m++)  
         pos += freq[jk][m][i];  /************************lvector *******************************/
       if(pp[jk]>=1.e-10)  long *lvector(long nl,long nh)
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  {
       else    long *v;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     }    if (!v) nrerror("allocation failure in ivector");
     for(jk=1; jk <=nlstate ; jk++){    return v-nl+NR_END;
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)  }
         pp[jk] += freq[jk][m][i];  
     }  /******************free lvector **************************/
     for(jk=1,pos=0; jk <=nlstate ; jk++)  void free_lvector(long *v, long nl, long nh)
       pos += pp[jk];  {
     for(jk=1; jk <=nlstate ; jk++){    free((FREE_ARG)(v+nl-NR_END));
       if(pos>=1.e-5)  }
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
       else  /******************* imatrix *******************************/
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       if( i <= (int) agemax){       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         if(pos>=1.e-5)  { 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       else    int **m; 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    
       }    /* allocate pointers to rows */ 
     }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     for(jk=-1; jk <=nlstate+ndeath; jk++)    if (!m) nrerror("allocation failure 1 in matrix()"); 
       for(m=-1; m <=nlstate+ndeath; m++)    m += NR_END; 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    m -= nrl; 
     if(i <= (int) agemax)    
       fprintf(ficresp,"\n");    
     printf("\n");    /* allocate rows and set pointers to them */ 
     }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
  }    m[nrl] += NR_END; 
      m[nrl] -= ncl; 
   fclose(ficresp);    
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   free_vector(pp,1,nlstate);    
     /* return pointer to array of pointers to rows */ 
 }  /* End of Freq */    return m; 
   } 
 /************* Waves Concatenation ***************/  
   /****************** free_imatrix *************************/
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  void free_imatrix(m,nrl,nrh,ncl,nch)
 {        int **m;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        long nch,ncl,nrh,nrl; 
      Death is a valid wave (if date is known).       /* free an int matrix allocated by imatrix() */ 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  { 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      and mw[mi+1][i]. dh depends on stepm.    free((FREE_ARG) (m+nrl-NR_END)); 
      */  } 
   
   int i, mi, m;  /******************* matrix *******************************/
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  double **matrix(long nrl, long nrh, long ncl, long nch)
 float sum=0.;  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   for(i=1; i<=imx; i++){    double **m;
     mi=0;  
     m=firstpass;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     while(s[m][i] <= nlstate){    if (!m) nrerror("allocation failure 1 in matrix()");
       if(s[m][i]>=1)    m += NR_END;
         mw[++mi][i]=m;    m -= nrl;
       if(m >=lastpass)  
         break;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       else    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         m++;    m[nrl] += NR_END;
     }/* end while */    m[nrl] -= ncl;
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       /* if(mi==0)  never been interviewed correctly before death */    return m;
          /* Only death is a correct wave */    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
       mw[mi][i]=m;  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     }  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
      */
     wav[i]=mi;  }
     if(mi==0)  
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  /*************************free matrix ************************/
   }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
   for(i=1; i<=imx; i++){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for(mi=1; mi<wav[i];mi++){    free((FREE_ARG)(m+nrl-NR_END));
       if (stepm <=0)  }
         dh[mi][i]=1;  
       else{  /******************* ma3x *******************************/
         if (s[mw[mi+1][i]][i] > nlstate) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  {
           if(j=0) j=1;  /* Survives at least one month after exam */    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         }    double ***m;
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
           k=k+1;    if (!m) nrerror("allocation failure 1 in matrix()");
           if (j >= jmax) jmax=j;    m += NR_END;
           else if (j <= jmin)jmin=j;    m -= nrl;
           sum=sum+j;  
         }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         jk= j/stepm;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         jl= j -jk*stepm;    m[nrl] += NR_END;
         ju= j -(jk+1)*stepm;    m[nrl] -= ncl;
         if(jl <= -ju)  
           dh[mi][i]=jk;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         else  
           dh[mi][i]=jk+1;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         if(dh[mi][i]==0)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
           dh[mi][i]=1; /* At least one step */    m[nrl][ncl] += NR_END;
       }    m[nrl][ncl] -= nll;
     }    for (j=ncl+1; j<=nch; j++) 
   }      m[nrl][j]=m[nrl][j-1]+nlay;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);    
 }    for (i=nrl+1; i<=nrh; i++) {
 /*********** Tricode ****************************/      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 void tricode(int *Tvar, int **nbcode, int imx)      for (j=ncl+1; j<=nch; j++) 
 {        m[i][j]=m[i][j-1]+nlay;
   int Ndum[80],ij, k, j, i;    }
   int cptcode=0;    return m; 
   for (k=0; k<79; k++) Ndum[k]=0;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   for (k=1; k<=7; k++) ncodemax[k]=0;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
      */
   for (j=1; j<=cptcovn; j++) {  }
     for (i=1; i<=imx; i++) {  
       ij=(int)(covar[Tvar[j]][i]);  /*************************free ma3x ************************/
       Ndum[ij]++;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       if (ij > cptcode) cptcode=ij;  {
     }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for (i=0; i<=cptcode; i++) {    free((FREE_ARG)(m+nrl-NR_END));
       if(Ndum[i]!=0) ncodemax[j]++;  }
     }  
    /*************** function subdirf ***********/
     ij=1;  char *subdirf(char fileres[])
     for (i=1; i<=ncodemax[j]; i++) {  {
       for (k=0; k<=79; k++) {    /* Caution optionfilefiname is hidden */
         if (Ndum[k] != 0) {    strcpy(tmpout,optionfilefiname);
           nbcode[Tvar[j]][ij]=k;    strcat(tmpout,"/"); /* Add to the right */
           ij++;    strcat(tmpout,fileres);
         }    return tmpout;
         if (ij > ncodemax[j]) break;  }
       }    
     }  /*************** function subdirf2 ***********/
   }    char *subdirf2(char fileres[], char *preop)
   {
   }    
     /* Caution optionfilefiname is hidden */
 /*********** Health Expectancies ****************/    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    strcat(tmpout,preop);
 {    strcat(tmpout,fileres);
   /* Health expectancies */    return tmpout;
   int i, j, nhstepm, hstepm, h;  }
   double age, agelim,hf;  
   double ***p3mat;  /*************** function subdirf3 ***********/
    char *subdirf3(char fileres[], char *preop, char *preop2)
   fprintf(ficreseij,"# Health expectancies\n");  {
   fprintf(ficreseij,"# Age");    
   for(i=1; i<=nlstate;i++)    /* Caution optionfilefiname is hidden */
     for(j=1; j<=nlstate;j++)    strcpy(tmpout,optionfilefiname);
       fprintf(ficreseij," %1d-%1d",i,j);    strcat(tmpout,"/");
   fprintf(ficreseij,"\n");    strcat(tmpout,preop);
     strcat(tmpout,preop2);
   hstepm=1*YEARM; /*  Every j years of age (in month) */    strcat(tmpout,fileres);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    return tmpout;
   }
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  char *asc_diff_time(long time_sec, char ascdiff[])
     /* nhstepm age range expressed in number of stepm */  {
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    long sec_left, days, hours, minutes;
     /* Typically if 20 years = 20*12/6=40 stepm */    days = (time_sec) / (60*60*24);
     if (stepm >= YEARM) hstepm=1;    sec_left = (time_sec) % (60*60*24);
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    hours = (sec_left) / (60*60) ;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    sec_left = (sec_left) %(60*60);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    minutes = (sec_left) /60;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    sec_left = (sec_left) % (60);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++)  /***************** f1dim *************************/
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){  extern int ncom; 
           eij[i][j][(int)age] +=p3mat[i][j][h];  extern double *pcom,*xicom;
         }  extern double (*nrfunc)(double []); 
       
     hf=1;  double f1dim(double x) 
     if (stepm >= YEARM) hf=stepm/YEARM;  { 
     fprintf(ficreseij,"%.0f",age );    int j; 
     for(i=1; i<=nlstate;i++)    double f;
       for(j=1; j<=nlstate;j++){    double *xt; 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);   
       }    xt=vector(1,ncom); 
     fprintf(ficreseij,"\n");    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    f=(*nrfunc)(xt); 
   }    free_vector(xt,1,ncom); 
 }    return f; 
   } 
 /************ Variance ******************/  
 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)  /*****************brent *************************/
 {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   /* Variance of health expectancies */  {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
   double **newm;     * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
   double **dnewm,**doldm;     * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
   int i, j, nhstepm, hstepm, h;     * the minimum is returned as xmin, and the minimum function value is returned as brent , the
   int k, cptcode;     * returned function value. 
    double *xp;    */
   double **gp, **gm;    int iter; 
   double ***gradg, ***trgradg;    double a,b,d,etemp;
   double ***p3mat;    double fu=0,fv,fw,fx;
   double age,agelim;    double ftemp=0.;
   int theta;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
    fprintf(ficresvij,"# Covariances of life expectancies\n");   
   fprintf(ficresvij,"# Age");    a=(ax < cx ? ax : cx); 
   for(i=1; i<=nlstate;i++)    b=(ax > cx ? ax : cx); 
     for(j=1; j<=nlstate;j++)    x=w=v=bx; 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    fw=fv=fx=(*f)(x); 
   fprintf(ficresvij,"\n");    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
   xp=vector(1,npar);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   dnewm=matrix(1,nlstate,1,npar);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   doldm=matrix(1,nlstate,1,nlstate);      printf(".");fflush(stdout);
        fprintf(ficlog,".");fflush(ficlog);
   hstepm=1*YEARM; /* Every year of age */  #ifdef DEBUGBRENT
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      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);
   agelim = AGESUP;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  #endif
     if (stepm >= YEARM) hstepm=1;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        *xmin=x; 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        return fx; 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      } 
     gp=matrix(0,nhstepm,1,nlstate);      ftemp=fu;
     gm=matrix(0,nhstepm,1,nlstate);      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
     for(theta=1; theta <=npar; theta++){        q=(x-v)*(fx-fw); 
       for(i=1; i<=npar; i++){ /* Computes gradient */        p=(x-v)*q-(x-w)*r; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        q=2.0*(q-r); 
       }        if (q > 0.0) p = -p; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          q=fabs(q); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        etemp=e; 
       for(j=1; j<= nlstate; j++){        e=d; 
         for(h=0; h<=nhstepm; h++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        else { 
         }          d=p/q; 
       }          u=x+d; 
              if (u-a < tol2 || b-u < tol2) 
       for(i=1; i<=npar; i++) /* Computes gradient */            d=SIGN(tol1,xm-x); 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        } 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        } else { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for(j=1; j<= nlstate; j++){      } 
         for(h=0; h<=nhstepm; h++){      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      fu=(*f)(u); 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      if (fu <= fx) { 
         }        if (u >= x) a=x; else b=x; 
       }        SHFT(v,w,x,u) 
       for(j=1; j<= nlstate; j++)        SHFT(fv,fw,fx,fu) 
         for(h=0; h<=nhstepm; h++){      } else { 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        if (u < x) a=u; else b=u; 
         }        if (fu <= fw || w == x) { 
     } /* End theta */          v=w; 
           w=u; 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          fv=fw; 
           fw=fu; 
     for(h=0; h<=nhstepm; h++)        } else if (fu <= fv || v == x || v == w) { 
       for(j=1; j<=nlstate;j++)          v=u; 
         for(theta=1; theta <=npar; theta++)          fv=fu; 
           trgradg[h][j][theta]=gradg[h][theta][j];        } 
       } 
     for(i=1;i<=nlstate;i++)    } 
       for(j=1;j<=nlstate;j++)    nrerror("Too many iterations in brent"); 
         vareij[i][j][(int)age] =0.;    *xmin=x; 
     for(h=0;h<=nhstepm;h++){    return fx; 
       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]);  /****************** mnbrak ***********************/
         for(i=1;i<=nlstate;i++)  
           for(j=1;j<=nlstate;j++)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
             vareij[i][j][(int)age] += doldm[i][j];              double (*func)(double)) 
       }  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
     }  the downhill direction (defined by the function as evaluated at the initial points) and returns
     h=1;  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
     if (stepm >= YEARM) h=stepm/YEARM;  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
     fprintf(ficresvij,"%.0f ",age );     */
     for(i=1; i<=nlstate;i++)    double ulim,u,r,q, dum;
       for(j=1; j<=nlstate;j++){    double fu; 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  
       }    double scale=10.;
     fprintf(ficresvij,"\n");    int iterscale=0;
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);    *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */    /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
      /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
   free_vector(xp,1,npar);    /*   *bx = *ax - (*ax - *bx)/scale; */
   free_matrix(doldm,1,nlstate,1,npar);    /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
   free_matrix(dnewm,1,nlstate,1,nlstate);    /* } */
   
 }    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
 /************ Variance of prevlim ******************/      SHFT(dum,*fb,*fa,dum) 
 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)    } 
 {    *cx=(*bx)+GOLD*(*bx-*ax); 
   /* Variance of prevalence limit */    *fc=(*func)(*cx); 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  #ifdef DEBUG
   double **newm;    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
   double **dnewm,**doldm;    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
   int i, j, nhstepm, hstepm;  #endif
   int k, cptcode;    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
   double *xp;      r=(*bx-*ax)*(*fb-*fc); 
   double *gp, *gm;      q=(*bx-*cx)*(*fb-*fa); 
   double **gradg, **trgradg;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double age,agelim;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
   int theta;      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
          if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        fu=(*func)(u); 
   fprintf(ficresvpl,"# Age");  #ifdef DEBUG
   for(i=1; i<=nlstate;i++)        /* f(x)=A(x-u)**2+f(u) */
       fprintf(ficresvpl," %1d-%1d",i,i);        double A, fparabu; 
   fprintf(ficresvpl,"\n");        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         fparabu= *fa - A*(*ax-u)*(*ax-u);
   xp=vector(1,npar);        printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
   dnewm=matrix(1,nlstate,1,npar);        fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
   doldm=matrix(1,nlstate,1,nlstate);        /* And thus,it can be that fu > *fc even if fparabu < *fc */
          /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
   hstepm=1*YEARM; /* Every year of age */          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
   agelim = AGESUP;  #endif 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  #ifdef MNBRAKORIGINAL
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  #else
     if (stepm >= YEARM) hstepm=1;  /*       if (fu > *fc) { */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  /* #ifdef DEBUG */
     gradg=matrix(1,npar,1,nlstate);  /*       printf("mnbrak4  fu > fc \n"); */
     gp=vector(1,nlstate);  /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
     gm=vector(1,nlstate);  /* #endif */
   /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
     for(theta=1; theta <=npar; theta++){  /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
       for(i=1; i<=npar; i++){ /* Computes gradient */  /*      dum=u; /\* Shifting c and u *\/ */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /*      u = *cx; */
       }  /*      *cx = dum; */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /*      dum = fu; */
       for(i=1;i<=nlstate;i++)  /*      fu = *fc; */
         gp[i] = prlim[i][i];  /*      *fc =dum; */
      /*       } else { /\* end *\/ */
       for(i=1; i<=npar; i++) /* Computes gradient */  /* #ifdef DEBUG */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  /*       printf("mnbrak3  fu < fc \n"); */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
       for(i=1;i<=nlstate;i++)  /* #endif */
         gm[i] = prlim[i][i];  /*      dum=u; /\* Shifting c and u *\/ */
   /*      u = *cx; */
       for(i=1;i<=nlstate;i++)  /*      *cx = dum; */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  /*      dum = fu; */
     } /* End theta */  /*      fu = *fc; */
   /*      *fc =dum; */
     trgradg =matrix(1,nlstate,1,npar);  /*       } */
   #ifdef DEBUG
     for(j=1; j<=nlstate;j++)        printf("mnbrak34  fu < or >= fc \n");
       for(theta=1; theta <=npar; theta++)        fprintf(ficlog, "mnbrak34 fu < fc\n");
         trgradg[j][theta]=gradg[theta][j];  #endif
         dum=u; /* Shifting c and u */
     for(i=1;i<=nlstate;i++)        u = *cx;
       varpl[i][(int)age] =0.;        *cx = dum;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        dum = fu;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        fu = *fc;
     for(i=1;i<=nlstate;i++)        *fc =dum;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  #endif
       } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
     fprintf(ficresvpl,"%.0f ",age );  #ifdef DEBUG
     for(i=1; i<=nlstate;i++)        printf("mnbrak2  u after c but before ulim\n");
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
     fprintf(ficresvpl,"\n");  #endif
     free_vector(gp,1,nlstate);        fu=(*func)(u); 
     free_vector(gm,1,nlstate);        if (fu < *fc) { 
     free_matrix(gradg,1,npar,1,nlstate);  #ifdef DEBUG
     free_matrix(trgradg,1,nlstate,1,npar);        printf("mnbrak2  u after c but before ulim AND fu < fc\n");
   } /* End age */        fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
   #endif
   free_vector(xp,1,npar);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   free_matrix(doldm,1,nlstate,1,npar);          SHFT(*fb,*fc,fu,(*func)(u)) 
   free_matrix(dnewm,1,nlstate,1,nlstate);        } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
 }  #ifdef DEBUG
         printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
         fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
   #endif
 /***********************************************/        u=ulim; 
 /**************** Main Program *****************/        fu=(*func)(u); 
 /***********************************************/      } else { /* u could be left to b (if r > q parabola has a maximum) */
   #ifdef DEBUG
 /*int main(int argc, char *argv[])*/        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
 int main()        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
 {  #endif
         u=(*cx)+GOLD*(*cx-*bx); 
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;        fu=(*func)(u); 
   double agedeb, agefin,hf;      } /* end tests */
   double agemin=1.e20, agemax=-1.e20;      SHFT(*ax,*bx,*cx,u) 
       SHFT(*fa,*fb,*fc,fu) 
   double fret;  #ifdef DEBUG
   double **xi,tmp,delta;        printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
         fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
   double dum; /* Dummy variable */  #endif
   double ***p3mat;    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
   int *indx;  } 
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];  /*************** linmin ************************/
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   char filerest[FILENAMELENGTH];  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
   char fileregp[FILENAMELENGTH];  the value of func at the returned location p . This is actually all accomplished by calling the
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  routines mnbrak and brent .*/
   int firstobs=1, lastobs=10;  int ncom; 
   int sdeb, sfin; /* Status at beginning and end */  double *pcom,*xicom;
   int c,  h , cpt,l;  double (*nrfunc)(double []); 
   int ju,jl, mi;   
   int i1,j1, k1,jk,aa,bb, stepsize;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  { 
      double brent(double ax, double bx, double cx, 
   int hstepm, nhstepm;                 double (*f)(double), double tol, double *xmin); 
   double bage, fage, age, agelim, agebase;    double f1dim(double x); 
   double ftolpl=FTOL;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   double **prlim;                double *fc, double (*func)(double)); 
   double *severity;    int j; 
   double ***param; /* Matrix of parameters */    double xx,xmin,bx,ax; 
   double  *p;    double fx,fb,fa;
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */    double scale=10., axs, xxs, xxss; /* Scale added for infinity */
   double *delti; /* Scale */   
   double ***eij, ***vareij;    ncom=n; 
   double **varpl; /* Variances of prevalence limits by age */    pcom=vector(1,n); 
   double *epj, vepp;    xicom=vector(1,n); 
   char version[80]="Imach version 0.64, May 2000, INED-EUROREVES ";    nrfunc=func; 
   char *alph[]={"a","a","b","c","d","e"}, str[4];    for (j=1;j<=n;j++) { 
   char z[1]="c", occ;      pcom[j]=p[j]; 
 #include <sys/time.h>      xicom[j]=xi[j]; 
 #include <time.h>    } 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
   /* long total_usecs;    /* axs=0.0; */
   struct timeval start_time, end_time;    /* xxss=1; /\* 1 and using scale *\/ */
      xxs=1;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    /* do{ */
       ax=0.;
       xx= xxs;
   printf("\nIMACH, Version 0.64a");      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
   printf("\nEnter the parameter file name: ");      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
       /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
 #ifdef windows      /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
   scanf("%s",pathtot);      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
   cygwin_split_path(pathtot,path,optionfile);      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);      /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
      chdir(path);    /*   if (fx != fx){ */
      /*    xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
   /*size=30;    /*    printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx); */
   getcwd(pathcd, size);      /*   } */
   printf("pathcd=%s, path=%s, optionfile=%s\n",pathcd,path,optionfile);    /* }while(fx != fx); */
   cutv(path,optionfile,pathtot,'\\');  
   chdir(path);  #ifdef DEBUGLINMIN
   replace(pathc,path);    printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
   printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);  #endif
   */    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
 #endif    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
 #ifdef unix    /* fmin = f(p[j] + xmin * xi[j]) */
   scanf("%s",optionfile);    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
 #endif    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
   #ifdef DEBUG
 /*-------- arguments in the command line --------*/    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   strcpy(fileres,"r");  #endif
   strcat(fileres, optionfile);  #ifdef DEBUGLINMIN
     printf("linmin end ");
   /*---------arguments file --------*/  #endif
     for (j=1;j<=n;j++) { 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
     printf("Problem with optionfile %s\n",optionfile);      xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
     goto end;      /* if(xxs <1.0) */
   }      /*   printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */
       p[j] += xi[j]; /* Parameters values are updated accordingly */
   strcpy(filereso,"o");    } 
   strcat(filereso,fileres);    /* printf("\n"); */
   if((ficparo=fopen(filereso,"w"))==NULL) {  #ifdef DEBUGLINMIN
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
   }    for (j=1;j<=n;j++) { 
       printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
   /* Reads comments: lines beginning with '#' */      if(j % ncovmodel == 0)
   while((c=getc(ficpar))=='#' && c!= EOF){        printf("\n");
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);  #endif
     puts(line);    free_vector(xicom,1,n); 
     fputs(line,ficparo);    free_vector(pcom,1,n); 
   }  } 
   ungetc(c,ficpar);  
   
   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);  /*************** powell ************************/
   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);  /*
   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);  Minimization of a function func of n variables. Input consists of an initial starting point
   p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
   covar=matrix(1,NCOVMAX,1,n);      rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
   if (strlen(model)<=1) cptcovn=0;  such that failure to decrease by more than this amount on one iteration signals doneness. On
   else {  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
     j=0;  function value at p , and iter is the number of iterations taken. The routine linmin is used.
     j=nbocc(model,'+');   */
     cptcovn=j+1;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   }              double (*func)(double [])) 
   { 
   ncovmodel=2+cptcovn;    void linmin(double p[], double xi[], int n, double *fret, 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                double (*func)(double [])); 
      int i,ibig,j; 
   /* Read guess parameters */    double del,t,*pt,*ptt,*xit;
   /* Reads comments: lines beginning with '#' */    double directest;
   while((c=getc(ficpar))=='#' && c!= EOF){    double fp,fptt;
     ungetc(c,ficpar);    double *xits;
     fgets(line, MAXLINE, ficpar);    int niterf, itmp;
     puts(line);  
     fputs(line,ficparo);    pt=vector(1,n); 
   }    ptt=vector(1,n); 
   ungetc(c,ficpar);    xit=vector(1,n); 
      xits=vector(1,n); 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    *fret=(*func)(p); 
     for(i=1; i <=nlstate; i++)    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for(j=1; j <=nlstate+ndeath-1; j++){      rcurr_time = time(NULL);  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    for (*iter=1;;++(*iter)) { 
       fprintf(ficparo,"%1d%1d",i1,j1);      fp=(*fret); /* From former iteration or initial value */
       printf("%1d%1d",i,j);      ibig=0; 
       for(k=1; k<=ncovmodel;k++){      del=0.0; 
         fscanf(ficpar," %lf",&param[i][j][k]);      rlast_time=rcurr_time;
         printf(" %lf",param[i][j][k]);      /* (void) gettimeofday(&curr_time,&tzp); */
         fprintf(ficparo," %lf",param[i][j][k]);      rcurr_time = time(NULL);  
       }      curr_time = *localtime(&rcurr_time);
       fscanf(ficpar,"\n");      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       printf("\n");      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
       fprintf(ficparo,"\n");  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
     }      for (i=1;i<=n;i++) {
          printf(" %d %.12f",i, p[i]);
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        fprintf(ficlog," %d %.12lf",i, p[i]);
   p=param[1][1];        fprintf(ficrespow," %.12lf", p[i]);
        }
   /* Reads comments: lines beginning with '#' */      printf("\n");
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"\n");
     ungetc(c,ficpar);      fprintf(ficrespow,"\n");fflush(ficrespow);
     fgets(line, MAXLINE, ficpar);      if(*iter <=3){
     puts(line);        tml = *localtime(&rcurr_time);
     fputs(line,ficparo);        strcpy(strcurr,asctime(&tml));
   }        rforecast_time=rcurr_time; 
   ungetc(c,ficpar);        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          strcurr[itmp-1]='\0';
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   for(i=1; i <=nlstate; i++){        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
     for(j=1; j <=nlstate+ndeath-1; j++){        for(niterf=10;niterf<=30;niterf+=10){
       fscanf(ficpar,"%1d%1d",&i1,&j1);          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
       printf("%1d%1d",i,j);          forecast_time = *localtime(&rforecast_time);
       fprintf(ficparo,"%1d%1d",i1,j1);          strcpy(strfor,asctime(&forecast_time));
       for(k=1; k<=ncovmodel;k++){          itmp = strlen(strfor);
         fscanf(ficpar,"%le",&delti3[i][j][k]);          if(strfor[itmp-1]=='\n')
         printf(" %le",delti3[i][j][k]);          strfor[itmp-1]='\0';
         fprintf(ficparo," %le",delti3[i][j][k]);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       fscanf(ficpar,"\n");        }
       printf("\n");      }
       fprintf(ficparo,"\n");      for (i=1;i<=n;i++) { /* For each direction i */
     }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
   }        fptt=(*fret); 
   delti=delti3[1][1];  #ifdef DEBUG
              printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   /* Reads comments: lines beginning with '#' */            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   while((c=getc(ficpar))=='#' && c!= EOF){  #endif
     ungetc(c,ficpar);            printf("%d",i);fflush(stdout); /* print direction (parameter) i */
     fgets(line, MAXLINE, ficpar);        fprintf(ficlog,"%d",i);fflush(ficlog);
     puts(line);        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
     fputs(line,ficparo);                                      /* Outputs are fret(new point p) p is updated and xit rescaled */
   }        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
   ungetc(c,ficpar);          /* because that direction will be replaced unless the gain del is small */
            /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
   matcov=matrix(1,npar,1,npar);          /* Unless the n directions are conjugate some gain in the determinant may be obtained */
   for(i=1; i <=npar; i++){          /* with the new direction. */
     fscanf(ficpar,"%s",&str);          del=fabs(fptt-(*fret)); 
     printf("%s",str);          ibig=i; 
     fprintf(ficparo,"%s",str);        } 
     for(j=1; j <=i; j++){  #ifdef DEBUG
       fscanf(ficpar," %le",&matcov[i][j]);        printf("%d %.12e",i,(*fret));
       printf(" %.5le",matcov[i][j]);        fprintf(ficlog,"%d %.12e",i,(*fret));
       fprintf(ficparo," %.5le",matcov[i][j]);        for (j=1;j<=n;j++) {
     }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     fscanf(ficpar,"\n");          printf(" x(%d)=%.12e",j,xit[j]);
     printf("\n");          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     fprintf(ficparo,"\n");        }
   }        for(j=1;j<=n;j++) {
   for(i=1; i <=npar; i++)          printf(" p(%d)=%.12e",j,p[j]);
     for(j=i+1;j<=npar;j++)          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
       matcov[i][j]=matcov[j][i];        }
            printf("\n");
   printf("\n");        fprintf(ficlog,"\n");
   #endif
       } /* end loop on each direction i */
    if(mle==1){      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
     /*-------- data file ----------*/      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
     if((ficres =fopen(fileres,"w"))==NULL) {      /* New value of last point Pn is not computed, P(n-1) */
       printf("Problem with resultfile: %s\n", fileres);goto end;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
     }        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
     fprintf(ficres,"#%s\n",version);        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
            /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
     if((fic=fopen(datafile,"r"))==NULL)    {        /* decreased of more than 3.84  */
       printf("Problem with datafile: %s\n", datafile);goto end;        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
     }        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
         /* By adding 10 parameters more the gain should be 18.31 */
     n= lastobs;  
     severity = vector(1,maxwav);        /* Starting the program with initial values given by a former maximization will simply change */
     outcome=imatrix(1,maxwav+1,1,n);        /* the scales of the directions and the directions, because the are reset to canonical directions */
     num=ivector(1,n);        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
     moisnais=vector(1,n);        /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
     annais=vector(1,n);  #ifdef DEBUG
     moisdc=vector(1,n);        int k[2],l;
     andc=vector(1,n);        k[0]=1;
     agedc=vector(1,n);        k[1]=-1;
     cod=ivector(1,n);        printf("Max: %.12e",(*func)(p));
     weight=vector(1,n);        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for (j=1;j<=n;j++) {
     mint=matrix(1,maxwav,1,n);          printf(" %.12e",p[j]);
     anint=matrix(1,maxwav,1,n);          fprintf(ficlog," %.12e",p[j]);
     s=imatrix(1,maxwav+1,1,n);        }
     adl=imatrix(1,maxwav+1,1,n);            printf("\n");
     tab=ivector(1,NCOVMAX);        fprintf(ficlog,"\n");
     ncodemax=ivector(1,8);        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
     i=1;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     while (fgets(line, MAXLINE, fic) != NULL)    {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       if ((i >= firstobs) && (i <=lastobs)) {            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                  }
         for (j=maxwav;j>=1;j--){          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           strcpy(line,stra);        }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  #endif
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }  
                free_vector(xit,1,n); 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        free_vector(xits,1,n); 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        return; 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      } /* enough precision */ 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
         for (j=ncov;j>=1;j--){        ptt[j]=2.0*p[j]-pt[j]; 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        xit[j]=p[j]-pt[j]; 
         }        pt[j]=p[j]; 
         num[i]=atol(stra);      } 
       fptt=(*func)(ptt); /* f_3 */
         /*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]));*/  #ifdef POWELLF1F3
   #else
         i=i+1;      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
       }  #endif
     }        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
         /* From x1 (P0) distance of x2 is at h and x3 is 2h */
     /*scanf("%d",i);*/        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
   imx=i-1; /* Number of individuals */        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
         /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
   /* Calculation of the number of parameter from char model*/        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
   Tvar=ivector(1,8);            /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
      #ifdef NRCORIGINAL
   if (strlen(model) >1){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
     j=0;  #else
     j=nbocc(model,'+');        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
     cptcovn=j+1;        t= t- del*SQR(fp-fptt);
      #endif
     strcpy(modelsav,model);        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
     if (j==0) {  #ifdef DEBUG
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);        printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
     }        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
     else {        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
       for(i=j; i>=1;i--){               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         cutv(stra,strb,modelsav,'+');        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
         if (strchr(strb,'*')) {               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
           cutv(strd,strc,strb,'*');        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
           cutv(strb,strc,strd,'V');  #endif
           for (k=1; k<=lastobs;k++)  #ifdef POWELLORIGINAL
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        if (t < 0.0) { /* Then we use it for new direction */
         }  #else
         else {cutv(strd,strc,strb,'V');        if (directest*t < 0.0) { /* Contradiction between both tests */
         Tvar[i+1]=atoi(strc);          printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
         }          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         strcpy(modelsav,stra);            fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
       }          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       cutv(strd,strc,stra,'V');        } 
       Tvar[1]=atoi(strc);        if (directest < 0.0) { /* Then we use it for new direction */
     }  #endif
   }  #ifdef DEBUGLINMIN
   /*printf("tvar=%d ",Tvar[1]);          printf("Before linmin in direction P%d-P0\n",n);
   scanf("%d ",i);*/          for (j=1;j<=n;j++) { 
     fclose(fic);            printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
             if(j % ncovmodel == 0)
     if (weightopt != 1) { /* Maximisation without weights*/              printf("\n");
       for(i=1;i<=n;i++) weight[i]=1.0;          }
     }  #endif
     /*-calculation of age at interview from date of interview and age at death -*/          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
     agev=matrix(1,maxwav,1,imx);  #ifdef DEBUGLINMIN
              for (j=1;j<=n;j++) { 
     for (i=1; i<=imx; i++)  {            printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            if(j % ncovmodel == 0)
       for(m=1; (m<= maxwav); m++){              printf("\n");
         if(s[m][i] >0){          }
           if (s[m][i] == nlstate+1) {  #endif
             if(agedc[i]>0)          for (j=1;j<=n;j++) { 
               if(moisdc[i]!=99 && andc[i]!=9999)            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
               agev[m][i]=agedc[i];            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
             else{          }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
               agev[m][i]=-1;          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
             }  
           }  #ifdef DEBUG
           else if(s[m][i] !=9){ /* Should no more exist */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
             if(mint[m][i]==99 || anint[m][i]==9999)          for(j=1;j<=n;j++){
               agev[m][i]=1;            printf(" %.12e",xit[j]);
             else if(agev[m][i] <agemin){            fprintf(ficlog," %.12e",xit[j]);
               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);*/          printf("\n");
             }          fprintf(ficlog,"\n");
             else if(agev[m][i] >agemax){  #endif
               agemax=agev[m][i];        } /* end of t or directest negative */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  #ifdef POWELLF1F3
             }  #else
             /*agev[m][i]=anint[m][i]-annais[i];*/      } /* end if (fptt < fp)  */
             /*   agev[m][i] = age[i]+2*m;*/  #endif
           }    } /* loop iteration */ 
           else { /* =9 */  } 
             agev[m][i]=1;  
             s[m][i]=-1;  /**** Prevalence limit (stable or period prevalence)  ****************/
           }  
         }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         else /*= 0 Unknown */  {
           agev[m][i]=1;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       }       matrix by transitions matrix until convergence is reached */
        
     }    int i, ii,j,k;
     for (i=1; i<=imx; i++)  {    double min, max, maxmin, maxmax,sumnew=0.;
       for(m=1; (m<= maxwav); m++){    /* double **matprod2(); */ /* test */
         if (s[m][i] > (nlstate+ndeath)) {    double **out, cov[NCOVMAX+1], **pmij();
           printf("Error: Wrong value in nlstate or ndeath\n");      double **newm;
           goto end;    double agefin, delaymax=50 ; /* Max number of years to converge */
         }    
       }    for (ii=1;ii<=nlstate+ndeath;ii++)
     }      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      }
     
     free_vector(severity,1,maxwav);    cov[1]=1.;
     free_imatrix(outcome,1,maxwav+1,1,n);    
     free_vector(moisnais,1,n);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     free_vector(annais,1,n);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     free_matrix(mint,1,maxwav,1,n);      newm=savm;
     free_matrix(anint,1,maxwav,1,n);      /* Covariates have to be included here again */
     free_vector(moisdc,1,n);      cov[2]=agefin;
     free_vector(andc,1,n);      if(nagesqr==1)
         cov[3]= agefin*agefin;;
          for (k=1; k<=cptcovn;k++) {
     wav=ivector(1,imx);        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      }
          /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     /* Concatenates waves */      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2];
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      for (k=1; k<=cptcovprod;k++) /* Useless */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];
       
 Tcode=ivector(1,100);      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
    nbcode=imatrix(1,nvar,1,8);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
    ncodemax[1]=1;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
        /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
    codtab=imatrix(1,100,1,10);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
    h=0;      
    m=pow(2,cptcovn);      savm=oldm;
        oldm=newm;
    for(k=1;k<=cptcovn; k++){      maxmax=0.;
      for(i=1; i <=(m/pow(2,k));i++){      for(j=1;j<=nlstate;j++){
        for(j=1; j <= ncodemax[k]; j++){        min=1.;
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){        max=0.;
            h++;        for(i=1; i<=nlstate; i++) {
            if (h>m) h=1;codtab[h][k]=j;          sumnew=0;
          }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
        }          prlim[i][j]= newm[i][j]/(1-sumnew);
      }          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
    }          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
    /*for(i=1; i <=m ;i++){        }
      for(k=1; k <=cptcovn; k++){        maxmin=max-min;
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);        maxmax=FMAX(maxmax,maxmin);
      }      } /* j loop */
      printf("\n");      if(maxmax < ftolpl){
    }*/        return prlim;
    /*scanf("%d",i);*/      }
        } /* age loop */
    /* Calculates basic frequencies. Computes observed prevalence at single age    return prlim; /* should not reach here */
        and prints on file fileres'p'. */  }
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);  
   /*************** transition probabilities ***************/ 
   
   /*scanf("%d ",i);*/  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
     /* According to parameters values stored in x and the covariate's values stored in cov,
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       computes the probability to be observed in state j being in state i by appying the
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       model to the ncovmodel covariates (including constant and age).
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       ncth covariate in the global vector x is given by the formula:
           j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
     /* For Powell, parameters are in a vector p[] starting at p[1]       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
           Outputs ps[i][j] the probability to be observed in j being in j according to
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     */
        double s1, lnpijopii;
     /*--------- results files --------------*/    /*double t34;*/
     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);    int i,j, nc, ii, jj;
      
    jk=1;      for(i=1; i<= nlstate; i++){
    fprintf(ficres,"# Parameters\n");        for(j=1; j<i;j++){
    printf("# Parameters\n");          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
    for(i=1,jk=1; i <=nlstate; i++){            /*lnpijopii += param[i][j][nc]*cov[nc];*/
      for(k=1; k <=(nlstate+ndeath); k++){            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
        if (k != i)  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
          {          }
            printf("%d%d ",i,k);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
            fprintf(ficres,"%1d%1d ",i,k);  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
            for(j=1; j <=ncovmodel; j++){        }
              printf("%f ",p[jk]);        for(j=i+1; j<=nlstate+ndeath;j++){
              fprintf(ficres,"%f ",p[jk]);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
              jk++;            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
            }            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
            printf("\n");  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
            fprintf(ficres,"\n");          }
          }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
      }        }
    }      }
       
     /* Computing hessian and covariance matrix */      for(i=1; i<= nlstate; i++){
     ftolhess=ftol; /* Usually correct */        s1=0;
     hesscov(matcov, p, npar, delti, ftolhess, func);        for(j=1; j<i; j++){
     fprintf(ficres,"# Scales\n");          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     printf("# Scales\n");          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
      for(i=1,jk=1; i <=nlstate; i++){        }
       for(j=1; j <=nlstate+ndeath; j++){        for(j=i+1; j<=nlstate+ndeath; j++){
         if (j!=i) {          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           fprintf(ficres,"%1d%1d",i,j);          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           printf("%1d%1d",i,j);        }
           for(k=1; k<=ncovmodel;k++){        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
             printf(" %.5e",delti[jk]);        ps[i][i]=1./(s1+1.);
             fprintf(ficres," %.5e",delti[jk]);        /* Computing other pijs */
             jk++;        for(j=1; j<i; j++)
           }          ps[i][j]= exp(ps[i][j])*ps[i][i];
           printf("\n");        for(j=i+1; j<=nlstate+ndeath; j++)
           fprintf(ficres,"\n");          ps[i][j]= exp(ps[i][j])*ps[i][i];
         }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       }      } /* end i */
       }      
          for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     k=1;        for(jj=1; jj<= nlstate+ndeath; jj++){
     fprintf(ficres,"# Covariance\n");          ps[ii][jj]=0;
     printf("# Covariance\n");          ps[ii][ii]=1;
     for(i=1;i<=npar;i++){        }
       /*  if (k>nlstate) k=1;      }
       i1=(i-1)/(ncovmodel*nlstate)+1;      
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      
       printf("%s%d%d",alph[k],i1,tab[i]);*/      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       fprintf(ficres,"%3d",i);      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
       printf("%3d",i);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       for(j=1; j<=i;j++){      /*   } */
         fprintf(ficres," %.5e",matcov[i][j]);      /*   printf("\n "); */
         printf(" %.5e",matcov[i][j]);      /* } */
       }      /* printf("\n ");printf("%lf ",cov[2]);*/
       fprintf(ficres,"\n");      /*
       printf("\n");        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       k++;        goto end;*/
     }      return ps;
      }
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);  /**************** Product of 2 matrices ******************/
       fgets(line, MAXLINE, ficpar);  
       puts(line);  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       fputs(line,ficparo);  {
     }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     ungetc(c,ficpar);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      /* in, b, out are matrice of pointers which should have been initialized 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       before: only the contents of out is modified. The function returns
           a pointer to pointers identical to out */
     if (fage <= 2) {    int i, j, k;
       bage = agemin;    for(i=nrl; i<= nrh; i++)
       fage = agemax;      for(k=ncolol; k<=ncoloh; k++){
     }        out[i][k]=0.;
         for(j=ncl; j<=nch; j++)
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          out[i][k] +=in[i][j]*b[j][k];
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      }
 /*------------ gnuplot -------------*/    return out;
 chdir(pathcd);  }
   if((ficgp=fopen("graph.plt","w"))==NULL) {  
     printf("Problem with file graph.plt");goto end;  
   }  /************* Higher Matrix Product ***************/
 #ifdef windows  
   fprintf(ficgp,"cd \"%s\" \n",pathc);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 #endif  {
 m=pow(2,cptcovn);    /* Computes the transition matrix starting at age 'age' over 
         'nhstepm*hstepm*stepm' months (i.e. until
  /* 1eme*/       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   for (cpt=1; cpt<= nlstate ; cpt ++) {       nhstepm*hstepm matrices. 
    for (k1=1; k1<= m ; k1 ++) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
 #ifdef windows       for the memory).
     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);       Model is determined by parameters x and covariates have to be 
 #endif       included manually here. 
 #ifdef unix  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);       */
 #endif  
     int i, j, d, h, k;
 for (i=1; i<= nlstate ; i ++) {    double **out, cov[NCOVMAX+1];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double **newm;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double agexact;
 }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    /* Hstepm could be zero and should return the unit matrix */
     for (i=1; i<= nlstate ; i ++) {    for (i=1;i<=nlstate+ndeath;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for (j=1;j<=nlstate+ndeath;j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        oldm[i][j]=(i==j ? 1.0 : 0.0);
 }        po[i][j][0]=(i==j ? 1.0 : 0.0);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      }
      for (i=1; i<= nlstate ; i ++) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for(h=1; h <=nhstepm; h++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(d=1; d <=hstepm; d++){
 }          newm=savm;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        /* Covariates have to be included here again */
 #ifdef unix        cov[1]=1.;
 fprintf(ficgp,"\nset ter gif small size 400,300");        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 #endif        cov[2]=agexact;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        if(nagesqr==1)
    }          cov[3]= agexact*agexact;
   }        for (k=1; k<=cptcovn;k++) 
   /*2 eme*/          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];
         for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
   for (k1=1; k1<= m ; k1 ++) {          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2];
            for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
     for (i=1; i<= nlstate+1 ; i ++) {          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 }                       pmij(pmmij,cov,ncovmodel,x,nlstate));
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        savm=oldm;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        oldm=newm;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      }
       for (j=1; j<= nlstate+1 ; j ++) {      for(i=1; i<=nlstate+ndeath; i++)
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1;j<=nlstate+ndeath;j++) {
         else fprintf(ficgp," \%%*lf (\%%*lf)");          po[i][j][h]=newm[i][j];
 }            /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       fprintf(ficgp,"\" t\"\" w l 0,");        }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      /*printf("h=%d ",h);*/
       for (j=1; j<= nlstate+1 ; j ++) {    } /* end h */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  /*     printf("\n H=%d \n",h); */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    return po;
 }    }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");  #ifdef NLOPT
     }    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    double fret;
   }    double *xt;
      int j;
   /*3eme*/    myfunc_data *d2 = (myfunc_data *) pd;
   /* xt = (p1-1); */
    for (k1=1; k1<= m ; k1 ++) {    xt=vector(1,n); 
     for (cpt=1; cpt<= nlstate ; cpt ++) {    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
       k=2+nlstate*(cpt-1);  
       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);    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
       for (i=1; i< nlstate ; i ++) {    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
         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);    printf("Function = %.12lf ",fret);
       }    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    printf("\n");
     }   free_vector(xt,1,n);
    }    return fret;
    }
   /* CV preval stat */  #endif
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {  /*************** log-likelihood *************/
       k=3;  double func( double *x)
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  {
       for (i=1; i< nlstate ; i ++)    int i, ii, j, k, mi, d, kk;
         fprintf(ficgp,"+$%d",k+i+1);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    double **out;
          double sw; /* Sum of weights */
       l=3+(nlstate+ndeath)*cpt;    double lli; /* Individual log likelihood */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    int s1, s2;
       for (i=1; i< nlstate ; i ++) {    double bbh, survp;
         l=3+(nlstate+ndeath)*cpt;    long ipmx;
         fprintf(ficgp,"+$%d",l+i+1);    double agexact;
       }    /*extern weight */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      /* We are differentiating ll according to initial status */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     }    /*for(i=1;i<imx;i++) 
   }      printf(" %d\n",s[4][i]);
      */
   /* proba elementaires */  
   for(i=1,jk=1; i <=nlstate; i++){    ++countcallfunc;
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {    cov[1]=1.;
         /*  fprintf(ficgp,"%1d%1d ",i,k);*/  
         for(j=1; j <=ncovmodel; j++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
           fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);  
           jk++;    if(mle==1){
           fprintf(ficgp,"\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        /* Computes the values of the ncovmodel covariates of the model
       }           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
     }           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   }           to be observed in j being in i according to the model.
   for(jk=1; jk <=m; jk++) {         */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
   for(i=1; i <=nlstate; i++) {            cov[2+nagesqr+k]=covar[Tvar[k]][i];
     for(k=1; k <=(nlstate+ndeath); k++){        }
       if (k != i) {        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
         fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
         for(j=3; j <=ncovmodel; j++)           has been calculated etc */
           fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for(mi=1; mi<= wav[i]-1; mi++){
         fprintf(ficgp,")/(1");          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(k1=1; k1 <=(nlstate+ndeath); k1++)            for (j=1;j<=nlstate+ndeath;j++){
           if (k1 != i) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             for(j=3; j <=ncovmodel; j++)            }
               fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for(d=0; d<dh[mi][i]; d++){
             fprintf(ficgp,")");            newm=savm;
           }            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
         fprintf(ficgp,") t \"p%d%d\" ", i,k);            cov[2]=agexact;
       if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            if(nagesqr==1)
       }              cov[3]= agexact*agexact;
     }            for (kk=1; kk<=cptcovage;kk++) {
   }              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              }
   }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  fclose(ficgp);            savm=oldm;
             oldm=newm;
     chdir(path);          } /* end mult */
     free_matrix(agev,1,maxwav,1,imx);        
     free_ivector(wav,1,imx);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          /* But now since version 0.9 we anticipate for bias at large stepm.
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);           * 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 
     free_imatrix(s,1,maxwav+1,1,n);           * the nearest (and in case of equal distance, to the lowest) interval but now
               * we keep into memory the bias bh[mi][i] and also the previous matrix product
               * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     free_ivector(num,1,n);           * probability in order to take into account the bias as a fraction of the way
     free_vector(agedc,1,n);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     free_vector(weight,1,n);           * -stepm/2 to stepm/2 .
     /*free_matrix(covar,1,NCOVMAX,1,n);*/           * For stepm=1 the results are the same as for previous versions of Imach.
     fclose(ficparo);           * For stepm > 1 the results are less biased than in previous versions. 
     fclose(ficres);           */
    }          s1=s[mw[mi][i]][i];
              s2=s[mw[mi+1][i]][i];
    /*________fin mle=1_________*/          bbh=(double)bh[mi][i]/(double)stepm; 
              /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
             */
     /* No more information from the sample is required now */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   /* Reads comments: lines beginning with '#' */          if( s2 > nlstate){ 
   while((c=getc(ficpar))=='#' && c!= EOF){            /* i.e. if s2 is a death state and if the date of death is known 
     ungetc(c,ficpar);               then the contribution to the likelihood is the probability to 
     fgets(line, MAXLINE, ficpar);               die between last step unit time and current  step unit time, 
     puts(line);               which is also equal to probability to die before dh 
     fputs(line,ficparo);               minus probability to die before dh-stepm . 
   }               In version up to 0.92 likelihood was computed
   ungetc(c,ficpar);          as if date of death was unknown. Death was treated as any other
            health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          to consider that at each interview the state was recorded
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);          (healthy, disable or death) and IMaCh was corrected; but when we
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          introduced the exact date of death then we should have modified
 /*--------- index.htm --------*/          the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
   if((fichtm=fopen("index.htm","w"))==NULL)    {          stepm. It is no more the probability to die between last interview
     printf("Problem with index.htm \n");goto end;          and month of death but the probability to survive from last
   }          interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
  fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n          Jackson for correcting this bug.  Former versions increased
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          mortality artificially. The bad side is that we add another loop
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          which slows down the processing. The difference can be up to 10%
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>          lower mortality.
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          /* If, at the beginning of the maximization mostly, the
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>             cumulative probability or probability to be dead is
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>             constant (ie = 1) over time d, the difference is equal to
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>             0.  out[s1][3] = savm[s1][3]: probability, being at state
         - 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);             s1 at precedent wave, to be dead a month before current
              wave is equal to probability, being at state s1 at
  fprintf(fichtm," <li>Graphs</li>\n<p>");             precedent wave, to be dead at mont of the current
              wave. Then the observed probability (that this person died)
  m=cptcovn;             is null according to current estimated parameter. In fact,
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}             it should be very low but not zero otherwise the log go to
              infinity.
  j1=0;          */
  for(k1=1; k1<=m;k1++){  /* #ifdef INFINITYORIGINAL */
    for(i1=1; i1<=ncodemax[k1];i1++){  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
        j1++;  /* #else */
        if (cptcovn > 0) {  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
          fprintf(fichtm,"<hr>************ Results for covariates");  /*          lli=log(mytinydouble); */
          for (cpt=1; cpt<=cptcovn;cpt++)  /*        else */
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
          fprintf(fichtm," ************\n<hr>");  /* #endif */
        }              lli=log(out[s1][s2] - savm[s1][s2]);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              } else if  (s2==-2) {
        for(cpt=1; cpt<nlstate;cpt++){            for (j=1,survp=0. ; j<=nlstate; j++) 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            /*survp += out[s1][j]; */
        }            lli= log(survp);
     for(cpt=1; cpt<=nlstate;cpt++) {          }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          
 interval) in state (%d): v%s%d%d.gif <br>          else if  (s2==-4) { 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              for (j=3,survp=0. ; j<=nlstate; j++)  
      }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
      for(cpt=1; cpt<=nlstate;cpt++) {            lli= log(survp); 
         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);  
      }          else if  (s2==-5) { 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            for (j=1,survp=0. ; j<=2; j++)  
 health expectancies in states (1) and (2): e%s%d.gif<br>              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            lli= log(survp); 
 fprintf(fichtm,"\n</body>");          } 
    }          
  }          else{
 fclose(fichtm);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             /*  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 */
   /*--------------- Prevalence limit --------------*/          } 
            /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   strcpy(filerespl,"pl");          /*if(lli ==000.0)*/
   strcat(filerespl,fileres);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          ipmx +=1;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          /* if (lli < log(mytinydouble)){ */
   fprintf(ficrespl,"#Prevalence limit\n");          /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
   fprintf(ficrespl,"#Age ");          /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          /* } */
   fprintf(ficrespl,"\n");        } /* end of wave */
        } /* end of individual */
   prlim=matrix(1,nlstate,1,nlstate);    }  else if(mle==2){
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(mi=1; mi<= wav[i]-1; mi++){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (ii=1;ii<=nlstate+ndeath;ii++)
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            for (j=1;j<=nlstate+ndeath;j++){
   k=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   agebase=agemin;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   agelim=agemax;            }
   ftolpl=1.e-10;          for(d=0; d<=dh[mi][i]; d++){
   i1=cptcovn;            newm=savm;
   if (cptcovn < 1){i1=1;}            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
   for(cptcov=1;cptcov<=i1;cptcov++){            if(nagesqr==1)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              cov[3]= agexact*agexact;
         k=k+1;            for (kk=1; kk<=cptcovage;kk++) {
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
         fprintf(ficrespl,"\n#****** ");            }
         for(j=1;j<=cptcovn;j++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         fprintf(ficrespl,"******\n");            savm=oldm;
                    oldm=newm;
         for (age=agebase; age<=agelim; age++){          } /* end mult */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        
           fprintf(ficrespl,"%.0f",age );          s1=s[mw[mi][i]][i];
           for(i=1; i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
           fprintf(ficrespl," %.5f", prlim[i][i]);          bbh=(double)bh[mi][i]/(double)stepm; 
           fprintf(ficrespl,"\n");          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         }          ipmx +=1;
       }          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fclose(ficrespl);        } /* end of wave */
   /*------------- h Pij x at various ages ------------*/      } /* end of individual */
      }  else if(mle==3){  /* exponential inter-extrapolation */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   printf("Computing pij: result on file '%s' \n", filerespij);            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   stepsize=(int) (stepm+YEARM-1)/YEARM;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (stepm<=24) stepsize=2;            }
           for(d=0; d<dh[mi][i]; d++){
   agelim=AGESUP;            newm=savm;
   hstepm=stepsize*YEARM; /* Every year of age */            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            cov[2]=agexact;
              if(nagesqr==1)
   k=0;              cov[3]= agexact*agexact;
   for(cptcov=1;cptcov<=i1;cptcov++){            for (kk=1; kk<=cptcovage;kk++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
       k=k+1;            }
         fprintf(ficrespij,"\n#****** ");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(j=1;j<=cptcovn;j++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);            savm=oldm;
         fprintf(ficrespij,"******\n");            oldm=newm;
                  } /* end mult */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          s1=s[mw[mi][i]][i];
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          s2=s[mw[mi+1][i]][i];
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          bbh=(double)bh[mi][i]/(double)stepm; 
           oldm=oldms;savm=savms;          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 */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            ipmx +=1;
           fprintf(ficrespij,"# Age");          sw += weight[i];
           for(i=1; i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             for(j=1; j<=nlstate+ndeath;j++)        } /* end of wave */
               fprintf(ficrespij," %1d-%1d",i,j);      } /* end of individual */
           fprintf(ficrespij,"\n");    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           for (h=0; h<=nhstepm; h++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
             for(i=1; i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
               for(j=1; j<=nlstate+ndeath;j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            for (j=1;j<=nlstate+ndeath;j++){
             fprintf(ficrespij,"\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
           fprintf(ficrespij,"\n");          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
     }            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            cov[2]=agexact;
             if(nagesqr==1)
   fclose(ficrespij);              cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
   /*---------- Health expectancies and variances ------------*/              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             }
   strcpy(filerest,"t");          
   strcat(filerest,fileres);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   if((ficrest=fopen(filerest,"w"))==NULL) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            savm=oldm;
   }            oldm=newm;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          } /* end mult */
         
           s1=s[mw[mi][i]][i];
   strcpy(filerese,"e");          s2=s[mw[mi+1][i]][i];
   strcat(filerese,fileres);          if( s2 > nlstate){ 
   if((ficreseij=fopen(filerese,"w"))==NULL) {            lli=log(out[s1][s2] - savm[s1][s2]);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          }else{
   }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          }
           ipmx +=1;
  strcpy(fileresv,"v");          sw += weight[i];
   strcat(fileresv,fileres);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  /*      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]); */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        } /* end of wave */
   }      } /* end of individual */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   k=0;        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
   for(cptcov=1;cptcov<=i1;cptcov++){        for(mi=1; mi<= wav[i]-1; mi++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (ii=1;ii<=nlstate+ndeath;ii++)
       k=k+1;            for (j=1;j<=nlstate+ndeath;j++){
       fprintf(ficrest,"\n#****** ");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1;j<=cptcovn;j++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);            }
       fprintf(ficrest,"******\n");          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
       fprintf(ficreseij,"\n#****** ");            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(j=1;j<=cptcovn;j++)            cov[2]=agexact;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            if(nagesqr==1)
       fprintf(ficreseij,"******\n");              cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficresvij,"\n#****** ");              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
       for(j=1;j<=cptcovn;j++)            }
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          
       fprintf(ficresvij,"******\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            savm=oldm;
       oldm=oldms;savm=savms;            oldm=newm;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            } /* end mult */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        
       oldm=oldms;savm=savms;          s1=s[mw[mi][i]][i];
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          s2=s[mw[mi+1][i]][i];
                lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          ipmx +=1;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          sw += weight[i];
       fprintf(ficrest,"\n");          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]);*/
       hf=1;        } /* end of wave */
       if (stepm >= YEARM) hf=stepm/YEARM;      } /* end of individual */
       epj=vector(1,nlstate+1);    } /* End of if */
       for(age=bage; age <=fage ;age++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         fprintf(ficrest," %.0f",age);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    return -l;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  }
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  
           }  /*************** log-likelihood *************/
           epj[nlstate+1] +=epj[j];  double funcone( double *x)
         }  {
         for(i=1, vepp=0.;i <=nlstate;i++)    /* Same as likeli but slower because of a lot of printf and if */
           for(j=1;j <=nlstate;j++)    int i, ii, j, k, mi, d, kk;
             vepp += vareij[i][j][(int)age];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    double **out;
         for(j=1;j <=nlstate;j++){    double lli; /* Individual log likelihood */
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    double llt;
         }    int s1, s2;
         fprintf(ficrest,"\n");    double bbh, survp;
       }    double agexact;
     }    /*extern weight */
   }    /* We are differentiating ll according to initial status */
            /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
  fclose(ficreseij);    /*for(i=1;i<imx;i++) 
  fclose(ficresvij);      printf(" %d\n",s[4][i]);
   fclose(ficrest);    */
   fclose(ficpar);    cov[1]=1.;
   free_vector(epj,1,nlstate+1);  
   /*scanf("%d ",i); */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   /*------- Variance limit prevalence------*/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
 strcpy(fileresvpl,"vpl");      for(mi=1; mi<= wav[i]-1; mi++){
   strcat(fileresvpl,fileres);        for (ii=1;ii<=nlstate+ndeath;ii++)
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          for (j=1;j<=nlstate+ndeath;j++){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     exit(0);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }          }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
  k=0;          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
  for(cptcov=1;cptcov<=i1;cptcov++){          cov[2]=agexact;
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          if(nagesqr==1)
      k=k+1;            cov[3]= agexact*agexact;
      fprintf(ficresvpl,"\n#****** ");          for (kk=1; kk<=cptcovage;kk++) {
      for(j=1;j<=cptcovn;j++)            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);          }
      fprintf(ficresvpl,"******\n");  
                /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
      varpl=matrix(1,nlstate,(int) bage, (int) fage);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      oldm=oldms;savm=savms;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
    }          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
  }          savm=oldm;
           oldm=newm;
   fclose(ficresvpl);        } /* end mult */
         
   /*---------- End : free ----------------*/        s1=s[mw[mi][i]][i];
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm; 
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        /* bias is positive if real duration
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);         * is higher than the multiple of stepm and negative otherwise.
           */
          if( s2 > nlstate && (mle <5) ){  /* Jackson */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          lli=log(out[s1][s2] - savm[s1][s2]);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        } else if  (s2==-2) {
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          for (j=1,survp=0. ; j<=nlstate; j++) 
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            lli= log(survp);
   free_matrix(matcov,1,npar,1,npar);        }else if (mle==1){
   free_vector(delti,1,npar);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          } else if(mle==2){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          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 */
         } else if(mle==3){  /* exponential inter-extrapolation */
   printf("End of Imach\n");          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 */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
            lli=log(out[s1][s2]); /* Original formula */
   /* 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);*/        } else{  /* mle=0 back to 1 */
   /*printf("Total time was %d uSec.\n", total_usecs);*/          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   /*------ End -----------*/          /*lli=log(out[s1][s2]); */ /* Original formula */
         } /* End of if */
  end:        ipmx +=1;
 #ifdef windows        sw += weight[i];
  chdir(pathcd);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 #endif        /*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]); */
  system("wgnuplot graph.plt");        if(globpr){
           fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
 #ifdef windows   %11.6f %11.6f %11.6f ", \
   while (z[0] != 'q') {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     chdir(pathcd);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     scanf("%s",z);            llt +=ll[k]*gipmx/gsw;
     if (z[0] == 'c') system("./imach");            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     else if (z[0] == 'e') {          }
       chdir(path);          fprintf(ficresilk," %10.6f\n", -llt);
       system("index.htm");        }
     }      } /* end of wave */
     else if (z[0] == 'q') exit(0);    } /* end of individual */
   }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 #endif    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
       gsw=sw;
     }
     return -l;
   }
   
   
   /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
     /* This routine should help understanding what is done with 
        the selection of individuals/waves and
        to check the exact contribution to the likelihood.
        Plotting could be done.
      */
     int k;
   
     if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
       fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   
     *fretone=(*funcone)(p);
     if(*globpri !=0){
       fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
     } 
     return;
   }
   
   
   /*********** Maximum Likelihood Estimation ***************/
   
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
     int i,j, iter=0;
     double **xi;
     double fret;
     double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   
   #ifdef NLOPT
     int creturn;
     nlopt_opt opt;
     /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     double *lb;
     double minf; /* the minimum objective value, upon return */
     double * p1; /* Shifted parameters from 0 instead of 1 */
     myfunc_data dinst, *d = &dinst;
   #endif
   
   
     xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     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");
   #ifdef POWELL
     powell(p,xi,npar,ftol,&iter,&fret,func);
   #endif
   
   #ifdef NLOPT
   #ifdef NEWUOA
     opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
     opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   #endif
     lb=vector(0,npar-1);
     for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     nlopt_set_lower_bounds(opt, lb);
     nlopt_set_initial_step1(opt, 0.1);
     
     p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     d->function = func;
     printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     nlopt_set_min_objective(opt, myfunc, d);
     nlopt_set_xtol_rel(opt, ftol);
     if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       printf("nlopt failed! %d\n",creturn); 
     }
     else {
       printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       iter=1; /* not equal */
     }
     nlopt_destroy(opt);
   #endif
     free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
     printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
   }
   
   /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
     double  **a,**y,*x,pd;
     double **hess;
     int i, j;
     int *indx;
   
     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);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
   
     printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
      
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
       /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
     
     for (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
         if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j,func,npar);
           
           hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
         }
       }
     }
     printf("\n");
     fprintf(ficlog,"\n");
   
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
     a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
     x=vector(1,npar);
     indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
   
     for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
       lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
       }
     }
   
     printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
       }
       printf("\n");
       fprintf(ficlog,"\n");
     }
   
     /* Recompute Inverse */
     for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
   
     /*  printf("\n#Hessian matrix recomputed#\n");
   
     for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
       lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
       }
       printf("\n");
       fprintf(ficlog,"\n");
     }
     */
   
     free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
     free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
   
   
   }
   
   /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   {
     int i;
     int l=1, lmax=20;
     double k1,k2;
     double p2[MAXPARM+1]; /* identical to x */
     double res;
     double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
     int k=0,kmax=10;
     double l1;
   
     fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
       l1=pow(10,l);
       delts=delt;
       for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
         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 */
         
   #ifdef DEBUGHESS
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         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);
   #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
         }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10;
         }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
         }
       }
     }
     delti[theta]=delts;
     return res; 
     
   }
   
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   {
     int i;
     int l=1, lmax=20;
     double k1,k2,k3,k4,res,fx;
     double p2[MAXPARM+1];
     int k;
   
     fx=func(x);
     for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
     
       p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
     
       p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
     
       p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   #endif
     }
     return res;
   }
   
   /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
   { 
     int i,imax,j,k; 
     double big,dum,sum,temp; 
     double *vv; 
    
     vv=vector(1,n); 
     *d=1.0; 
     for (i=1;i<=n;i++) { 
       big=0.0; 
       for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
     } 
     for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
         sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
       } 
       big=0.0; 
       for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
         for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
           imax=i; 
         } 
       } 
       if (j != imax) { 
         for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
         } 
         *d = -(*d); 
         vv[imax]=vv[j]; 
       } 
       indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
         dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
     } 
     free_vector(vv,1,n);  /* Doesn't work */
   ;
   } 
   
   void lubksb(double **a, int n, int *indx, double b[]) 
   { 
     int i,ii=0,ip,j; 
     double sum; 
    
     for (i=1;i<=n;i++) { 
       ip=indx[i]; 
       sum=b[ip]; 
       b[ip]=b[i]; 
       if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
       b[i]=sum; 
     } 
     for (i=n;i>=1;i--) { 
       sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
     } 
   } 
   
   void pstamp(FILE *fichier)
   {
     fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
   }
   
   /************ Frequencies ********************/
   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 */
     
     int i, m, jk, j1, bool, z1,j;
     int first;
     double ***freq; /* Frequencies */
     double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
     
     pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
     strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
     }
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
     
     j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
     first=1;
   
     /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
     /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
     /*    j1++; */
     for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
           for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
         
         for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0;
         
         dateintsum=0;
         k2cpt=0;
         for (i=1; i<=imx; i++) {
           bool=1;
           if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
             for (z1=1; z1<=cptcoveff; z1++)       
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
                   /* Tests if the value of each of the covariates of i is equal to filter j1 */
                 bool=0;
                 /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
                   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
                   j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                 /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
               } 
           }
    
           if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 if (m<lastpass) {
                   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];
                 }
                 
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
                   k2cpt++;
                 }
                 /*}*/
             }
           }
         } /* end i */
          
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         pstamp(ficresp);
         if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
           fprintf(ficresp, "**********\n#");
           fprintf(ficlog, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
           fprintf(ficlog, "**********\n#");
         }
         for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
         
         for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
             fprintf(ficlog,"Total");
           }else{
             if(first==1){
               first=0;
               printf("See log file for details...\n");
             }
             fprintf(ficlog,"Age %d", i);
           }
           for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
           }
           for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
               if(first==1){
                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
               if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
           }
   
           for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
           }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
             posprop += prop[jk][i];
           }
           for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
               if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
               if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               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);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
               else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
           }
           
           for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
               if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
           if(i <= iagemax)
             fprintf(ficresp,"\n");
           if(first==1)
             printf("Others in log...\n");
           fprintf(ficlog,"\n");
         }
         /*}*/
     }
     dateintmean=dateintsum/k2cpt; 
    
     fclose(ficresp);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
   }
   
   /************ Prevalence ********************/
   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
     */
    
     int i, m, jk, j1, bool, z1,j;
   
     double **prop;
     double posprop; 
     double  y2; /* in fractional years */
     int iagemin, iagemax;
     int first; /** to stop verbosity which is redirected to log file */
   
     iagemin= (int) agemin;
     iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
     
     /*j=cptcoveff;*/
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
     first=1;
     for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
       /*for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;*/
         
         for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
        
         for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
           if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
                 bool=0;
           } 
           if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
               }
             } /* end selection of waves */
           }
         }
         for(i=iagemin; i <= iagemax+3; i++){  
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
           } 
           
           for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
               } else{
                 if(first==1){
                   first=0;
                   printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
                 }
               }
             } 
           }/* end jk */ 
         }/* end i */ 
       /*} *//* end i1 */
     } /* end j1 */
     
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   
   /************* 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)
   {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
        */
   
     int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
     int first;
     int j, k=0,jk, ju, jl;
     double sum=0.;
     first=0;
     jmin=100000;
     jmax=-1;
     jmean=0.;
     for(i=1; i<=imx; i++){
       mi=0;
       m=firstpass;
       while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           mw[++mi][i]=m;
         if(m >=lastpass)
           break;
         else
           m++;
       }/* end while */
       if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
         mw[mi][i]=m;
       }
   
       wav[i]=mi;
       if(mi==0){
         nbwarn++;
         if(first==0){
           printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
         }
         if(first==1){
           fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
       } /* end mi==0 */
     } /* End individuals */
   
     for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
           dh[mi][i]=1;
         else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
                 nberr++;
                 printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 j=1; /* Temporary Dangerous patch */
                 printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                 fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }
               k=k+1;
               if (j >= jmax){
                 jmax=j;
                 ijmax=i;
               }
               if (j <= jmin){
                 jmin=j;
                 ijmin=i;
               }
               sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
           }
           else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   
             k=k+1;
             if (j >= jmax) {
               jmax=j;
               ijmax=i;
             }
             else if (j <= jmin){
               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]);*/
             if(j<0){
               nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }
             sum=sum+j;
           }
           jk= j/stepm;
           jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
               dh[mi][i]=jk;
               bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
                     * to avoid the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
           }else{
             if(jl <= -ju){
               dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
                                    */
             }
             else{
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
             if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
               /*  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);*/
             }
           } /* end if mle */
         }
       } /* end wave */
     }
     jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
    }
   
   /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   {
     /**< Uses cptcovn+2*cptcovprod as the number of covariates */
     /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
      * Boring subroutine which should only output nbcode[Tvar[j]][k]
      * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
      * nbcode[Tvar[j]][1]= 
     */
   
     int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     int modmaxcovj=0; /* Modality max of covariates j */
     int cptcode=0; /* Modality max of covariates j */
     int modmincovj=0; /* Modality min of covariates j */
   
   
     cptcoveff=0; 
    
     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
     /* Loop on covariates without age and products */
     for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
       for (k=-1; k < maxncov; k++) Ndum[k]=0;
       for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
                                  modality of this covariate Vj*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                       * If product of Vn*Vm, still boolean *:
                                       * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                       * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                         modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
           modmaxcovj=ij; 
         else if (ij < modmincovj) 
           modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
           printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
           exit(1);
         }else
         Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         /* getting the maximum value of the modality of the covariate
            (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
            female is 1, then modmaxcovj=1.*/
       } /* end for loop on individuals i */
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       cptcode=modmaxcovj;
       /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
      /*for (i=0; i<=cptcode; i++) {*/
       for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
         printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
         fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
         if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
           if( k != -1){
             ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered excluding 
                                undefined. Usually 2: 0 and 1. */
           }
           ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered including 
                                undefined. Usually 3: -1, 0 and 1. */
         }
         /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
            historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
       } /* Ndum[-1] number of undefined modalities */
   
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
       /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
          If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
          modmincovj=3; modmaxcovj = 7;
          There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
          which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
          defining two dummy variables: variables V1_1 and V1_2.
          nbcode[Tvar[j]][ij]=k;
          nbcode[Tvar[j]][1]=0;
          nbcode[Tvar[j]][2]=1;
          nbcode[Tvar[j]][3]=2;
          To be continued (not working yet).
       */
       ij=0; /* ij is similar to i but can jump over null modalities */
       for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
           if (Ndum[i] == 0) { /* If nobody responded to this modality k */
             break;
           }
           ij++;
           nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
           cptcode = ij; /* New max modality for covar j */
       } /* end of loop on modality i=-1 to 1 or more */
         
       /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
       /*  /\*recode from 0 *\/ */
       /*                               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; */
       /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
       /*  } */
       /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
       /*  if (ij > ncodemax[j]) { */
       /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
       /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
       /*    break; */
       /*  } */
       /*   }  /\* end of loop on modality k *\/ */
     } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     
    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     
     for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
      ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
      Ndum[ij]++; /* Might be supersed V1 + V1*age */
    } 
   
    ij=0;
    for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      if((Ndum[i]!=0) && (i<=ncovcol)){
        ij++;
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
      }else{
          /* Tvaraff[ij]=0; */
      }
    }
    /* ij--; */
    cptcoveff=ij; /*Number of total covariates*/
   
   }
   
   
   /*********** Health Expectancies ****************/
   
   void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
   {
     /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3mat;
     double eip;
   
     pstamp(ficreseij);
     fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
       }
       fprintf(ficreseij," e%1d. ",i);
     }
     fprintf(ficreseij,"\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 */ 
   
     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;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
     int movingaverage();
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k;
     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,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   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 lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 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 **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     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,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     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, cov[NCOVMAX+1];
     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 one-step probabilities (drawings)</a></h4></br>this page is important in order to visualize confidence intervals and especially correlation between disability and recovery</li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, 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; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*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]][codtabm(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]][codtabm(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]][codtabm(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]][codtabm(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]][codtabm(j1,z1)]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         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 (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           if(nagesqr==1)
             cov[3]= age*age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];
           
       
           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);
   
           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++;
               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++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 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 */
         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);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;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;first2=2;
         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.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* 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 size 320, 240");
                       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=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
            printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
          }
          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%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      /* } /\* end i1 *\/ */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
    - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \
   But because parameters are usually highly correlated (a higher incidence of disability \
   and a higher incidence of recovery can give very close observed transition) it might \
   be very useful to look not only at linear confidence intervals estimated from the \
   variances but at the covariance matrix. And instead of looking at the estimated coefficients \
   (parameters) of the logistic regression, it might be more meaningful to visualize the \
   covariance matrix of the one-step probabilities. \
   See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
   
    fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      /* } /\* end i1 *\/ */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
     for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficgp,"# initial state %d\n",i);
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           fprintf(ficgp,"#   current state %d\n",k);
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
             jk++; 
           }
           fprintf(ficgp,"\n");
         }
       }
      }
     fprintf(ficgp,"##############\n#\n");
   
     /*goto avoid;*/
     fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
     fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
     fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
     fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
     fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
     fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
     fprintf(ficgp,"#\n");
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        fprintf(ficgp,"# ng=%d\n",ng);
        fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"#    jk=%d\n",jk);
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  if(nagesqr==0)
                    fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                else
                  if(nagesqr==0)
                    fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel-nagesqr; j++) {
                  /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                  if(ij <=cptcovage) { /* Bug valgrind */
                    if((j-2)==Tage[ij]) { /* Bug valgrind */
                      fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);
                      ij++;
                    }
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){ 
                  if(nagesqr==0)
                    fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
     
                  ij=1;
                  for(j=3; j <=ncovmodel-nagesqr; j++){
                    if(ij <=cptcovage) { /* Bug valgrind */
                      if((j-2)==Tage[ij]) { /* Bug valgrind */
                        fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);
                        ij++;
                      }
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(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]][codtabm(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*************/
   void 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]][codtabm(k,j)]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
      * - nagesqr = 1 if age*age in the model, otherwise 0.
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
      * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
     char *strpt;
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       strcpy(modelsav,model); 
       if ((strpt=strstr(model,"age*age")) !=0){
         printf(" strpt=%s, model=%s\n",strpt, model);
         if(strpt != model){
         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
    corresponding column of parameters.\n",model);
         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
    'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
    corresponding column of parameters.\n",model); fflush(ficlog);
         return 1;
       }
   
         nagesqr=1;
         if (strstr(model,"+age*age") !=0)
           substrchaine(modelsav, model, "+age*age");
         else if (strstr(model,"age*age+") !=0)
           substrchaine(modelsav, model, "age*age+");
         else 
           substrchaine(modelsav, model, "age*age");
       }else
         nagesqr=0;
       if (strlen(modelsav) >1){
         j=nbocc(modelsav,'+'); /**< j=Number of '+' */
         j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
         cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
         cptcovt= j+1; /* Number of total covariates in the model, not including
                      * cst, age and age*age 
                      * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated 
                     * separately: ncovn=4- 2=2 (V1+V3). */
         cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
         cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
   
       
         /*   Design
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
          *  <          ncovcol=8                >
          * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
          *   k=  1    2      3       4     5       6      7        8
          *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
          *  covar[k,i], value of kth covariate if not including age for individual i:
          *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
          *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
          *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
          *  Tage[++cptcovage]=k
          *       if products, new covar are created after ncovcol with k1
          *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
          *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
          *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
          *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
          *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
          *  <          ncovcol=8                >
          *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
          *          k=  1    2      3       4     5       6      7        8    9   10   11  12
          *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
          * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          * p Tprod[1]@2={                         6, 5}
          *p Tvard[1][1]@4= {7, 8, 5, 6}
          * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
          *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          *How to reorganize?
          * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
          * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          *       {2,   1,     4,      8,    5,      6,     3,       7}
          * Struct []
          */
   
         /* This loop fills the array Tvar from the string 'model'.*/
         /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
         /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
         /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
         /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
         /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
         /*        k=1 Tvar[1]=2 (from V2) */
         /*        k=5 Tvar[5] */
         /* for (k=1; k<=cptcovn;k++) { */
         /*        cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
         /*        } */
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
         /*
          * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
         for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
         cptcovage=0;
         for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                            modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
           if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
           /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
           /*scanf("%d",i);*/
           if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
             cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
             if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
               /* covar is not filled and then is empty */
               cptcovprod--;
               cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
               Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
               cptcovage++; /* Sums the number of covariates which include age as a product */
               Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
               /*printf("stre=%s ", stre);*/
             } else if (strcmp(strd,"age")==0) { /* or age*Vn */
               cptcovprod--;
               cutl(stre,strb,strc,'V');
               Tvar[k]=atoi(stre);
               cptcovage++;
               Tage[cptcovage]=k;
             } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
               /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
               cptcovn++;
               cptcovprodnoage++;k1++;
               cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
               Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                      because this model-covariate is a construction we invent a new column
                                      ncovcol + k1
                                      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                      Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
               cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
               Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
               Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
               Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
               k2=k2+2;
               Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
               Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
               for (i=1; i<=lastobs;i++){
                 /* Computes the new covariate which is a product of
                    covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
                 covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
               }
             } /* End age is not in the model */
           } /* End if model includes a product */
           else { /* no more sum */
             /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
             /*  scanf("%d",i);*/
             cutl(strd,strc,strb,'V');
             ks++; /**< Number of simple covariates */
             cptcovn++;
             Tvar[k]=atoi(strd);
           }
           strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
           /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
             scanf("%d",i);*/
         } /* end of loop + on total covariates */
       } /* end if strlen(modelsave == 0) age*age might exist */
     } /* end if strlen(model == 0) */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           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;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo(int logged)
    {
      /* #include "syscompilerinfo.h"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
         "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
         "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
         "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
         /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
         /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
         uiAccess='false'"
         /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
         /NOLOGO /TLBID:1
      */
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              if(logged) fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for "); if (logged) fprintf(ficlog, " for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");if(logged) fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
            if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       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);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(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]][codtabm(k,j)]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; 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]][codtabm(k,j)]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
           return 0;
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       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 ");
       i1= pow(2,cptcoveff);
      /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
      /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
      /*   k=k+1;  */
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(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++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             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");
         }
         /*}*/
       }
           return 0;
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int num_filled;
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb=0.;
   
     double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
   
     double fret;
     double dum=0.; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
     char model[MAXLINE], modeltemp[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt, c2;
     int jl=0;
     int i1, j1, jk, stepsize=0;
     int count=0;
   
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm=0, nhstepm=0;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110., age, agelim=0., agebase=0.;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
     syscompilerinfo(0);
     printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
     chdir(path); /* Can be a relative path */
     if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
   #endif
     printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %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 --------*/
   
     /* Main 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,"Version %s %s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo(1);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /* Main ---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
   
       /* First parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
                           title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
       if (num_filled != 5) {
         printf("Should be 5 parameters\n");
       }
       numlinepar++;
       printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
     }
     /* Second parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                           &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
       if (num_filled != 8) {
         printf("Not 8\n");
       }
       printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
     }
   
     /* Third parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"model=1+age%[^.\n]\n", model)) !=EOF){
       if (num_filled != 1) {
         printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         model[0]='\0';
         goto end;
       }
       else{
         if (model[0]=='+'){
           for(i=1; i<=strlen(model);i++)
             modeltemp[i-1]=model[i];
         }
         strcpy(model,modeltemp); 
       }
       printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout);
     }
     /* 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=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
     /* numlinepar=numlinepar+3; /\* In general *\/ */
     /* 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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
     if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
       model[strlen(model)-1]='\0';
     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=1+age%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=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     /* if(model[0]=='#'|| model[0]== '\0'){ */
     if(model[0]=='#'){
       printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
    'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
    'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
       if(mle != -1){
         printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
         exit(1);
       }
     }
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
         z[0]=line[1];
       }
       /* printf("****line [1] = %c \n",line[1]); */
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
     else
       ncovmodel=2; /* Constant and age */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You chose 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) { /* Main Wizard */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) || (j1 != jj)){
             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,jj);
           fprintf(ficlog,"%1d%1d",i,jj);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       /* Scans npar lines */
       for(i=1; i <=npar; i++){
         count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
         if(count != 3){
           printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
   This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
           fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
   This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
           exit(1);
         }else
         if(mle==1)
           printf("%1d%1d%1d",i1,j1,jk);
         fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
         fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
         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");
       }
       /* End of read covariance matrix npar lines */
       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 */
   
     /*  Main data
      */
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
     ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
   /* Main decodemodel */
   
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     /* Nbcode gives the value of the lth modality of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] is the maximum value of this jth covariate */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              * For k=4 covariates, h goes from 1 to 2**k
              * codtabm(h,k)=  1 & (h-1) >> (k-1) ;
              *     h\k   1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     2
              *    10     2     1     1     2
              *    11 i=6 1     2     1     2
              *    12     2     2     1     2
              *    13 i=7 1 i=4 1     2     2    
              *    14     2     1     2     2
              *    15 i=8 1     2     2     2
              *    16     2     2     2     2
              */
     for(h=1; h <=100 ;h++){ 
       /* printf("h=%2d ", h); */
        for(k=1; k <=10; k++){
          /* printf("k=%d %d ",k,codtabm(h,k)); */
          codtab[h][k]=codtabm(h,k);
        }
        /* printf("\n"); */
     }
     /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
     /*   for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/  */
     /*     for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
     /*    for(cpt=1; cpt <=pow(2,k-1); cpt++){  /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/  */
     /*      h++; */
     /*      if (h>m)  */
     /*        h=1; */
     /*      codtab[h][k]=j; */
     /*      /\* codtab[12][3]=1; *\/ */
     /*      /\*codtab[h][Tvar[k]]=j;*\/ */
     /*      /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */
     /*    }  */
     /*     } */
     /*   } */
     /* }  */
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){  */
     /*    for(k=1; k <=cptcovn; k++){ */
     /*      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
     /*    } */
     /*    printf("\n"); */
     /* } */
     /*   scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /* Initialisation of ----------- gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
   
   
     /* Initialisation of --------- 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);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
     chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
     
     /* 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*/
     /* For mortality only */
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
       /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
       /*     gsl_vector_set(x, 0, 0.0268); */
       /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) {
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
         fprintf(ficlog,"%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 / */
       if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
           printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
           fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
       }else
         printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 mortality only */
     /* Standard maximisation */
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       /* Computes likelihood for initial parameters */
       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; /* again, 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, Real Maximisation */
         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=1+age+%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("%12.7f ",p[jk]);
               fprintf(ficlog,"%12.7f ",p[jk]);
               fprintf(ficres,"%12.7f ",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);
       }
       printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
       fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\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);
             for(j=1; j <=ncovmodel; j++){
               printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
               fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
           }
         }
       }
   
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
   
       /* Other stuffs, more or less useful */    
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficlog,"pop_based=%d\n",popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
           printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
           fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
       }else
         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);
   
   
       /* Other results (useful)*/
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
    
       /* ------ Other prevalence ratios------------ */
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(ncodemaxwundef,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
   #ifdef WIN32
      if (_chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n",path);
      if(_getcwd(pathcd,MAXLINE) > 0)
   #else
      if(chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n", path);
      if (getcwd(pathcd, MAXLINE) > 0)
   #endif 
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: "); fflush(stdout);
       scanf("%s",z);
     }
   }

Removed from v.1.4  
changed lines
  Added in v.1.198


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