Diff for /imach/src/imach.c between versions 1.166 and 1.226

version 1.166, 2014/12/22 11:40:47 version 1.226, 2016/07/12 18:42:34
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.226  2016/07/12 18:42:34  brouard
     Summary: temp
   
     Revision 1.225  2016/07/12 08:40:03  brouard
     Summary: saving but not running
   
     Revision 1.224  2016/07/01 13:16:01  brouard
     Summary: Fixes
   
     Revision 1.223  2016/02/19 09:23:35  brouard
     Summary: temporary
   
     Revision 1.222  2016/02/17 08:14:50  brouard
     Summary: Probably last 0.98 stable version 0.98r6
   
     Revision 1.221  2016/02/15 23:35:36  brouard
     Summary: minor bug
   
     Revision 1.219  2016/02/15 00:48:12  brouard
     *** empty log message ***
   
     Revision 1.218  2016/02/12 11:29:23  brouard
     Summary: 0.99 Back projections
   
     Revision 1.217  2015/12/23 17:18:31  brouard
     Summary: Experimental backcast
   
     Revision 1.216  2015/12/18 17:32:11  brouard
     Summary: 0.98r4 Warning and status=-2
   
     Version 0.98r4 is now:
      - displaying an error when status is -1, date of interview unknown and date of death known;
      - permitting a status -2 when the vital status is unknown at a known date of right truncation.
     Older changes concerning s=-2, dating from 2005 have been supersed.
   
     Revision 1.215  2015/12/16 08:52:24  brouard
     Summary: 0.98r4 working
   
     Revision 1.214  2015/12/16 06:57:54  brouard
     Summary: temporary not working
   
     Revision 1.213  2015/12/11 18:22:17  brouard
     Summary: 0.98r4
   
     Revision 1.212  2015/11/21 12:47:24  brouard
     Summary: minor typo
   
     Revision 1.211  2015/11/21 12:41:11  brouard
     Summary: 0.98r3 with some graph of projected cross-sectional
   
     Author: Nicolas Brouard
   
     Revision 1.210  2015/11/18 17:41:20  brouard
     Summary: Start working on projected prevalences
   
     Revision 1.209  2015/11/17 22:12:03  brouard
     Summary: Adding ftolpl parameter
     Author: N Brouard
   
     We had difficulties to get smoothed confidence intervals. It was due
     to the period prevalence which wasn't computed accurately. The inner
     parameter ftolpl is now an outer parameter of the .imach parameter
     file after estepm. If ftolpl is small 1.e-4 and estepm too,
     computation are long.
   
     Revision 1.208  2015/11/17 14:31:57  brouard
     Summary: temporary
   
     Revision 1.207  2015/10/27 17:36:57  brouard
     *** empty log message ***
   
     Revision 1.206  2015/10/24 07:14:11  brouard
     *** empty log message ***
   
     Revision 1.205  2015/10/23 15:50:53  brouard
     Summary: 0.98r3 some clarification for graphs on likelihood contributions
   
     Revision 1.204  2015/10/01 16:20:26  brouard
     Summary: Some new graphs of contribution to likelihood
   
     Revision 1.203  2015/09/30 17:45:14  brouard
     Summary: looking at better estimation of the hessian
   
     Also a better criteria for convergence to the period prevalence And
     therefore adding the number of years needed to converge. (The
     prevalence in any alive state shold sum to one
   
     Revision 1.202  2015/09/22 19:45:16  brouard
     Summary: Adding some overall graph on contribution to likelihood. Might change
   
     Revision 1.201  2015/09/15 17:34:58  brouard
     Summary: 0.98r0
   
     - Some new graphs like suvival functions
     - Some bugs fixed like model=1+age+V2.
   
     Revision 1.200  2015/09/09 16:53:55  brouard
     Summary: Big bug thanks to Flavia
   
     Even model=1+age+V2. did not work anymore
   
     Revision 1.199  2015/09/07 14:09:23  brouard
     Summary: 0.98q6 changing default small png format for graph to vectorized svg.
   
     Revision 1.198  2015/09/03 07:14:39  brouard
     Summary: 0.98q5 Flavia
   
     Revision 1.197  2015/09/01 18:24:39  brouard
     *** empty log message ***
   
     Revision 1.196  2015/08/18 23:17:52  brouard
     Summary: 0.98q5
   
     Revision 1.195  2015/08/18 16:28:39  brouard
     Summary: Adding a hack for testing purpose
   
     After reading the title, ftol and model lines, if the comment line has
     a q, starting with #q, the answer at the end of the run is quit. It
     permits to run test files in batch with ctest. The former workaround was
     $ echo q | imach foo.imach
   
     Revision 1.194  2015/08/18 13:32:00  brouard
     Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
   
     Revision 1.193  2015/08/04 07:17:42  brouard
     Summary: 0.98q4
   
     Revision 1.192  2015/07/16 16:49:02  brouard
     Summary: Fixing some outputs
   
     Revision 1.191  2015/07/14 10:00:33  brouard
     Summary: Some fixes
   
     Revision 1.190  2015/05/05 08:51:13  brouard
     Summary: Adding digits in output parameters (7 digits instead of 6)
   
     Fix 1+age+.
   
     Revision 1.189  2015/04/30 14:45:16  brouard
     Summary: 0.98q2
   
     Revision 1.188  2015/04/30 08:27:53  brouard
     *** empty log message ***
   
     Revision 1.187  2015/04/29 09:11:15  brouard
     *** empty log message ***
   
     Revision 1.186  2015/04/23 12:01:52  brouard
     Summary: V1*age is working now, version 0.98q1
   
     Some codes had been disabled in order to simplify and Vn*age was
     working in the optimization phase, ie, giving correct MLE parameters,
     but, as usual, outputs were not correct and program core dumped.
   
     Revision 1.185  2015/03/11 13:26:42  brouard
     Summary: Inclusion of compile and links command line for Intel Compiler
   
     Revision 1.184  2015/03/11 11:52:39  brouard
     Summary: Back from Windows 8. Intel Compiler
   
     Revision 1.183  2015/03/10 20:34:32  brouard
     Summary: 0.98q0, trying with directest, mnbrak fixed
   
     We use directest instead of original Powell test; probably no
     incidence on the results, but better justifications;
     We fixed Numerical Recipes mnbrak routine which was wrong and gave
     wrong results.
   
     Revision 1.182  2015/02/12 08:19:57  brouard
     Summary: Trying to keep directest which seems simpler and more general
     Author: Nicolas Brouard
   
     Revision 1.181  2015/02/11 23:22:24  brouard
     Summary: Comments on Powell added
   
     Author:
   
     Revision 1.180  2015/02/11 17:33:45  brouard
     Summary: Finishing move from main to function (hpijx and prevalence_limit)
   
     Revision 1.179  2015/01/04 09:57:06  brouard
     Summary: back to OS/X
   
     Revision 1.178  2015/01/04 09:35:48  brouard
     *** empty log message ***
   
     Revision 1.177  2015/01/03 18:40:56  brouard
     Summary: Still testing ilc32 on OSX
   
     Revision 1.176  2015/01/03 16:45:04  brouard
     *** empty log message ***
   
     Revision 1.175  2015/01/03 16:33:42  brouard
     *** empty log message ***
   
     Revision 1.174  2015/01/03 16:15:49  brouard
     Summary: Still in cross-compilation
   
     Revision 1.173  2015/01/03 12:06:26  brouard
     Summary: trying to detect cross-compilation
   
     Revision 1.172  2014/12/27 12:07:47  brouard
     Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   
     Revision 1.171  2014/12/23 13:26:59  brouard
     Summary: Back from Visual C
   
     Still problem with utsname.h on Windows
   
     Revision 1.170  2014/12/23 11:17:12  brouard
     Summary: Cleaning some \%% back to %%
   
     The escape was mandatory for a specific compiler (which one?), but too many warnings.
   
     Revision 1.169  2014/12/22 23:08:31  brouard
     Summary: 0.98p
   
     Outputs some informations on compiler used, OS etc. Testing on different platforms.
   
     Revision 1.168  2014/12/22 15:17:42  brouard
     Summary: update
   
     Revision 1.167  2014/12/22 13:50:56  brouard
     Summary: Testing uname and compiler version and if compiled 32 or 64
   
     Testing on Linux 64
   
   Revision 1.166  2014/12/22 11:40:47  brouard    Revision 1.166  2014/12/22 11:40:47  brouard
   *** empty log message ***    *** empty log message ***
   
Line 448 Line 675
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the period (stable) prevalence.     of the life expectancies. It also computes the period (stable) prevalence.
   
   Back prevalence and projections:
    - back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj)
       Computes the back prevalence limit  for any combination     of covariate values k
       at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,
      - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
    - hBijx Back Probability to be in state i at age x-h being in j at x
      Computes for any combination of covariates k and any age between bage and fage 
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                           oldm=oldms;savm=savms;
            - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
        Computes the transition matrix starting at age 'age' over
        'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
        nhstepm*hstepm matrices. Returns p3mat[i][j][h] after calling 
        p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\
        1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   Important routines
   
   - func (or funcone), computes logit (pij) distinguishing
     o fixed variables (single or product dummies or quantitative);
     o varying variables by:
      (1) wave (single, product dummies, quantitative), 
      (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
          % fixed dummy (treated) or quantitative (not done because time-consuming);
          % varying dummy (not done) or quantitative (not done);
   - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
     and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
   - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
     o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
       race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
   
   
       
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
Line 505 Line 766
  end   end
 */  */
   
   /* #define DEBUG */
   /* #define DEBUGBRENT */
   /* #define DEBUGLINMIN */
   /* #define DEBUGHESS */
   #define DEBUGHESSIJ
   /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
 #define POWELL /* Instead of NLOPT */  #define POWELL /* Instead of NLOPT */
   #define POWELLNOF3INFF1TEST /* Skip test */
   /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
   /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
   
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <string.h>  #include <string.h>
   #include <ctype.h>
   
 #ifdef _WIN32  #ifdef _WIN32
 #include <io.h>  #include <io.h>
   #include <windows.h>
   #include <tchar.h>
 #else  #else
 #include <unistd.h>  #include <unistd.h>
 #endif  #endif
   
 #include <limits.h>  #include <limits.h>
 #include <sys/types.h>  #include <sys/types.h>
   
   #if defined(__GNUC__)
   #include <sys/utsname.h> /* Doesn't work on Windows */
   #endif
   
 #include <sys/stat.h>  #include <sys/stat.h>
 #include <errno.h>  #include <errno.h>
 /* extern int errno; */  /* extern int errno; */
Line 538 Line 816
 #include <gsl/gsl_multimin.h>  #include <gsl/gsl_multimin.h>
 #endif  #endif
   
   
 #ifdef NLOPT  #ifdef NLOPT
 #include <nlopt.h>  #include <nlopt.h>
 typedef struct {  typedef struct {
Line 564  typedef struct { Line 843  typedef struct {
 #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
 #define codtabm(h,k)  1 & (h-1) >> (k-1) ;  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
   /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
   #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /**< Number of months per year */  #define YEARM 12. /**< Number of months per year */
 #define AGESUP 130  /* #define AGESUP 130 */
   #define AGESUP 150
   #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
 #define AGEBASE 40  #define AGEBASE 40
   #define AGEOVERFLOW 1.e20
 #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 #ifdef _WIN32  #ifdef _WIN32
 #define DIRSEPARATOR '\\'  #define DIRSEPARATOR '\\'
Line 582  typedef struct { Line 866  typedef struct {
   
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   #include "version.h"
 char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";  char version[]=__IMACH_VERSION__;
   char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar=0, nforce=0; /* Number of variables, number of forces */  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
 /* Number of covariates model=V2+V1+ V3*age+V2*V4 */  /* 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) */  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
 int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
 int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */  int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
   int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
 int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
 int cptcovprodnoage=0; /**< Number of covariate products without age */     int cptcovprodnoage=0; /**< Number of covariate products without age */   
 int cptcoveff=0; /* Total number of covariates to vary for printing results */  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   int ncoveff=0; /* Total number of effective covariates in the model */
   int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
   int ntveff=0; /**< ntveff number of effective time varying variables */
   int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
 int cptcov=0; /* Working variable */  int cptcov=0; /* Working variable */
   int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead 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 ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */ 
 int popbased=0;  int popbased=0;
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
Line 619  double jmean=1; /* Mean space between 2 Line 911  double jmean=1; /* Mean space between 2
 double **matprod2(); /* test */  double **matprod2(); /* test */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
   
 /*FILE *fic ; */ /* Used in readdata only */  /*FILE *fic ; */ /* Used in readdata only */
 FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
 FILE *ficlog, *ficrespow;  FILE *ficlog, *ficrespow;
 int globpr=0; /* Global variable for printing or not */  int globpr=0; /* Global variable for printing or not */
 double fretone; /* Only one call to likelihood */  double fretone; /* Only one call to likelihood */
Line 643  char fileresv[FILENAMELENGTH]; Line 937  char fileresv[FILENAMELENGTH];
 FILE  *ficresvpl;  FILE  *ficresvpl;
 char fileresvpl[FILENAMELENGTH];  char fileresvpl[FILENAMELENGTH];
 char title[MAXLINE];  char title[MAXLINE];
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
 char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 char command[FILENAMELENGTH];  char command[FILENAMELENGTH];
 int  outcmd=0;  int  outcmd=0;
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char fileresu[FILENAMELENGTH]; /* fileres without r in front */
 char filelog[FILENAMELENGTH]; /* Log file */  char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];  char filerest[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];  char fileregp[FILENAMELENGTH];
Line 699  static double maxarg1,maxarg2; Line 993  static double maxarg1,maxarg2;
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #define rint(a) floor(a+0.5)  #define rint(a) floor(a+0.5)
 /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
 /* #define mytinydouble 1.0e-16 */  #define mytinydouble 1.0e-16
 /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
 /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
 /* static double dsqrarg; */  /* static double dsqrarg; */
Line 718  int estepm; Line 1012  int estepm;
   
 int m,nb;  int m,nb;
 long *num;  long *num;
 int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;  int firstpass=0, lastpass=4,*cod, *cens;
   int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
                      covariate for which somebody answered excluding 
                      undefined. Usually 2: 0 and 1. */
   int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered including 
                                undefined. Usually 3: -1, 0 and 1. */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;  double **pmmij, ***probs; /* Global pointer */
   double ***mobaverage, ***mobaverages; /* New global variable */
 double *ageexmed,*agecens;  double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
   
Line 729  int **s; /* Status */ Line 1030  int **s; /* Status */
 double *agedc;  double *agedc;
 double  **covar; /**< covar[j,i], value of jth covariate for individual i,  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                   * covar=matrix(0,NCOVMAX,1,n);                     * covar=matrix(0,NCOVMAX,1,n); 
                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
   double **coqvar; /* Fixed quantitative covariate iqv */
   double ***cotvar; /* Time varying covariate itv */
   double ***cotqvar; /* Time varying quantitative covariate itqv */
 double  idx;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
   int *Fixed; /** Fixed[Tvar[k]] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ 
   int *Dummy; /** Dummy[Tvar[k]] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
   int *Tage;
 int *Ndum; /** Freq of modality (tricode */  int *Ndum; /** Freq of modality (tricode */
 int **codtab; /**< codtab=imatrix(1,100,1,10); */  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
 int **Tvard, *Tprod, cptcovprod, *Tvaraff;  int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;
 double *lsurv, *lpop, *tpop;  double *lsurv, *lpop, *tpop;
   
 double ftol=FTOL; /**< Tolerance for computing Max Likelihood */  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
Line 747  static int split( char *path, char *dirc Line 1055  static int split( char *path, char *dirc
      the name of the file (name), its extension only (ext) and its first part of the name (finame)       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   */     */ 
   char  *ss;                            /* pointer */    char  *ss;                            /* pointer */
   int   l1, l2;                         /* length counters */    int   l1=0, l2=0;                             /* length counters */
   
   l1 = strlen(path );                   /* length of path */    l1 = strlen(path );                   /* length of path */
   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
Line 758  static int split( char *path, char *dirc Line 1066  static int split( char *path, char *dirc
       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     /* get current working directory */      /* get current working directory */
     /*    extern  char* getcwd ( char *buf , int len);*/      /*    extern  char* getcwd ( char *buf , int len);*/
     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #ifdef WIN32
       if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
   #else
           if (getcwd(dirc, FILENAME_MAX) == NULL) {
   #endif
       return( GLOCK_ERROR_GETCWD );        return( GLOCK_ERROR_GETCWD );
     }      }
     /* got dirc from getcwd*/      /* got dirc from getcwd*/
     printf(" DIRC = %s \n",dirc);      printf(" DIRC = %s \n",dirc);
   } else {                              /* strip direcotry from path */    } else {                              /* strip directory from path */
     ss++;                               /* after this, the filename */      ss++;                               /* after this, the filename */
     l2 = strlen( ss );                  /* length of filename */      l2 = strlen( ss );                  /* length of filename */
     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     strcpy( name, ss );         /* save file name */      strcpy( name, ss );         /* save file name */
     strncpy( dirc, path, l1 - l2 );     /* now the directory */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     dirc[l1-l2] = 0;                    /* add zero */      dirc[l1-l2] = '\0';                 /* add zero */
     printf(" DIRC2 = %s \n",dirc);      printf(" DIRC2 = %s \n",dirc);
   }    }
   /* We add a separator at the end of dirc if not exists */    /* We add a separator at the end of dirc if not exists */
Line 821  char *trimbb(char *out, char *in) Line 1133  char *trimbb(char *out, char *in)
   return s;    return s;
 }  }
   
   /* char *substrchaine(char *out, char *in, char *chain) */
   /* { */
   /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
   /*   char *s, *t; */
   /*   t=in;s=out; */
   /*   while ((*in != *chain) && (*in != '\0')){ */
   /*     *out++ = *in++; */
   /*   } */
   
   /*   /\* *in matches *chain *\/ */
   /*   while ((*in++ == *chain++) && (*in != '\0')){ */
   /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   /*   } */
   /*   in--; chain--; */
   /*   while ( (*in != '\0')){ */
   /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   /*     *out++ = *in++; */
   /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
   /*   } */
   /*   *out='\0'; */
   /*   out=s; */
   /*   return out; */
   /* } */
   char *substrchaine(char *out, char *in, char *chain)
   {
     /* Substract chain 'chain' from 'in', return and output 'out' */
     /* in="V1+V1*age+age*age+V2", chain="age*age" */
   
     char *strloc;
   
     strcpy (out, in); 
     strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
     printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
     if(strloc != NULL){ 
       /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
       memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
       /* strcpy (strloc, strloc +strlen(chain));*/
     }
     printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
     return out;
   }
   
   
 char *cutl(char *blocc, char *alocc, char *in, char occ)  char *cutl(char *blocc, char *alocc, char *in, char occ)
 {  {
   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'     /* 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')       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
      gives blocc="abcdef2ghi" and alocc="j".       gives blocc="abcdef" and alocc="ghi2j".
      If occ is not found blocc is null and alocc is equal to in. Returns blocc       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   */    */
   char *s, *t;    char *s, *t;
Line 851  char *cutl(char *blocc, char *alocc, cha Line 1206  char *cutl(char *blocc, char *alocc, cha
 }  }
 char *cutv(char *blocc, char *alocc, char *in, char occ)  char *cutv(char *blocc, char *alocc, char *in, char occ)
 {  {
   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'     /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
      gives blocc="abcdef2ghi" and alocc="j".       gives blocc="abcdef2ghi" and alocc="j".
      If occ is not found blocc is null and alocc is equal to in. Returns alocc       If occ is not found blocc is null and alocc is equal to in. Returns alocc
Line 1128  char *subdirf3(char fileres[], char *pre Line 1483  char *subdirf3(char fileres[], char *pre
   strcat(tmpout,fileres);    strcat(tmpout,fileres);
   return tmpout;    return tmpout;
 }  }
    
   /*************** function subdirfext ***********/
   char *subdirfext(char fileres[], char *preop, char *postop)
   {
     
     strcpy(tmpout,preop);
     strcat(tmpout,fileres);
     strcat(tmpout,postop);
     return tmpout;
   }
   
   /*************** function subdirfext3 ***********/
   char *subdirfext3(char fileres[], char *preop, char *postop)
   {
     
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,fileres);
     strcat(tmpout,postop);
     return tmpout;
   }
    
 char *asc_diff_time(long time_sec, char ascdiff[])  char *asc_diff_time(long time_sec, char ascdiff[])
 {  {
   long sec_left, days, hours, minutes;    long sec_left, days, hours, minutes;
Line 1162  double f1dim(double x) Line 1540  double f1dim(double x)
   
 /*****************brent *************************/  /*****************brent *************************/
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 {   {
     /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
      * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
      * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
      * the minimum is returned as xmin, and the minimum function value is returned as brent , the
      * returned function value. 
     */
   int iter;     int iter; 
   double a,b,d,etemp;    double a,b,d,etemp;
   double fu=0,fv,fw,fx;    double fu=0,fv,fw,fx;
Line 1200  double brent(double ax, double bx, doubl Line 1584  double brent(double ax, double bx, doubl
       etemp=e;         etemp=e; 
       e=d;         e=d; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))         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));                                   d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       else {         else { 
         d=p/q;                                   d=p/q; 
         u=x+d;                                   u=x+d; 
         if (u-a < tol2 || b-u < tol2)                                   if (u-a < tol2 || b-u < tol2) 
           d=SIGN(tol1,xm-x);                                           d=SIGN(tol1,xm-x); 
       }         } 
     } else {       } else { 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
Line 1215  double brent(double ax, double bx, doubl Line 1599  double brent(double ax, double bx, doubl
     if (fu <= fx) {       if (fu <= fx) { 
       if (u >= x) a=x; else b=x;         if (u >= x) a=x; else b=x; 
       SHFT(v,w,x,u)         SHFT(v,w,x,u) 
         SHFT(fv,fw,fx,fu)         SHFT(fv,fw,fx,fu) 
         } else {       } else { 
           if (u < x) a=u; else b=u;         if (u < x) a=u; else b=u; 
           if (fu <= fw || w == x) {         if (fu <= fw || w == x) { 
             v=w;                                   v=w; 
             w=u;                                   w=u; 
             fv=fw;                                   fv=fw; 
             fw=fu;                                   fw=fu; 
           } else if (fu <= fv || v == x || v == w) {         } else if (fu <= fv || v == x || v == w) { 
             v=u;                                   v=u; 
             fv=fu;                                   fv=fu; 
           }         } 
         }       } 
   }     } 
   nrerror("Too many iterations in brent");     nrerror("Too many iterations in brent"); 
   *xmin=x;     *xmin=x; 
Line 1238  double brent(double ax, double bx, doubl Line 1622  double brent(double ax, double bx, doubl
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
             double (*func)(double))               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
   new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
   values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
      */
   double ulim,u,r,q, dum;    double ulim,u,r,q, dum;
   double fu;     double fu; 
    
   *fa=(*func)(*ax);     double scale=10.;
   *fb=(*func)(*bx);     int iterscale=0;
   
     *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
     *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
   
   
     /* 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++); */
     /*   *bx = *ax - (*ax - *bx)/scale; */
     /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
     /* } */
   
   if (*fb > *fa) {     if (*fb > *fa) { 
     SHFT(dum,*ax,*bx,dum)       SHFT(dum,*ax,*bx,dum) 
       SHFT(dum,*fb,*fa,dum)       SHFT(dum,*fb,*fa,dum) 
       }     } 
   *cx=(*bx)+GOLD*(*bx-*ax);     *cx=(*bx)+GOLD*(*bx-*ax); 
   *fc=(*func)(*cx);     *fc=(*func)(*cx); 
   while (*fb > *fc) { /* Declining fa, fb, fc */  #ifdef DEBUG
     printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
     fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
   #endif
     while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
     r=(*bx-*ax)*(*fb-*fc);       r=(*bx-*ax)*(*fb-*fc); 
     q=(*bx-*cx)*(*fb-*fa);       q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
     if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
       fu=(*func)(u);         fu=(*func)(u); 
 #ifdef DEBUG  #ifdef DEBUG
       /* f(x)=A(x-u)**2+f(u) */        /* f(x)=A(x-u)**2+f(u) */
       double A, fparabu;         double A, fparabu; 
       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
       fparabu= *fa - A*(*ax-u)*(*ax-u);        fparabu= *fa - A*(*ax-u)*(*ax-u);
       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);        printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
       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);        fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
         /* 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),
           (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
         /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
 #endif   #endif 
   #ifdef MNBRAKORIGINAL
   #else
   /*       if (fu > *fc) { */
   /* #ifdef DEBUG */
   /*       printf("mnbrak4  fu > fc \n"); */
   /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
   /* #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 *\\/  *\/ */
   /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
   /*      dum=u; /\* Shifting c and u *\/ */
   /*      u = *cx; */
   /*      *cx = dum; */
   /*      dum = fu; */
   /*      fu = *fc; */
   /*      *fc =dum; */
   /*       } else { /\* end *\/ */
   /* #ifdef DEBUG */
   /*       printf("mnbrak3  fu < fc \n"); */
   /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
   /* #endif */
   /*      dum=u; /\* Shifting c and u *\/ */
   /*      u = *cx; */
   /*      *cx = dum; */
   /*      dum = fu; */
   /*      fu = *fc; */
   /*      *fc =dum; */
   /*       } */
   #ifdef DEBUGMNBRAK
                    double A, fparabu; 
        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
        fparabu= *fa - A*(*ax-u)*(*ax-u);
        printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
        fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
   #endif
         dum=u; /* Shifting c and u */
         u = *cx;
         *cx = dum;
         dum = fu;
         fu = *fc;
         *fc =dum;
   #endif
     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   #ifdef DEBUG
         printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
         fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
   #endif
       fu=(*func)(u);         fu=(*func)(u); 
       if (fu < *fc) {         if (fu < *fc) { 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))   #ifdef DEBUG
           SHFT(*fb,*fc,fu,(*func)(u))                                   printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
           }                             fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
   #endif
                             SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
                                   SHFT(*fb,*fc,fu,(*func)(u)) 
   #ifdef DEBUG
                                           printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
   #endif
         } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   #ifdef DEBUG
         printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
         fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
   #endif
       u=ulim;         u=ulim; 
       fu=(*func)(u);         fu=(*func)(u); 
     } else {       } else { /* u could be left to b (if r > q parabola has a maximum) */
   #ifdef DEBUG
         printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
         fprintf(ficlog,"\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
   #endif
       u=(*cx)+GOLD*(*cx-*bx);         u=(*cx)+GOLD*(*cx-*bx); 
       fu=(*func)(u);         fu=(*func)(u); 
     }   #ifdef DEBUG
         printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
         fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
   #endif
       } /* end tests */
     SHFT(*ax,*bx,*cx,u)       SHFT(*ax,*bx,*cx,u) 
       SHFT(*fa,*fb,*fc,fu)       SHFT(*fa,*fb,*fc,fu) 
       }   #ifdef DEBUG
         printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
         fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
   #endif
     } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
 }   } 
   
 /*************** linmin ************************/  /*************** linmin ************************/
Line 1294  int ncom; Line 1769  int ncom;
 double *pcom,*xicom;  double *pcom,*xicom;
 double (*nrfunc)(double []);   double (*nrfunc)(double []); 
     
   #ifdef LINMINORIGINAL
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   #else
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat) 
   #endif
 {   { 
   double brent(double ax, double bx, double cx,     double brent(double ax, double bx, double cx, 
                double (*f)(double), double tol, double *xmin);                  double (*f)(double), double tol, double *xmin); 
Line 1304  void linmin(double p[], double xi[], int Line 1783  void linmin(double p[], double xi[], int
   int j;     int j; 
   double xx,xmin,bx,ax;     double xx,xmin,bx,ax; 
   double fx,fb,fa;    double fx,fb,fa;
    
   #ifdef LINMINORIGINAL
   #else
     double scale=10., axs, xxs; /* Scale added for infinity */
   #endif
     
   ncom=n;     ncom=n; 
   pcom=vector(1,n);     pcom=vector(1,n); 
   xicom=vector(1,n);     xicom=vector(1,n); 
   nrfunc=func;     nrfunc=func; 
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
     pcom[j]=p[j];       pcom[j]=p[j]; 
     xicom[j]=xi[j];       xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
   }     } 
   ax=0.0;   
   xx=1.0;   #ifdef LINMINORIGINAL
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */    xx=1.;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */  #else
     axs=0.0;
     xxs=1.;
     do{
       xx= xxs;
   #endif
       ax=0.;
       mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
       /* 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))   */
       /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
       /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
       /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
       /* 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]]*/
   #ifdef LINMINORIGINAL
   #else
       if (fx != fx){
                           xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
                           printf("|");
                           fprintf(ficlog,"|");
   #ifdef DEBUGLINMIN
                           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);
   #endif
       }
     }while(fx != fx && xxs > 1.e-5);
   #endif
     
   #ifdef DEBUGLINMIN
     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);
     fprintf(ficlog,"\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);
   #endif
   #ifdef LINMINORIGINAL
   #else
           if(fb == fx){ /* Flat function in the direction */
                   xmin=xx;
       *flat=1;
           }else{
       *flat=0;
   #endif
                   /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
     /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
     /* fmin = f(p[j] + xmin * xi[j]) */
     /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
     /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
 #ifdef DEBUG  #ifdef DEBUG
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
   #endif
   #ifdef LINMINORIGINAL
   #else
                           }
   #endif
   #ifdef DEBUGLINMIN
     printf("linmin end ");
     fprintf(ficlog,"linmin end ");
 #endif  #endif
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
   #ifdef LINMINORIGINAL
     xi[j] *= xmin;       xi[j] *= xmin; 
     p[j] += xi[j];   #else
   #ifdef DEBUGLINMIN
       if(xxs <1.0)
         printf(" before xi[%d]=%12.8f", j,xi[j]);
   #endif
       xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
   #ifdef DEBUGLINMIN
       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 );
   #endif
   #endif
       p[j] += xi[j]; /* Parameters values are updated accordingly */
   }     } 
   #ifdef DEBUGLINMIN
     printf("\n");
     printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
     fprintf(ficlog,"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]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
       fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
       if(j % ncovmodel == 0){
         printf("\n");
         fprintf(ficlog,"\n");
       }
     }
   #else
   #endif
   free_vector(xicom,1,n);     free_vector(xicom,1,n); 
   free_vector(pcom,1,n);     free_vector(pcom,1,n); 
 }   } 
Line 1339  such that failure to decrease by more th Line 1901  such that failure to decrease by more th
 output, p is set to the best point found, xi is the then-current direction set, fret is the returned  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
 function value at p , and iter is the number of iterations taken. The routine linmin is used.  function value at p , and iter is the number of iterations taken. The routine linmin is used.
  */   */
   #ifdef LINMINORIGINAL
   #else
           int *flatdir; /* Function is vanishing in that direction */
           int flat=0, flatd=0; /* Function is vanishing in that direction */
   #endif
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
             double (*func)(double []))               double (*func)(double [])) 
 {   { 
   void linmin(double p[], double xi[], int n, double *fret,   #ifdef LINMINORIGINAL
    void linmin(double p[], double xi[], int n, double *fret, 
               double (*func)(double []));                 double (*func)(double [])); 
   #else 
    void linmin(double p[], double xi[], int n, double *fret, 
                                                    double (*func)(double []),int *flat); 
   #endif
   int i,ibig,j;     int i,ibig,j; 
   double del,t,*pt,*ptt,*xit;    double del,t,*pt,*ptt,*xit;
     double directest;
   double fp,fptt;    double fp,fptt;
   double *xits;    double *xits;
   int niterf, itmp;    int niterf, itmp;
   #ifdef LINMINORIGINAL
   #else
   
     flatdir=ivector(1,n); 
     for (j=1;j<=n;j++) flatdir[j]=0; 
   #endif
   
   pt=vector(1,n);     pt=vector(1,n); 
   ptt=vector(1,n);     ptt=vector(1,n); 
Line 1356  void powell(double p[], double **xi, int Line 1935  void powell(double p[], double **xi, int
   xits=vector(1,n);     xits=vector(1,n); 
   *fret=(*func)(p);     *fret=(*func)(p); 
   for (j=1;j<=n;j++) pt[j]=p[j];     for (j=1;j<=n;j++) pt[j]=p[j]; 
     rcurr_time = time(NULL);      rcurr_time = time(NULL);  
   for (*iter=1;;++(*iter)) {     for (*iter=1;;++(*iter)) { 
     fp=(*fret);       fp=(*fret); /* From former iteration or initial value */
     ibig=0;       ibig=0; 
     del=0.0;       del=0.0; 
     rlast_time=rcurr_time;      rlast_time=rcurr_time;
Line 1368  void powell(double p[], double **xi, int Line 1947  void powell(double p[], double **xi, int
     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
     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(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
 /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
    for (i=1;i<=n;i++) {      for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);        printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);        fprintf(ficlog," %d %.12lf",i, p[i]);
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
Line 1382  void powell(double p[], double **xi, int Line 1961  void powell(double p[], double **xi, int
       rforecast_time=rcurr_time;         rforecast_time=rcurr_time; 
       itmp = strlen(strcurr);        itmp = strlen(strcurr);
       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         strcurr[itmp-1]='\0';                                  strcurr[itmp-1]='\0';
       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for(niterf=10;niterf<=30;niterf+=10){        for(niterf=10;niterf<=30;niterf+=10){
         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);                                  rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         forecast_time = *localtime(&rforecast_time);                                  forecast_time = *localtime(&rforecast_time);
         strcpy(strfor,asctime(&forecast_time));                                  strcpy(strfor,asctime(&forecast_time));
         itmp = strlen(strfor);                                  itmp = strlen(strfor);
         if(strfor[itmp-1]=='\n')                                  if(strfor[itmp-1]=='\n')
         strfor[itmp-1]='\0';                                          strfor[itmp-1]='\0';
         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);                                  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);                                  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);
       }        }
     }      }
     for (i=1;i<=n;i++) {       for (i=1;i<=n;i++) { /* For each direction i */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];         for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
       fptt=(*fret);         fptt=(*fret); 
 #ifdef DEBUG  #ifdef DEBUG
           printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);        printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);        fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
 #endif  #endif
       printf("%d",i);fflush(stdout);        printf("%d",i);fflush(stdout); /* print direction (parameter) i */
       fprintf(ficlog,"%d",i);fflush(ficlog);        fprintf(ficlog,"%d",i);fflush(ficlog);
       linmin(p,xit,n,fret,func);   #ifdef LINMINORIGINAL
       if (fabs(fptt-(*fret)) > del) {         linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
         del=fabs(fptt-(*fret));   #else
         ibig=i;         linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                           flatdir[i]=flat; /* Function is vanishing in that direction i */
   #endif
                           /* 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 */
                                   /* 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. */
                                   /* Unless the n directions are conjugate some gain in the determinant may be obtained */
                                   /* with the new direction. */
                                   del=fabs(fptt-(*fret)); 
                                   ibig=i; 
       }         } 
 #ifdef DEBUG  #ifdef DEBUG
       printf("%d %.12e",i,(*fret));        printf("%d %.12e",i,(*fret));
       fprintf(ficlog,"%d %.12e",i,(*fret));        fprintf(ficlog,"%d %.12e",i,(*fret));
       for (j=1;j<=n;j++) {        for (j=1;j<=n;j++) {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);                                  xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         printf(" x(%d)=%.12e",j,xit[j]);                                  printf(" x(%d)=%.12e",j,xit[j]);
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);                                  fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
       for(j=1;j<=n;j++) {        for(j=1;j<=n;j++) {
         printf(" p(%d)=%.12e",j,p[j]);                                  printf(" p(%d)=%.12e",j,p[j]);
         fprintf(ficlog," p(%d)=%.12e",j,p[j]);                                  fprintf(ficlog," p(%d)=%.12e",j,p[j]);
       }        }
       printf("\n");        printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
 #endif  #endif
     } /* end i */      } /* end loop on each direction i */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
       /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
       /* New value of last point Pn is not computed, P(n-1) */
         for(j=1;j<=n;j++) {
                                   if(flatdir[j] >0){
                                           printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
                                           fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
                                   }
                                   /* printf("\n"); */
                                   /* fprintf(ficlog,"\n"); */
                           }
       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 */
         /* 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 */
         /* decreased of more than 3.84  */
         /* 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 */
                           
         /* Starting the program with initial values given by a former maximization will simply change */
         /* the scales of the directions and the directions, because the are reset to canonical directions */
         /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
         /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
 #ifdef DEBUG  #ifdef DEBUG
       int k[2],l;        int k[2],l;
       k[0]=1;        k[0]=1;
Line 1450  void powell(double p[], double **xi, int Line 2062  void powell(double p[], double **xi, int
       }        }
 #endif  #endif
   
   #ifdef LINMINORIGINAL
   #else
         free_ivector(flatdir,1,n); 
   #endif
       free_vector(xit,1,n);         free_vector(xit,1,n); 
       free_vector(xits,1,n);         free_vector(xits,1,n); 
       free_vector(ptt,1,n);         free_vector(ptt,1,n); 
       free_vector(pt,1,n);         free_vector(pt,1,n); 
       return;         return; 
     }       } /* enough precision */ 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++) { /* Computes an extrapolated point */      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
       ptt[j]=2.0*p[j]-pt[j];         ptt[j]=2.0*p[j]-pt[j]; 
       xit[j]=p[j]-pt[j];         xit[j]=p[j]-pt[j]; 
       pt[j]=p[j];         pt[j]=p[j]; 
     }       } 
     fptt=(*func)(ptt);       fptt=(*func)(ptt); /* f_3 */
   #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
                   if (*iter <=4) {
   #else
   #endif
   #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
   #else
     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */      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) */        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
       /* From x1 (P0) distance of x2 is at h and x3 is 2h */        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
       /* Let f"(x2) be the 2nd derivative equal everywhere.  */        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */        /* 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 */        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
       /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
       /* Thus we compare delta(2h) with observed f1-f3 */        /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
       /* or best gain on one ancient line 'del' with total  */        /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
       /* gain f1-f2 = f1 - f2 - 'del' with del  */  
       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
         /*  Even if f3 <f1, directest can be negative and t >0 */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);        /* mu² and del² are equal when f3=f1 */
                           /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
                           /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
                           /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
                           /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
   #ifdef NRCORIGINAL
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
   #else
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
       t= t- del*SQR(fp-fptt);        t= t- del*SQR(fp-fptt);
       printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);  #endif
       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
 #ifdef DEBUG  #ifdef DEBUG
         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);
       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
Line 1488  void powell(double p[], double **xi, int Line 2119  void powell(double p[], double **xi, int
       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);        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);
       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);        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);
 #endif  #endif
       if (t < 0.0) { /* Then we use it for last direction */  #ifdef POWELLORIGINAL
         linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/        if (t < 0.0) { /* Then we use it for new direction */
         for (j=1;j<=n;j++) {   #else
           xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */        if (directest*t < 0.0) { /* Contradiction between both tests */
           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */                                  printf("directest= %.12lf (if <0 we include P0 Pn as new direction), 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);
         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
         fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         } 
         if (directest < 0.0) { /* Then we use it for new direction */
   #endif
   #ifdef DEBUGLINMIN
                                   printf("Before linmin in direction P%d-P0\n",n);
                                   for (j=1;j<=n;j++) {
                                           printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                           fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                           if(j % ncovmodel == 0){
                                                   printf("\n");
                                                   fprintf(ficlog,"\n");
                                           }
                                   }
   #endif
   #ifdef LINMINORIGINAL
                                   linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
   #else
                                   linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
                                   flatdir[i]=flat; /* Function is vanishing in that direction i */
   #endif
   
   #ifdef DEBUGLINMIN
                                   for (j=1;j<=n;j++) { 
                                           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                           if(j % ncovmodel == 0){
                                                   printf("\n");
                                                   fprintf(ficlog,"\n");
                                           }
                                   }
   #endif
                                   for (j=1;j<=n;j++) { 
                                           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
                                           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
                                   }
   #ifdef LINMINORIGINAL
   #else
                                   for (j=1, flatd=0;j<=n;j++) {
                                           if(flatdir[j]>0)
                                                   flatd++;
                                   }
                                   if(flatd >0){
                                           printf("%d flat directions\n",flatd);
                                           fprintf(ficlog,"%d flat directions\n",flatd);
                                           for (j=1;j<=n;j++) { 
                                                   if(flatdir[j]>0){
                                                           printf("%d ",j);
                                                           fprintf(ficlog,"%d ",j);
                                                   }
                                           }
                                           printf("\n");
                                           fprintf(ficlog,"\n");
                                   }
   #endif
                                   printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                                   fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                                   
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);                                  printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);                                  fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         for(j=1;j<=n;j++){                                  for(j=1;j<=n;j++){
           printf(" %.12e",xit[j]);                                          printf(" %lf",xit[j]);
           fprintf(ficlog," %.12e",xit[j]);                                          fprintf(ficlog," %lf",xit[j]);
         }                                  }
         printf("\n");                                  printf("\n");
         fprintf(ficlog,"\n");                                  fprintf(ficlog,"\n");
 #endif  #endif
       } /* end of t negative */        } /* end of t or directest negative */
   #ifdef POWELLNOF3INFF1TEST
   #else
     } /* end if (fptt < fp)  */      } /* end if (fptt < fp)  */
   }   #endif
   #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
                   } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
   #else
   #endif
     } /* loop iteration */ 
 }   } 
   
 /**** Prevalence limit (stable or period prevalence)  ****************/  /**** Prevalence limit (stable or period prevalence)  ****************/
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
      matrix by transitions matrix until convergence is reached */       matrix by transitions matrix until convergence is reached with precision ftolpl */
     /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
     /* Wx is row vector: population in state 1, population in state 2, population dead */
     /* or prevalence in state 1, prevalence in state 2, 0 */
     /* newm is the matrix after multiplications, its rows are identical at a factor */
     /* Initial matrix pimij */
     /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
     /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
     /*  0,                   0                  , 1} */
     /*
      * and after some iteration: */
     /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
     /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
     /*  0,                   0                  , 1} */
     /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
     /* {0.51571254859325999, 0.4842874514067399, */
     /*  0.51326036147820708, 0.48673963852179264} */
     /* If we start from prlim again, prlim tends to a constant matrix */
   
   int i, ii,j,k;    int i, ii,j,k;
   double min, max, maxmin, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **pmij();    double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
   double **newm;    double **newm;
   double agefin, delaymax=50 ; /* Max number of years to converge */    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
     int ncvloop=0;
     
     min=vector(1,nlstate);
     max=vector(1,nlstate);
     meandiff=vector(1,nlstate);
   
           /* Starting with matrix unity */
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
     
    cov[1]=1.;    cov[1]=1.;
      
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       ncvloop++;
     newm=savm;      newm=savm;
     /* Covariates have to be included here again */      /* Covariates have to be included here again */
     cov[2]=agefin;      cov[2]=agefin;
           if(nagesqr==1)
         cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;k++) {      for (k=1; k<=cptcovn;k++) {
       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/                          /* Here comes the value of the covariate 'ij' */
     }        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */        /* 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])]); */
     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */      }
     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
       for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
       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])]; */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
           
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */      /* 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 *\/ */      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
                   /* age and covariate values of ij are in 'cov' */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           
     savm=oldm;      savm=oldm;
     oldm=newm;      oldm=newm;
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){      for(j=1; j<=nlstate; j++){
       min=1.;        max[j]=0.;
       max=0.;        min[j]=1.;
       for(i=1; i<=nlstate; i++) {      }
         sumnew=0;      for(i=1;i<=nlstate;i++){
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        sumnew=0;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         for(j=1; j<=nlstate; j++){ 
         prlim[i][j]= newm[i][j]/(1-sumnew);          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[j]=FMAX(max[j],prlim[i][j]);
         max=FMAX(max,prlim[i][j]);          min[j]=FMIN(min[j],prlim[i][j]);
         min=FMIN(min,prlim[i][j]);  
       }        }
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);  
     }      }
   
       maxmax=0.;
       for(j=1; j<=nlstate; j++){
         meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
         maxmax=FMAX(maxmax,meandiff[j]);
         /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
       } /* j loop */
       *ncvyear= (int)age- (int)agefin;
       /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
     if(maxmax < ftolpl){      if(maxmax < ftolpl){
         /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
         free_vector(min,1,nlstate);
         free_vector(max,1,nlstate);
         free_vector(meandiff,1,nlstate);
       return prlim;        return prlim;
     }      }
   }    } /* age loop */
       /* After some age loop it doesn't converge */
     printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
   Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
     /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
     free_vector(min,1,nlstate);
     free_vector(max,1,nlstate);
     free_vector(meandiff,1,nlstate);
     
     return prlim; /* should not reach here */
   }
   
   
    /**** Back Prevalence limit (stable or period prevalence)  ****************/
   
    /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
    /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
    double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
   {
     /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
        matrix by transitions matrix until convergence is reached with precision ftolpl */
     /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
     /* Wx is row vector: population in state 1, population in state 2, population dead */
     /* or prevalence in state 1, prevalence in state 2, 0 */
     /* newm is the matrix after multiplications, its rows are identical at a factor */
     /* Initial matrix pimij */
     /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
     /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
     /*  0,                   0                  , 1} */
     /*
      * and after some iteration: */
     /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
     /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
     /*  0,                   0                  , 1} */
     /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
     /* {0.51571254859325999, 0.4842874514067399, */
     /*  0.51326036147820708, 0.48673963852179264} */
     /* If we start from prlim again, prlim tends to a constant matrix */
   
     int i, ii,j,k;
     double *min, *max, *meandiff, maxmax,sumnew=0.;
     /* double **matprod2(); */ /* test */
     double **out, cov[NCOVMAX+1], **bmij();
     double **newm;
     double         **dnewm, **doldm, **dsavm;  /* for use */
     double         **oldm, **savm;  /* for use */
   
     double agefin, delaymax=200. ; /* 100 Max number of years to converge */
     int ncvloop=0;
     
     min=vector(1,nlstate);
     max=vector(1,nlstate);
     meandiff=vector(1,nlstate);
   
           dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
           oldm=oldms; savm=savms;
   
           /* Starting with matrix unity */
           for (ii=1;ii<=nlstate+ndeath;ii++)
                   for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
     
     cov[1]=1.;
     
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
     /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
     for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
       ncvloop++;
       newm=savm; /* oldm should be kept from previous iteration or unity at start */
                   /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
       /* Covariates have to be included here again */
       cov[2]=agefin;
       if(nagesqr==1)
         cov[3]= agefin*agefin;;
       for (k=1; k<=cptcovn;k++) {
         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
         /* 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])]); */
       }
       /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
       for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
       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])]; */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
       
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* 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 *\/ */
                   /* ij should be linked to the correct index of cov */
                   /* age and covariate values ij are in 'cov', but we need to pass
                    * ij for the observed prevalence at age and status and covariate
                    * number:  prevacurrent[(int)agefin][ii][ij]
                    */
       /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
       /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
       savm=oldm;
       oldm=newm;
       for(j=1; j<=nlstate; j++){
         max[j]=0.;
         min[j]=1.;
       }
       for(j=1; j<=nlstate; j++){ 
         for(i=1;i<=nlstate;i++){
                                   /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
                                   bprlim[i][j]= newm[i][j];
                                   max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
                                   min[i]=FMIN(min[i],bprlim[i][j]);
         }
       }
                   
       maxmax=0.;
       for(i=1; i<=nlstate; i++){
         meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
         maxmax=FMAX(maxmax,meandiff[i]);
         /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
       } /* j loop */
       *ncvyear= -( (int)age- (int)agefin);
       /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
       if(maxmax < ftolpl){
         /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
         free_vector(min,1,nlstate);
         free_vector(max,1,nlstate);
         free_vector(meandiff,1,nlstate);
         return bprlim;
       }
     } /* age loop */
       /* After some age loop it doesn't converge */
     printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
   Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
     /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
     free_vector(min,1,nlstate);
     free_vector(max,1,nlstate);
     free_vector(meandiff,1,nlstate);
     
     return bprlim; /* should not reach here */
 }  }
   
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
Line 1598  double **pmij(double **ps, double *cov, Line 2476  double **pmij(double **ps, double *cov,
   /*double t34;*/    /*double t34;*/
   int i,j, nc, ii, jj;    int i,j, nc, ii, jj;
   
     for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){      for(j=1; j<i;j++){
         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           /*lnpijopii += param[i][j][nc]*cov[nc];*/          /*lnpijopii += param[i][j][nc]*cov[nc];*/
           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
 /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }        }
         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */        /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       }      }
       for(j=i+1; j<=nlstate+ndeath;j++){      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/          /*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];          lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         }        }
         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       }      }
     }    }
         
     for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
       s1=0;      s1=0;
       for(j=1; j<i; j++){      for(j=1; j<i; j++){
         s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       }      }
       for(j=i+1; j<=nlstate+ndeath; j++){      for(j=i+1; j<=nlstate+ndeath; j++){
         s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       }      }
       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       ps[i][i]=1./(s1+1.);      ps[i][i]=1./(s1+1.);
       /* Computing other pijs */      /* Computing other pijs */
       for(j=1; j<i; j++)      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)      for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     } /* end i */    } /* end i */
         
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){      for(jj=1; jj<= nlstate+ndeath; jj++){
         ps[ii][jj]=0;        ps[ii][jj]=0;
         ps[ii][ii]=1;        ps[ii][ii]=1;
       }
     }
     
     
     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     /*   } */
     /*   printf("\n "); */
     /* } */
     /* printf("\n ");printf("%lf ",cov[2]);*/
     /*
       for(i=1; i<= npar; i++) printf("%f ",x[i]);
                   goto end;*/
     return ps;
   }
   
   /*************** backward transition probabilities ***************/ 
   
    /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
   /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
    double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
   {
     /* Computes the backward probability at age agefin and covariate ij
      * and returns in **ps as well as **bmij.
      */
     int i, ii, j,k;
     
     double **out, **pmij();
     double sumnew=0.;
     double agefin;
     
     double **dnewm, **dsavm, **doldm;
     double **bbmij;
     
     doldm=ddoldms; /* global pointers */
     dnewm=ddnewms;
     dsavm=ddsavms;
     
     agefin=cov[2];
     /* bmij *//* age is cov[2], ij is included in cov, but we need for
        the observed prevalence (with this covariate ij) */
     dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
     /* We do have the matrix Px in savm  and we need pij */
     for (j=1;j<=nlstate+ndeath;j++){
       sumnew=0.; /* w1 p11 + w2 p21 only on live states */
       for (ii=1;ii<=nlstate;ii++){
         sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
       } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
       for (ii=1;ii<=nlstate+ndeath;ii++){
         if(sumnew >= 1.e-10){
           /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
           /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
           /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
           /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
           /* }else */
           doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
         }else{
           printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
       }        }
     }      } /*End ii */
         } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
         /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */    bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */    /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */    /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
     /*   } */    /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
     /*   printf("\n "); */    /* left Product of this matrix by diag matrix of prevalences (savm) */
     /* } */    for (j=1;j<=nlstate+ndeath;j++){
     /* printf("\n ");printf("%lf ",cov[2]);*/      for (ii=1;ii<=nlstate+ndeath;ii++){
     /*        dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
       for(i=1; i<= npar; i++) printf("%f ",x[i]);      }
       goto end;*/    } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
     return ps;    ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
     /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
     /* end bmij */
     return ps; 
   }
   /*************** transition probabilities ***************/ 
   
   double **bpmij(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,
        computes the probability to be observed in state j being in state i by appying the
        model to the ncovmodel covariates (including constant and age).
        lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
        and, according on how parameters are entered, the position of the coefficient xij(nc) of the
        ncth covariate in the global vector x is given by the formula:
        j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
        j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        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
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     */
     double s1, lnpijopii;
     /*double t34;*/
     int i,j, nc, ii, jj;
   
           for(i=1; i<= nlstate; i++){
                   for(j=1; j<i;j++){
                           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                   /*lnpijopii += param[i][j][nc]*cov[nc];*/
                                   lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                                   /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                           }
                           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                           /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   }
                   for(j=i+1; j<=nlstate+ndeath;j++){
                           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                   /*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("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                           }
                           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   }
           }
           
           for(i=1; i<= nlstate; i++){
                   s1=0;
                   for(j=1; j<i; j++){
                           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                           /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   }
                   for(j=i+1; j<=nlstate+ndeath; j++){
                           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                           /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                   }
                   /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                   ps[i][i]=1./(s1+1.);
                   /* Computing other pijs */
                   for(j=1; j<i; j++)
                           ps[i][j]= exp(ps[i][j])*ps[i][i];
                   for(j=i+1; j<=nlstate+ndeath; j++)
                           ps[i][j]= exp(ps[i][j])*ps[i][i];
                   /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
           } /* end i */
           
           for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                   for(jj=1; jj<= nlstate+ndeath; jj++){
                           ps[ii][jj]=0;
                           ps[ii][ii]=1;
                   }
           }
           /* Added for backcast */ /* Transposed matrix too */
           for(jj=1; jj<= nlstate+ndeath; jj++){
                   s1=0.;
                   for(ii=1; ii<= nlstate+ndeath; ii++){
                           s1+=ps[ii][jj];
                   }
                   for(ii=1; ii<= nlstate; ii++){
                           ps[ii][jj]=ps[ii][jj]/s1;
                   }
           }
           /* Transposition */
           for(jj=1; jj<= nlstate+ndeath; jj++){
                   for(ii=jj; ii<= nlstate+ndeath; ii++){
                           s1=ps[ii][jj];
                           ps[ii][jj]=ps[jj][ii];
                           ps[jj][ii]=s1;
                   }
           }
           /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
           /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
           /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
           /*   } */
           /*   printf("\n "); */
           /* } */
           /* printf("\n ");printf("%lf ",cov[2]);*/
           /*
                   for(i=1; i<= npar; i++) printf("%f ",x[i]);
                   goto end;*/
           return ps;
 }  }
   
   
 /**************** Product of 2 matrices ******************/  /**************** Product of 2 matrices ******************/
   
 double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
Line 1683  double **matprod2(double **out, double * Line 2721  double **matprod2(double **out, double *
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 {  {
   /* Computes the transition matrix starting at age 'age' over     /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over 
      'nhstepm*hstepm*stepm' months (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
      nhstepm*hstepm matrices.        nhstepm*hstepm matrices. 
Line 1698  double ***hpxij(double ***po, int nhstep Line 2736  double ***hpxij(double ***po, int nhstep
   int i, j, d, h, k;    int i, j, d, h, k;
   double **out, cov[NCOVMAX+1];    double **out, cov[NCOVMAX+1];
   double **newm;    double **newm;
     double agexact;
     double agebegin, ageend;
   
   /* Hstepm could be zero and should return the unit matrix */    /* Hstepm could be zero and should return the unit matrix */
   for (i=1;i<=nlstate+ndeath;i++)    for (i=1;i<=nlstate+ndeath;i++)
Line 1711  double ***hpxij(double ***po, int nhstep Line 2751  double ***hpxij(double ***po, int nhstep
       newm=savm;        newm=savm;
       /* Covariates have to be included here again */        /* Covariates have to be included here again */
       cov[1]=1.;        cov[1]=1.;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
         cov[2]=agexact;
         if(nagesqr==1)
                                   cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++)         for (k=1; k<=cptcovn;k++) 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];                                  cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
       for (k=1; k<=cptcovage;k++)                          /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
                                   /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
                                   cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
                           /* 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 (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];                                  cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
                           /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
   
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                           /* right multiplication of oldm by the current matrix */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         /* if((int)age == 70){ */
         /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
         /*        for(i=1; i<=nlstate+ndeath; i++) { */
         /*          printf("%d pmmij ",i); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",pmmij[i][j]); */
         /*          } */
         /*          printf(" oldm "); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",oldm[i][j]); */
         /*          } */
         /*          printf("\n"); */
         /*        } */
         /* } */
         savm=oldm;
         oldm=newm;
       }
       for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
                                   po[i][j][h]=newm[i][j];
                                   /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
       /*printf("h=%d ",h);*/
     } /* end h */
           /*     printf("\n H=%d \n",h); */
     return po;
   }
   
   /************* Higher Back Matrix Product ***************/
   /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
   double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
   {
     /* Computes the transition matrix starting at age 'age' over
        'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
        nhstepm*hstepm matrices.
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step
        (typically every 2 years instead of every month which is too big
        for the memory).
        Model is determined by parameters x and covariates have to be
        included manually here.
   
     */
   
     int i, j, d, h, k;
     double **out, cov[NCOVMAX+1];
     double **newm;
     double agexact;
     double agebegin, ageend;
     double **oldm, **savm;
   
     oldm=oldms;savm=savms;
     /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
         newm=savm;
         /* Covariates have to be included here again */
         cov[1]=1.;
         agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
         /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
         cov[2]=agexact;
         if(nagesqr==1)
           cov[3]= agexact*agexact;
         for (k=1; k<=cptcovn;k++)
           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
         for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
           /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
         /* 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 */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
                           
                           
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         /* Careful transposed matrix */
         /* age is in cov[2] */
         /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
         /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
         out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
                      1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         /* if((int)age == 70){ */
         /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
         /*        for(i=1; i<=nlstate+ndeath; i++) { */
         /*          printf("%d pmmij ",i); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",pmmij[i][j]); */
         /*          } */
         /*          printf(" oldm "); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",oldm[i][j]); */
         /*          } */
         /*          printf("\n"); */
         /*        } */
         /* } */
       savm=oldm;        savm=oldm;
       oldm=newm;        oldm=newm;
     }      }
Line 1734  double ***hpxij(double ***po, int nhstep Line 2885  double ***hpxij(double ***po, int nhstep
       }        }
     /*printf("h=%d ",h);*/      /*printf("h=%d ",h);*/
   } /* end h */    } /* end h */
 /*     printf("\n H=%d \n",h); */    /*     printf("\n H=%d \n",h); */
   return po;    return po;
 }  }
   
   
 #ifdef NLOPT  #ifdef NLOPT
   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   double fret;    double fret;
Line 1762  double ***hpxij(double ***po, int nhstep Line 2914  double ***hpxij(double ***po, int nhstep
 double func( double *x)  double func( double *x)
 {  {
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
     int ioffset=0;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double sw; /* Sum of weights */    double sw; /* Sum of weights */
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
   int s1, s2;    int s1, s2;
     int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quatitative time varying covariate */
   double bbh, survp;    double bbh, survp;
   long ipmx;    long ipmx;
     double agexact;
   /*extern weight */    /*extern weight */
   /* We are differentiating ll according to initial status */    /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 1781  double func( double *x) Line 2936  double func( double *x)
   cov[1]=1.;    cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     ioffset=0;
   if(mle==1){    if(mle==1){
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       /* Computes the values of the ncovmodel covariates of the model        /* 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[]           depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability           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.           to be observed in j being in i according to the model.
        */        */
       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */        ioffset=2+nagesqr+cptcovage;
         cov[2+k]=covar[Tvar[k]][i];        /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
         for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
           cov[++ioffset]=covar[Tvar[k]][i];
       }        }
         for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
           cov[++ioffset]=coqvar[iqv][i];
         }
   
       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]            is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
          has been calculated etc */           has been calculated etc */
         /* For an individual i, wav[i] gives the number of effective waves */
         /* We compute the contribution to Likelihood of each effective transition
            mw[mi][i] is real wave of the mi th effectve wave */
         /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
            s2=s[mw[mi+1][i]][i];
            And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
            But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
            meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
         */
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
             cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
           }
           for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
             if(cotqvar[mw[mi][i]][iqtv][i] == -1){
               printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
             }
             cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
           }
           /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
Line 1803  double func( double *x) Line 2983  double func( double *x)
           }            }
         for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
           newm=savm;            newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;  /* Should be changed here */
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
           }            }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;            savm=oldm;
           oldm=newm;            oldm=newm;
         } /* end mult */          } /* end mult */
                                         
         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         /* But now since version 0.9 we anticipate for bias at large stepm.          /* But now since version 0.9 we anticipate for bias at large stepm.
          * If stepm is larger than one month (smallest stepm) and if the exact delay            * If stepm is larger than one month (smallest stepm) and if the exact delay 
Line 1840  double func( double *x) Line 3023  double func( double *x)
              which is also equal to probability to die before dh                which is also equal to probability to die before dh 
              minus probability to die before dh-stepm .                minus probability to die before dh-stepm . 
              In version up to 0.92 likelihood was computed               In version up to 0.92 likelihood was computed
         as if date of death was unknown. Death was treated as any other               as if date of death was unknown. Death was treated as any other
         health state: the date of the interview describes the actual state               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               and not the date of a change in health state. The former idea was
         to consider that at each interview the state was recorded               to consider that at each interview the state was recorded
         (healthy, disable or death) and IMaCh was corrected; but when we               (healthy, disable or death) and IMaCh was corrected; but when we
         introduced the exact date of death then we should have modified               introduced the exact date of death then we should have modified
         the contribution of an exact death to the likelihood. This new               the contribution of an exact death to the likelihood. This new
         contribution is smaller and very dependent of the step unit               contribution is smaller and very dependent of the step unit
         stepm. It is no more the probability to die between last interview               stepm. It is no more the probability to die between last interview
         and month of death but the probability to survive from last               and month of death but the probability to survive from last
         interview up to one month before death multiplied by the               interview up to one month before death multiplied by the
         probability to die within a month. Thanks to Chris               probability to die within a month. Thanks to Chris
         Jackson for correcting this bug.  Former versions increased               Jackson for correcting this bug.  Former versions increased
         mortality artificially. The bad side is that we add another loop               mortality artificially. The bad side is that we add another loop
         which slows down the processing. The difference can be up to 10%               which slows down the processing. The difference can be up to 10%
         lower mortality.               lower mortality.
             */
             /* If, at the beginning of the maximization mostly, the
                cumulative probability or probability to be dead is
                constant (ie = 1) over time d, the difference is equal to
                0.  out[s1][3] = savm[s1][3]: probability, being at state
                s1 at precedent wave, to be dead a month before current
                wave is equal to probability, being at state s1 at
                precedent wave, to be dead at mont of the current
                wave. Then the observed probability (that this person died)
                is null according to current estimated parameter. In fact,
                it should be very low but not zero otherwise the log go to
                infinity.
           */            */
   /* #ifdef INFINITYORIGINAL */
   /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /* #else */
   /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
   /*          lli=log(mytinydouble); */
   /*        else */
   /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /* #endif */
           lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
             
           } else if  ( s2==-1 ) { /* alive */
         } else if  (s2==-2) {  
           for (j=1,survp=0. ; j<=nlstate; j++)             for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           /*survp += out[s1][j]; */            /*survp += out[s1][j]; */
           lli= log(survp);            lli= log(survp);
         }          }
                   else if  (s2==-4) { 
         else if  (s2==-4) {   
           for (j=3,survp=0. ; j<=nlstate; j++)              for (j=3,survp=0. ; j<=nlstate; j++)  
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);             lli= log(survp); 
         }           } 
           else if  (s2==-5) { 
         else if  (s2==-5) {             for (j=1,survp=0. ; j<=2; j++)  
           for (j=1,survp=0. ; j<=2; j++)    
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);             lli= log(survp); 
         }           } 
           
         else{          else{
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */            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 */            /*  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 */
Line 1886  double func( double *x) Line 3085  double func( double *x)
         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         /*if(lli ==000.0)*/          /*if(lli ==000.0)*/
         /*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); */          /*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); */
         ipmx +=1;          ipmx +=1;
         sw += weight[i];          sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /* if (lli < log(mytinydouble)){ */
           /*   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(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]); */
           /* } */
       } /* end of wave */        } /* end of wave */
     } /* end of individual */      } /* end of individual */
   }  else if(mle==2){    }  else if(mle==2){
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
Line 1902  double func( double *x) Line 3105  double func( double *x)
           }            }
         for(d=0; d<=dh[mi][i]; d++){          for(d=0; d<=dh[mi][i]; d++){
           newm=savm;            newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           }            }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 1923  double func( double *x) Line 3129  double func( double *x)
     } /* end of individual */      } /* end of individual */
   }  else if(mle==3){  /* exponential inter-extrapolation */    }  else if(mle==3){  /* exponential inter-extrapolation */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
Line 1932  double func( double *x) Line 3138  double func( double *x)
           }            }
         for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
           newm=savm;            newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           }            }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 1953  double func( double *x) Line 3162  double func( double *x)
     } /* end of individual */      } /* end of individual */
   }else if (mle==4){  /* ml=4 no inter-extrapolation */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
Line 1962  double func( double *x) Line 3171  double func( double *x)
           }            }
         for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
           newm=savm;            newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           }            }
                   
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 1977  double func( double *x) Line 3189  double func( double *x)
         s2=s[mw[mi+1][i]][i];          s2=s[mw[mi+1][i]][i];
         if( s2 > nlstate){           if( s2 > nlstate){ 
           lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
           } else if  ( s2==-1 ) { /* alive */
             for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += out[s1][j];
             lli= log(survp);
         }else{          }else{
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          }
Line 1988  double func( double *x) Line 3204  double func( double *x)
     } /* end of individual */      } /* end of individual */
   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
Line 1997  double func( double *x) Line 3213  double func( double *x)
           }            }
         for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
           newm=savm;            newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           }            }
                   
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 2029  double funcone( double *x) Line 3248  double funcone( double *x)
 {  {
   /* Same as likeli but slower because of a lot of printf and if */    /* Same as likeli but slower because of a lot of printf and if */
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
           int ioffset=0;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
   double llt;    double llt;
   int s1, s2;    int s1, s2;
           int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
   double bbh, survp;    double bbh, survp;
     double agexact;
     double agebegin, ageend;
   /*extern weight */    /*extern weight */
   /* We are differentiating ll according to initial status */    /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 2044  double funcone( double *x) Line 3267  double funcone( double *x)
   cov[1]=1.;    cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     ioffset=0;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      ioffset=2+nagesqr+cptcovage;
     for(mi=1; mi<= wav[i]-1; mi++){      /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
       for (k=1; k<=ncoveff+nqfveff;k++){ /* Simple and product fixed covariates without age* products */
         cov[++ioffset]=covar[Tvar[k]][i];
       }
       for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitative fixed covariates */
         cov[++ioffset]=coqvar[Tvar[iqv]][i];
       }
       
       for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
         for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
           cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
         }
         for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
           cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
         }
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (ii=1;ii<=nlstate+ndeath;ii++)
         for (j=1;j<=nlstate+ndeath;j++){          for (j=1;j<=nlstate+ndeath;j++){
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           savm[ii][j]=(ii==j ? 1.0 : 0.0);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }          }
       for(d=0; d<dh[mi][i]; d++){        
         agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
         ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
         for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
           /*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.*/
         newm=savm;          newm=savm;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;
           if(nagesqr==1)
             cov[3]= agexact*agexact;
         for (kk=1; kk<=cptcovage;kk++) {          for (kk=1; kk<=cptcovage;kk++) {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
         }          }
           /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 2070  double funcone( double *x) Line 3316  double funcone( double *x)
               
       s1=s[mw[mi][i]][i];        s1=s[mw[mi][i]][i];
       s2=s[mw[mi+1][i]][i];        s2=s[mw[mi+1][i]][i];
         /* if(s2==-1){ */
         /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
         /*        /\* exit(1); *\/ */
         /* } */
       bbh=(double)bh[mi][i]/(double)stepm;         bbh=(double)bh[mi][i]/(double)stepm; 
       /* bias is positive if real duration        /* bias is positive if real duration
        * is higher than the multiple of stepm and negative otherwise.         * is higher than the multiple of stepm and negative otherwise.
        */         */
       if( s2 > nlstate && (mle <5) ){  /* Jackson */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         lli=log(out[s1][s2] - savm[s1][s2]);          lli=log(out[s1][s2] - savm[s1][s2]);
       } else if  (s2==-2) {        } else if  ( s2==-1 ) { /* alive */
         for (j=1,survp=0. ; j<=nlstate; j++)           for (j=1,survp=0. ; j<=nlstate; j++) 
           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         lli= log(survp);          lli= log(survp);
Line 2097  double funcone( double *x) Line 3347  double funcone( double *x)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        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]); */        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       if(globpr){        if(globpr){
         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\          fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
  %11.6f %11.6f %11.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],                  num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
                 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         for(k=1,llt=0.,l=0.; k<=nlstate; k++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           llt +=ll[k]*gipmx/gsw;            llt +=ll[k]*gipmx/gsw;
Line 2131  void likelione(FILE *ficres,double p[], Line 3381  void likelione(FILE *ficres,double p[],
   int k;    int k;
   
   if(*globpri !=0){ /* Just counts and sums, no printings */    if(*globpri !=0){ /* Just counts and sums, no printings */
     strcpy(fileresilk,"ilk");       strcpy(fileresilk,"ILK_"); 
     strcat(fileresilk,fileres);      strcat(fileresilk,fileresu);
     if((ficresilk=fopen(fileresilk,"w"))==NULL) {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresilk);        printf("Problem with resultfile: %s\n", fileresilk);
       fprintf(ficlog,"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, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -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 ");      fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%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]); */      /*  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++)       for(k=1; k<=nlstate; k++) 
       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
Line 2148  void likelione(FILE *ficres,double p[], Line 3398  void likelione(FILE *ficres,double p[],
   *fretone=(*funcone)(p);    *fretone=(*funcone)(p);
   if(*globpri !=0){    if(*globpri !=0){
     fclose(ficresilk);      fclose(ficresilk);
     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));      if (mle ==0)
     fflush(fichtm);         fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
   }       else if(mle >=1)
         fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
       fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       
         
       for (k=1; k<= nlstate ; k++) {
         fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
   <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
       }
       fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
   <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
   <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       fflush(fichtm);
     }
   return;    return;
 }  }
   
Line 2181  void mlikeli(FILE *ficres,double p[], in Line 3445  void mlikeli(FILE *ficres,double p[], in
     for (j=1;j<=npar;j++)      for (j=1;j<=npar;j++)
       xi[i][j]=(i==j ? 1.0 : 0.0);        xi[i][j]=(i==j ? 1.0 : 0.0);
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcpy(filerespow,"pow");     strcpy(filerespow,"POW_"); 
   strcat(filerespow,fileres);    strcat(filerespow,fileres);
   if((ficrespow=fopen(filerespow,"w"))==NULL) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", filerespow);      printf("Problem with resultfile: %s\n", filerespow);
Line 2226  void mlikeli(FILE *ficres,double p[], in Line 3490  void mlikeli(FILE *ficres,double p[], in
   fclose(ficrespow);    fclose(ficrespow);
   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
 }  }
   
 /**** Computes Hessian and covariance matrix ***/  /**** Computes Hessian and covariance matrix ***/
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 {  {
   double  **a,**y,*x,pd;    double  **a,**y,*x,pd;
   double **hess;    /* double **hess; */
   int i, j;    int i, j;
   int *indx;    int *indx;
   
   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);    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);    double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
   void lubksb(double **a, int npar, int *indx, double b[]) ;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double gompertz(double p[]);    double gompertz(double p[]);
   hess=matrix(1,npar,1,npar);    /* hess=matrix(1,npar,1,npar); */
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for (i=1;i<=npar;i++){    for (i=1;i<=npar;i++){
     printf("%d",i);fflush(stdout);      printf("%d-",i);fflush(stdout);
     fprintf(ficlog,"%d",i);fflush(ficlog);      fprintf(ficlog,"%d-",i);fflush(ficlog);
         
      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
           
Line 2260  void hesscov(double **matcov, double p[] Line 3524  void hesscov(double **matcov, double p[]
   for (i=1;i<=npar;i++) {    for (i=1;i<=npar;i++) {
     for (j=1;j<=npar;j++)  {      for (j=1;j<=npar;j++)  {
       if (j>i) {         if (j>i) { 
         printf(".%d%d",i,j);fflush(stdout);          printf(".%d-%d",i,j);fflush(stdout);
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);          fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
         hess[i][j]=hessij(p,delti,i,j,func,npar);          hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
                   
         hess[j][i]=hess[i][j];              hess[j][i]=hess[i][j];    
         /*printf(" %lf ",hess[i][j]);*/          /*printf(" %lf ",hess[i][j]);*/
Line 2296  void hesscov(double **matcov, double p[] Line 3560  void hesscov(double **matcov, double p[]
   fprintf(ficlog,"\n#Hessian matrix#\n");    fprintf(ficlog,"\n#Hessian matrix#\n");
   for (i=1;i<=npar;i++) {     for (i=1;i<=npar;i++) { 
     for (j=1;j<=npar;j++) {       for (j=1;j<=npar;j++) { 
       printf("%.3e ",hess[i][j]);        printf("%.6e ",hess[i][j]);
       fprintf(ficlog,"%.3e ",hess[i][j]);        fprintf(ficlog,"%.6e ",hess[i][j]);
     }      }
     printf("\n");      printf("\n");
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
   }    }
   
     /* printf("\n#Covariance matrix#\n"); */
     /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
     /* for (i=1;i<=npar;i++) {  */
     /*   for (j=1;j<=npar;j++) {  */
     /*     printf("%.6e ",matcov[i][j]); */
     /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
     /*   } */
     /*   printf("\n"); */
     /*   fprintf(ficlog,"\n"); */
     /* } */
   
   /* Recompute Inverse */    /* Recompute Inverse */
   for (i=1;i<=npar;i++)    /* for (i=1;i<=npar;i++) */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
   ludcmp(a,npar,indx,&pd);    /* 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"); */
     /* } */
   
     /* Verifying the inverse matrix */
   #ifdef DEBUGHESS
     y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
   
   /*  printf("\n#Hessian matrix recomputed#\n");     printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
      fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
   
   for (j=1;j<=npar;j++) {    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++){       for (i=1;i<=npar;i++){ 
       y[i][j]=x[i];        printf("%.2f ",y[i][j]);
       printf("%.3e ",y[i][j]);        fprintf(ficlog,"%.2f ",y[i][j]);
       fprintf(ficlog,"%.3e ",y[i][j]);  
     }      }
     printf("\n");      printf("\n");
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
   }    }
   */  #endif
   
   free_matrix(a,1,npar,1,npar);    free_matrix(a,1,npar,1,npar);
   free_matrix(y,1,npar,1,npar);    free_matrix(y,1,npar,1,npar);
   free_vector(x,1,npar);    free_vector(x,1,npar);
   free_ivector(indx,1,npar);    free_ivector(indx,1,npar);
   free_matrix(hess,1,npar,1,npar);    /* free_matrix(hess,1,npar,1,npar); */
   
   
 }  }
   
 /*************** hessian matrix ****************/  /*************** hessian matrix ****************/
 double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 {  { /* Around values of x, computes the function func and returns the scales delti and hessian */
   int i;    int i;
   int l=1, lmax=20;    int l=1, lmax=20;
   double k1,k2;    double k1,k2, res, fx;
   double p2[MAXPARM+1]; /* identical to x */    double p2[MAXPARM+1]; /* identical to x */
   double res;  
   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double fx;  
   int k=0,kmax=10;    int k=0,kmax=10;
   double l1;    double l1;
   
Line 2358  double hessii(double x[], double delta, Line 3647  double hessii(double x[], double delta,
       p2[theta]=x[theta]-delt;        p2[theta]=x[theta]-delt;
       k2=func(p2)-fx;        k2=func(p2)-fx;
       /*res= (k1-2.0*fx+k2)/delt/delt; */        /*res= (k1-2.0*fx+k2)/delt/delt; */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
               
 #ifdef DEBUGHESS  #ifdef DEBUGHESSII
       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);        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);        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  #endif
Line 2374  double hessii(double x[], double delta, Line 3663  double hessii(double x[], double delta,
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         delts=delt;          delts=delt;
       }        }
     }      } /* End loop k */
   }    }
   delti[theta]=delts;    delti[theta]=delts;
   return res;     return res; 
       
 }  }
   
 double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)  double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {  {
   int i;    int i;
   int l=1, lmax=20;    int l=1, lmax=20;
   double k1,k2,k3,k4,res,fx;    double k1,k2,k3,k4,res,fx;
   double p2[MAXPARM+1];    double p2[MAXPARM+1];
   int k;    int k, kmax=1;
     double v1, v2, cv12, lc1, lc2;
   
     int firstime=0;
     
   fx=func(x);    fx=func(x);
   for (k=1; k<=2; k++) {    for (k=1; k<=kmax; k=k+10) {
     for (i=1;i<=npar;i++) p2[i]=x[i];      for (i=1;i<=npar;i++) p2[i]=x[i];
     p2[thetai]=x[thetai]+delti[thetai]/k;      p2[thetai]=x[thetai]+delti[thetai]*k;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      p2[thetaj]=x[thetaj]+delti[thetaj]*k;
     k1=func(p2)-fx;      k1=func(p2)-fx;
       
     p2[thetai]=x[thetai]+delti[thetai]/k;      p2[thetai]=x[thetai]+delti[thetai]*k;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      p2[thetaj]=x[thetaj]-delti[thetaj]*k;
     k2=func(p2)-fx;      k2=func(p2)-fx;
       
     p2[thetai]=x[thetai]-delti[thetai]/k;      p2[thetai]=x[thetai]-delti[thetai]*k;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      p2[thetaj]=x[thetaj]+delti[thetaj]*k;
     k3=func(p2)-fx;      k3=func(p2)-fx;
       
     p2[thetai]=x[thetai]-delti[thetai]/k;      p2[thetai]=x[thetai]-delti[thetai]*k;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      p2[thetaj]=x[thetaj]-delti[thetaj]*k;
     k4=func(p2)-fx;      k4=func(p2)-fx;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
 #ifdef DEBUG      if(k1*k2*k3*k4 <0.){
     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);        firstime=1;
     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);        kmax=kmax+10;
       }
       if(kmax >=10 || firstime ==1){
         printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
         fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
         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);
       }
   #ifdef DEBUGHESSIJ
       v1=hess[thetai][thetai];
       v2=hess[thetaj][thetaj];
       cv12=res;
       /* Computing eigen value of Hessian matrix */
       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) ){
         printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
         fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
         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  #endif
   }    }
   return res;    return res;
 }  }
   
       /* Not done yet: Was supposed to fix if not exactly at the maximum */
   /* 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]; */
   /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
   /*   int k=0,kmax=10; */
   /*   double l1; */
     
   /*   fx=func(x); */
   /*   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 = delti*(l1*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 DEBUGHESSIJ */
   /*       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 */
   /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
   /*      k=kmax; */
   /*       } */
   /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >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; */
   /*       } */
   /*     } /\* End loop k *\/ */
   /*   } */
   /*   delti[theta]=delts; */
   /*   return res;  */
   /* } */
   
   
 /************** Inverse of matrix **************/  /************** Inverse of matrix **************/
 void ludcmp(double **a, int n, int *indx, double *d)   void ludcmp(double **a, int n, int *indx, double *d) 
 {   { 
Line 2492  void lubksb(double **a, int n, int *indx Line 3858  void lubksb(double **a, int n, int *indx
   
 void pstamp(FILE *fichier)  void pstamp(FILE *fichier)
 {  {
   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }  }
   
 /************ Frequencies ********************/  /************ 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[])  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
                     int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                     int firstpass,  int lastpass, int stepm, int weightopt, char model[])
 {  /* Some frequencies */  {  /* Some frequencies */
       
   int i, m, jk, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j;
     int iind=0, iage=0;
     int mi; /* Effective wave */
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp, **prop;    double *meanq;
   double pos,posprop, k2, dateintsum=0,k2cpt=0;    double **meanqt;
   char fileresp[FILENAMELENGTH];    double *pp, **prop, *posprop, *pospropt;
       double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
     double agebegin, ageend;
       
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   prop=matrix(1,nlstate,iagemin,iagemax+3);    prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
   strcpy(fileresp,"p");    posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
   strcat(fileresp,fileres);    pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
     /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
     meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
     meanqt=matrix(1,lastpass,1,nqtveff);
     strcpy(fileresp,"P_");
     strcat(fileresp,fileresu);
     /*strcat(fileresphtm,fileresu);*/
   if((ficresp=fopen(fileresp,"w"))==NULL) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
     printf("Problem with prevalence resultfile: %s\n", fileresp);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     exit(0);      exit(0);
   }    }
   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);  
     strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
     if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
       printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
       fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
       fflush(ficlog);
       exit(70); 
     }
     else{
       fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %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=1+age+%s<br>\n",\
               fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
     fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
       
     strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
     if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
       printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
       fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
       fflush(ficlog);
       exit(70); 
     }
     else{
       fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %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=1+age+%s<br>\n",\
               fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
     fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
   
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
   j1=0;    j1=0;
       
   j=cptcoveff;    j=ncoveff;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
   first=1;    first=1;
   
   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */    /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */       reference=low_education V1=0,V2=0
   /*    j1++;       med_educ                V1=1 V2=0, 
 */       high_educ               V1=0 V2=1
   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){       Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    */
         scanf("%d", i);*/  
       for (i=-5; i<=nlstate+ndeath; i++)      for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination excluding varying and quantitatives */
         for (jk=-5; jk<=nlstate+ndeath; jk++)        posproptt=0.;
           for(m=iagemin; m <= iagemax+3; m++)      /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
             freq[i][jk][m]=0;        scanf("%d", i);*/
             for (i=-5; i<=nlstate+ndeath; i++)  
       for (i=1; i<=nlstate; i++)          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         for(m=iagemin; m <= iagemax+3; m++)          for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;            freq[i][jk][m]=0;
               
       dateintsum=0;      for (i=1; i<=nlstate; i++)  {
       k2cpt=0;        for(m=iagemin; m <= iagemax+3; m++)
       for (i=1; i<=imx; i++) {          prop[i][m]=0;
         bool=1;        posprop[i]=0;
         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */        pospropt[i]=0;
           for (z1=1; z1<=cptcoveff; z1++)             }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){      for (z1=1; z1<= nqfveff; z1++) {  
                 /* Tests if the value of each of the covariates of i is equal to filter j1 */        meanq[z1]+=0.;
               bool=0;        for(m=1;m<=lastpass;m++){
               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",           meanqt[m][z1]=0.;
                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],        }
                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/      }
               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/        
             }       dateintsum=0;
         }      k2cpt=0;
        /* For that comination of covariate j1, we count and print the frequencies */
         if (bool==1){      for (iind=1; iind<=imx; iind++) { /* For each individual iind */
           for(m=firstpass; m<=lastpass; m++){        bool=1;
             k2=anint[m][i]+(mint[m][i]/12.);        if (nqfveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
           for (z1=1; z1<= nqfveff; z1++) {  
             meanq[z1]+=coqvar[Tvar[z1]][iind];
           }
           for (z1=1; z1<=ncoveff; z1++) {  
             /* if(Tvaraff[z1] ==-20){ */
             /*     /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
             /* }else  if(Tvaraff[z1] ==-10){ */
             /*     /\* sumnew+=coqvar[z1][iind]; *\/ */
             /* }else  */
             if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
               /* Tests if this individual i responded to j1 (V4=1 V3=0) */
               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*/
             } 
           } /* end z1 */
         } /* cptcovn > 0 */
   
         if (bool==1){ /* We selected an individual iin satisfying combination j1 */
           /* for(m=firstpass; m<=lastpass; m++){ */
           for(mi=1; mi<wav[iind];mi++){
             m=mw[mi][iind];
             /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
                and mw[mi+1][iind]. dh depends on stepm. */
             agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
             ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
             if(m >=firstpass && m <=lastpass){
               k2=anint[m][iind]+(mint[m][iind]/12.);
             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
               if(agev[m][i]==0) agev[m][i]=iagemax+1;              if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
               if(agev[m][i]==1) agev[m][i]=iagemax+2;              if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];              if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
               if (m<lastpass) {                prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              if (m<lastpass) {
                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];                /* if(s[m][iind]==4 && s[m+1][iind]==4) */
               }                /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
                               if(s[m][iind]==-1)
               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {                  printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
                 dateintsum=dateintsum+k2;                freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                 k2cpt++;                /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
               }                freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
               /*}*/              }
             }  
             if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
               dateintsum=dateintsum+k2;
               k2cpt++;
               /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
           }            }
         }            /*}*/
       } /* end i */          } /* end m */
                } /* end bool */
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/      } /* end iind = 1 to imx */
       pstamp(ficresp);      /* prop[s][age] is feeded for any initial and valid live state as well as
       if  (cptcovn>0) {         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
         fprintf(ficresp, "\n#********** Variable ");   
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresp, "**********\n#");      /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         fprintf(ficlog, "\n#********** Variable ");       pstamp(ficresp);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      if  (ncoveff>0) {
         fprintf(ficlog, "**********\n#");        fprintf(ficresp, "\n#********** Variable "); 
       }        fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
       for(i=1; i<=nlstate;i++)         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        for (z1=1; z1<=ncoveff; z1++){
       fprintf(ficresp, "\n");          fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                 fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
       for(i=iagemin; i <= iagemax+3; i++){          fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         if(i==iagemax+3){        }
           fprintf(ficlog,"Total");        fprintf(ficresp, "**********\n#");
         }else{        fprintf(ficresphtm, "**********</h3>\n");
         fprintf(ficresphtmfr, "**********</h3>\n");
         fprintf(ficlog, "\n#********** Variable "); 
         for (z1=1; z1<=ncoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficlog, "**********\n");
       }
       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
       for(i=1; i<=nlstate;i++) {
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
       }
       fprintf(ficresp, "\n");
       fprintf(ficresphtm, "\n");
         
       /* Header of frequency table by age */
       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
       fprintf(ficresphtmfr,"<th>Age</th> ");
       for(jk=-1; jk <=nlstate+ndeath; jk++){
         for(m=-1; m <=nlstate+ndeath; m++){
           if(jk!=0 && m!=0)
             fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
         }
       }
       fprintf(ficresphtmfr, "\n");
         
       /* For each age */
       for(iage=iagemin; iage <= iagemax+3; iage++){
         fprintf(ficresphtm,"<tr>");
         if(iage==iagemax+1){
           fprintf(ficlog,"1");
           fprintf(ficresphtmfr,"<tr><th>0</th> ");
         }else if(iage==iagemax+2){
           fprintf(ficlog,"0");
           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
         }else if(iage==iagemax+3){
           fprintf(ficlog,"Total");
           fprintf(ficresphtmfr,"<tr><th>Total</th> ");
         }else{
           if(first==1){
             first=0;
             printf("See log file for details...\n");
           }
           fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
           fprintf(ficlog,"Age %d", iage);
         }
         for(jk=1; jk <=nlstate ; jk++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
             pp[jk] += freq[jk][m][iage]; 
         }
         for(jk=1; jk <=nlstate ; jk++){
           for(m=-1, pos=0; m <=0 ; m++)
             pos += freq[jk][m][iage];
           if(pp[jk]>=1.e-10){
           if(first==1){            if(first==1){
             first=0;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             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);  
           }            }
             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(jk=1; jk <=nlstate ; jk++){ 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          /* posprop[jk]=0; */
             pp[jk] += freq[jk][m][i];          for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
         }                   pp[jk] += freq[jk][m][iage];
         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){        } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
           pos += pp[jk];  
           posprop += prop[jk][i];        for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
           pos += pp[jk]; /* pos is the total number of transitions until this age */
           posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
                                             from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
           pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
                                           from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
         }
         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);
         }          }
         for(jk=1; jk <=nlstate ; jk++){          if( iage <= iagemax){
           if(pos>=1.e-5){            if(pos>=1.e-5){
             if(first==1)              fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              /*probs[iage][jk][j1]= pp[jk]/pos;*/
           }else{              /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
             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){            else{
             if(pos>=1.e-5){              fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);              fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
               /*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);  
           }            }
         }          }
                   pospropt[jk] +=posprop[jk];
         for(jk=-1; jk <=nlstate+ndeath; jk++)        } /* end loop jk */
           for(m=-1; m <=nlstate+ndeath; m++)        /* pospropt=0.; */
             if(freq[jk][m][i] !=0 ) {        for(jk=-1; jk <=nlstate+ndeath; jk++){
             if(first==1)          for(m=-1; m <=nlstate+ndeath; m++){
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            if(freq[jk][m][iage] !=0 ) { /* minimizing output */
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);              if(first==1){
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
             }              }
         if(i <= iagemax)              fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
           fprintf(ficresp,"\n");            }
         if(first==1)            if(jk!=0 && m!=0)
           printf("Others in log...\n");              fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
         fprintf(ficlog,"\n");          }
         } /* end loop jk */
         posproptt=0.; 
         for(jk=1; jk <=nlstate; jk++){
           posproptt += pospropt[jk];
         }
         fprintf(ficresphtmfr,"</tr>\n ");
         if(iage <= iagemax){
           fprintf(ficresp,"\n");
           fprintf(ficresphtm,"</tr>\n");
       }        }
       /*}*/        if(first==1)
   }          printf("Others in log...\n");
         fprintf(ficlog,"\n");
       } /* end loop age iage */
       fprintf(ficresphtm,"<tr><th>Tot</th>");
       for(jk=1; jk <=nlstate ; jk++){
         if(posproptt < 1.e-5){
           fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);   
         }else{
           fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);    
         }
       }
       fprintf(ficresphtm,"</tr>\n");
       fprintf(ficresphtm,"</table>\n");
       fprintf(ficresphtmfr,"</table>\n");
       if(posproptt < 1.e-5){
         fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
         fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
         fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
         invalidvarcomb[j1]=1;
       }else{
         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
         invalidvarcomb[j1]=0;
       }
       fprintf(ficresphtmfr,"</table>\n");
     } /* end selected combination of covariate j1 */
   dateintmean=dateintsum/k2cpt;     dateintmean=dateintsum/k2cpt; 
                     
   fclose(ficresp);    fclose(ficresp);
   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);    fclose(ficresphtm);
     fclose(ficresphtmfr);
     free_vector(meanq,1,nqfveff);
     free_matrix(meanqt,1,lastpass,1,nqtveff);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
     free_vector(pospropt,1,nlstate);
     free_vector(posprop,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
   free_matrix(prop,1,nlstate,iagemin, iagemax+3);    /* End of freqsummary */
   /* End of Freq */  
 }  }
   
 /************ Prevalence ********************/  /************ 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)   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     /* 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).        in each health status at the date of interview (if between dateprev1 and dateprev2).
      We still use firstpass and lastpass as another selection.        We still use firstpass and lastpass as another selection.
   */     */
     
   int i, m, jk, j1, bool, z1,j;     int i, m, jk, j1, bool, z1,j;
      int mi; /* Effective wave */
   double **prop;     int iage;
   double posprop;      double agebegin, ageend;
   double  y2; /* in fractional years */  
   int iagemin, iagemax;     double **prop;
   int first; /** to stop verbosity which is redirected to log file */     double posprop; 
      double  y2; /* in fractional years */
   iagemin= (int) agemin;     int iagemin, iagemax;
   iagemax= (int) agemax;     int first; /** to stop verbosity which is redirected to log file */
   /*pp=vector(1,nlstate);*/  
   prop=matrix(1,nlstate,iagemin,iagemax+3);      iagemin= (int) agemin;
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/     iagemax= (int) agemax;
   j1=0;     /*pp=vector(1,nlstate);*/
        prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
   /*j=cptcoveff;*/     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}     j1=0;
       
   first=1;     /*j=cptcoveff;*/
   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     /*for(i1=1; i1<=ncodemax[k1];i1++){    
       j1++;*/     first=1;
      for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
        for (i=1; i<=nlstate; i++)  
          for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
            prop[i][iage]=0.0;
       
        for (i=1; i<=imx; i++) { /* Each individual */
          bool=1;
          if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
            for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
                bool=0;
          } 
          if (bool==1) { /* For this combination of covariates values, this individual fits */
            /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
            for(mi=1; mi<wav[i];mi++){
              m=mw[mi][i];
              agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
              /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
              if(m >=firstpass && m <=lastpass){
                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-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
                    printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m); 
                    exit(1);
                  }
                  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];/* At age of beginning of transition, where status is known */
                    prop[s[m][i]][iagemax+3] += weight[i]; 
                  } /* end valid statuses */ 
                } /* end selection of dates */
              } /* end selection of waves */
            } /* end effective waves */
          } /* end bool */
        }
        for(i=iagemin; i <= iagemax+3; i++){  
          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
            posprop += prop[jk][i]; 
          } 
               
       for (i=1; i<=nlstate; i++)           for(jk=1; jk <=nlstate ; jk++){      
         for(m=iagemin; m <= iagemax+3; m++)           if( i <=  iagemax){ 
           prop[i][m]=0.0;             if(posprop>=1.e-5){ 
                     probs[i][jk][j1]= prop[jk][i]/posprop;
       for (i=1; i<=imx; i++) { /* Each individual */             } else{
         bool=1;               if(first==1){
         if  (cptcovn>0) {                 first=0;
           for (z1=1; z1<=cptcoveff; z1++)                  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]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])                }
               bool=0;             }
         }            } 
         if (bool==1) {          }/* end jk */ 
           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/       }/* end i */ 
             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */       /*} *//* end i1 */
             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */     } /* end j1 */
               if(agev[m][i]==0) agev[m][i]=iagemax+1;    
               if(agev[m][i]==1) agev[m][i]=iagemax+2;     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
               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);      /*free_vector(pp,1,nlstate);*/
               if (s[m][i]>0 && s[m][i]<=nlstate) {      free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
                 /*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]]);*/   }  /* End of prevalence */
                 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 ***************/  /************* Waves Concatenation ***************/
   
Line 2767  void  concatwav(int wav[], int **dh, int Line 4306  void  concatwav(int wav[], int **dh, int
      and mw[mi+1][i]. dh depends on stepm.       and mw[mi+1][i]. dh depends on stepm.
      */       */
   
   int i, mi, m;    int i=0, mi=0, m=0, mli=0;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      double sum=0., jmean=0.;*/       double sum=0., jmean=0.;*/
   int first;    int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
   int j, k=0,jk, ju, jl;    int j, k=0,jk, ju, jl;
   double sum=0.;    double sum=0.;
   first=0;    first=0;
     firstwo=0;
     firsthree=0;
     firstfour=0;
   jmin=100000;    jmin=100000;
   jmax=-1;    jmax=-1;
   jmean=0.;    jmean=0.;
   for(i=1; i<=imx; i++){  
     mi=0;  /* Treating live states */
     for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
       mi=0;  /* First valid wave */
                   mli=0; /* Last valid wave */
     m=firstpass;      m=firstpass;
     while(s[m][i] <= nlstate){      while(s[m][i] <= nlstate){  /* a live state */
       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)                          if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
         mw[++mi][i]=m;                                  mli=m-1;/* mw[++mi][i]=m-1; */
       if(m >=lastpass)                          }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
         break;                                  mw[++mi][i]=m;
       else                                  mli=m;
         m++;        } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
         if(m < lastpass){ /* m < lastpass, standard case */
                                   m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
         }
                           else{ /* m >= lastpass, eventual special issue with warning */
   #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
                                   break;
   #else
                                   if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
                                           if(firsthree == 0){
                                                   printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
                                                   firsthree=1;
                                           }
                                           fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
                                           mw[++mi][i]=m;
                                           mli=m;
                                   }
                                   if(s[m][i]==-2){ /* Vital status is really unknown */
                                           nbwarn++;
                                           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
                                                   printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
                                                   fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
                                           }
                                           break;
                                   }
                                   break;
   #endif
                           }/* End m >= lastpass */
     }/* end while */      }/* end while */
     if (s[m][i] > nlstate){  
           /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
       /* After last pass */
   /* Treating death states */
       if (s[m][i] > nlstate){  /* In a death state */
                           /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
                           /* } */
       mi++;     /* Death is another wave */        mi++;     /* Death is another wave */
       /* if(mi==0)  never been interviewed correctly before death */        /* if(mi==0)  never been interviewed correctly before death */
          /* Only death is a correct wave */                          /* Only death is a correct wave */
       mw[mi][i]=m;        mw[mi][i]=m;
     }      }
   #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
     wav[i]=mi;                  else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
         /* m++; */
         /* mi++; */
         /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
         /* mw[mi][i]=m; */
         if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
                                   if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
                                           nbwarn++;
                                           if(firstfiv==0){
                                                   printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
                                                   firstfiv=1;
                                           }else{
                                                   fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
                                           }
                                   }else{ /* Death occured afer last wave potential bias */
                                           nberr++;
                                           if(firstwo==0){
                                                   printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
                                                   firstwo=1;
                                           }
                                           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
                                   }
         }else{ /* end date of interview is known */
                                   /* death is known but not confirmed by death status at any wave */
                                   if(firstfour==0){
                                           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
                                           firstfour=1;
                                   }
                                   fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
         }
       } /* end if date of death is known */
   #endif
       wav[i]=mi; /* mi should be the last effective wave (or mli) */
       /* wav[i]=mw[mi][i]; */
     if(mi==0){      if(mi==0){
       nbwarn++;        nbwarn++;
       if(first==0){        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);                                  printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         first=1;                                  first=1;
       }        }
       if(first==1){        if(first==1){
         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);                                  fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       }        }
     } /* end mi==0 */      } /* end mi==0 */
   } /* End individuals */    } /* End individuals */
     /* wav and mw are no more changed */
           
     
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     for(mi=1; mi<wav[i];mi++){      for(mi=1; mi<wav[i];mi++){
       if (stepm <=0)        if (stepm <=0)
         dh[mi][i]=1;                                  dh[mi][i]=1;
       else{        else{
         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */                                  if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           if (agedc[i] < 2*AGESUP) {                                          if (agedc[i] < 2*AGESUP) {
             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                                                   j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(j==0) j=1;  /* Survives at least one month after exam */                                                  if(j==0) j=1;  /* Survives at least one month after exam */
             else if(j<0){                                                  else if(j<0){
               nberr++;                                                          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]);                                                          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 */                                                          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);                                                          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,"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);                                                          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;                                                  k=k+1;
             if (j >= jmax){                                                  if (j >= jmax){
               jmax=j;                                                          jmax=j;
               ijmax=i;                                                          ijmax=i;
             }                                                  }
             if (j <= jmin){                                                  if (j <= jmin){
               jmin=j;                                                          jmin=j;
               ijmin=i;                                                          ijmin=i;
             }                                                  }
             sum=sum+j;                                                  sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i);*/                                                  /*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);*/                                                  /*        printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           }                                          }
         }                                  }
         else{                                  else{
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                                          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]); */  /*        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;                                          k=k+1;
           if (j >= jmax) {                                          if (j >= jmax) {
             jmax=j;                                                  jmax=j;
             ijmax=i;                                                  ijmax=i;
           }                                          }
           else if (j <= jmin){                                          else if (j <= jmin){
             jmin=j;                                                  jmin=j;
             ijmin=i;                                                  ijmin=i;
           }                                          }
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,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]);*/                                          /*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){                                          if(j<0){
             nberr++;                                                  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]);                                                  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]);                                                  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;                                          sum=sum+j;
         }                                  }
         jk= j/stepm;                                  jk= j/stepm;
         jl= j -jk*stepm;                                  jl= j -jk*stepm;
         ju= j -(jk+1)*stepm;                                  ju= j -(jk+1)*stepm;
         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */                                  if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           if(jl==0){                                          if(jl==0){
             dh[mi][i]=jk;                                                  dh[mi][i]=jk;
             bh[mi][i]=0;                                                  bh[mi][i]=0;
           }else{ /* We want a negative bias in order to only have interpolation ie                                          }else{ /* We want a negative bias in order to only have interpolation ie
                   * to avoid the price of an extra matrix product in likelihood */                                                                          * to avoid the price of an extra matrix product in likelihood */
             dh[mi][i]=jk+1;                                                  dh[mi][i]=jk+1;
             bh[mi][i]=ju;                                                  bh[mi][i]=ju;
           }                                          }
         }else{                                  }else{
           if(jl <= -ju){                                          if(jl <= -ju){
             dh[mi][i]=jk;                                                  dh[mi][i]=jk;
             bh[mi][i]=jl;       /* bias is positive if real duration                                                  bh[mi][i]=jl;   /* bias is positive if real duration
                                  * is higher than the multiple of stepm and negative otherwise.                                                                                                           * is higher than the multiple of stepm and negative otherwise.
                                  */                                                                                                           */
           }                                          }
           else{                                          else{
             dh[mi][i]=jk+1;                                                  dh[mi][i]=jk+1;
             bh[mi][i]=ju;                                                  bh[mi][i]=ju;
           }                                          }
           if(dh[mi][i]==0){                                          if(dh[mi][i]==0){
             dh[mi][i]=1; /* At least one step */                                                  dh[mi][i]=1; /* At least one step */
             bh[mi][i]=ju; /* 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);*/                                                  /*  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 if mle */
       }        }
     } /* end wave */      } /* end wave */
   }    }
Line 2899  void  concatwav(int wav[], int **dh, int Line 4512  void  concatwav(int wav[], int **dh, int
  }   }
   
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)   void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
 {  {
   /**< Uses cptcovn+2*cptcovprod as the number of covariates */    /**< 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     /*      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]     * Boring subroutine which should only output nbcode[Tvar[j]][k]
    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)     * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
   /* nbcode[Tvar[j]][1]=      * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
   */    */
   
   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
Line 2914  void tricode(int *Tvar, int **nbcode, in Line 4527  void tricode(int *Tvar, int **nbcode, in
   int modmincovj=0; /* Modality min of covariates j */    int modmincovj=0; /* Modality min of covariates j */
   
   
   cptcoveff=0;     /* cptcoveff=0;  */
           /* *cptcov=0; */
     
   for (k=-1; k < maxncov; k++) Ndum[k]=0;  
   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
   /* Loop on covariates without age and products */    /* Loop on covariates without age and products and no quantitative variable */
   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */    /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the     for (j=1; j<=cptcovsnq; j++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
                                modality of this covariate Vj*/       for (k=-1; k < maxncov; k++) Ndum[k]=0;
       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i      for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
                                     * If product of Vn*Vm, still boolean *:                                  modality of this covariate Vj*/
                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables        switch(Typevar[j]) {
                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */        case 1: /* A real fixed dummy covariate */
       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the          ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                       modality of the nth covariate of individual i. */                                        * If product of Vn*Vm, still boolean *:
       if (ij > modmaxcovj)                                        * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
         modmaxcovj=ij;                                         * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
       else if (ij < modmincovj)           /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
         modmincovj=ij;              modality of the nth covariate of individual i. */
       if ((ij < -1) && (ij > NCOVMAX)){          if (ij > modmaxcovj)
         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );            modmaxcovj=ij; 
         exit(1);          else if (ij < modmincovj) 
       }else            modmincovj=ij; 
       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/          if ((ij < -1) && (ij > NCOVMAX)){
       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */            printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            exit(1);
       /* getting the maximum value of the modality of the covariate          }else
          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and            Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
          female is 1, then modmaxcovj=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 ies 1, then modmaxcovj=1.*/
           break;
         case 2:
           break;
   
         }
       } /* 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);      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;      cptcode=modmaxcovj;
     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
    /*for (i=0; i<=cptcode; i++) {*/      /*for (i=0; i<=cptcode; i++) {*/
     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */      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 V%d %d\n", j, Tvar[j], Ndum[i]);        printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */        fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */        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        /* 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 */         * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
     } /* Ndum[-1] number of undefined modalities */      } /* Ndum[-1] number of undefined modalities */
       
     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */      /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;         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;         modmincovj=3; modmaxcovj = 7;
        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;         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 3-1 digits are 0=00 1=01, 2=10; defining two dummy          which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
        variables V1_1 and V1_2.         defining two dummy variables: variables V1_1 and V1_2.
        nbcode[Tvar[j]][ij]=k;         nbcode[Tvar[j]][ij]=k;
        nbcode[Tvar[j]][1]=0;         nbcode[Tvar[j]][1]=0;
        nbcode[Tvar[j]][2]=1;         nbcode[Tvar[j]][2]=1;
        nbcode[Tvar[j]][3]=2;         nbcode[Tvar[j]][3]=2;
          To be continued (not working yet).
     */      */
     ij=1; /* ij is similar to i but can jumps over null modalities */      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 */      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*/
       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */        if (Ndum[i] == 0) { /* If nobody responded to this modality k */
         /*recode from 0 */          break;
         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */        }
           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.         ij++;
                                      k is a modality. If we have model=V1+V1*sex         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.*/
                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */        cptcode = ij; /* New max modality for covar j */
           ij++;      } /* end of loop on modality i=-1 to 1 or more */
         }      
         if (ij > ncodemax[j]) break;       /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
       }  /* end of loop on */      /*  /\*recode from 0 *\/ */
     } /* end of loop on modality */       /*                               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*/      } /* 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 (k=-1; k< maxncov; k++) Ndum[k]=0; 
       
   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */     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.*/       /* 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 */       ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
    Ndum[ij]++;       Ndum[ij]++; /* Might be supersed V1 + V1*age */
  }     } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
     
  ij=1;    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) */    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]);*/      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
    if((Ndum[i]!=0) && (i<=ncovcol)){      if((Ndum[i]!=0) && (i<=ncovcol)){
      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
      Tvaraff[ij]=i; /*For printing (unclear) */        Tvaraff[++ij]=i; /*For printing (unclear) */
      ij++;      }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){
    }else        Tvaraff[++ij]=-10; /* Dont'n know how to treat quantitative variables yet */
        Tvaraff[ij]=0;      }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){
  }        Tvaraff[++ij]=i; /*For printing (unclear) */
  ij--;      }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){
  cptcoveff=ij; /*Number of total covariates*/        Tvaraff[++ij]=-20; /* Dont'n know how to treat quantitative variables yet */
       }
     } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
     /* ij--; */
     /* cptcoveff=ij; /\*Number of total covariates*\/ */
     *cptcov=ij; /*Number of total real effective covariates: effective
                  * because they can be excluded from the model and real
                  * if in the model but excluded because missing values*/
 }  }
   
   
Line 3122  void cvevsij(double ***eij, double x[], Line 4770  void cvevsij(double ***eij, double x[],
   
 {  {
   /* Covariances of health expectancies eij and of total life expectancies according    /* Covariances of health expectancies eij and of total life expectancies according
    to initial status i, ei. .       to initial status i, ei. .
   */    */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
Line 3216  void cvevsij(double ***eij, double x[], Line 4864  void cvevsij(double ***eij, double x[],
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/      /* if (stepm >= YEARM) hstepm=1;*/
     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                   
     /* If stepm=6 months */      /* If stepm=6 months */
     /* Computed by stepm unit matrices, product of hstepma matrices, stored      /* Computed by stepm unit matrices, product of hstepma matrices, stored
        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   
     /* Computing  Variances of health expectancies */      /* Computing  Variances of health expectancies */
     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
        decrease memory allocation */         decrease memory allocation */
Line 3233  void cvevsij(double ***eij, double x[], Line 4881  void cvevsij(double ***eij, double x[],
       }        }
       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
                             
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
         for(i=1; i<=nlstate; i++){          for(i=1; i<=nlstate; i++){
           for(h=0; h<=nhstepm-1; h++){            for(h=0; h<=nhstepm-1; h++){
Line 3242  void cvevsij(double ***eij, double x[], Line 4890  void cvevsij(double ***eij, double x[],
           }            }
         }          }
       }        }
                                
       for(ij=1; ij<= nlstate*nlstate; ij++)        for(ij=1; ij<= nlstate*nlstate; ij++)
         for(h=0; h<=nhstepm-1; h++){          for(h=0; h<=nhstepm-1; h++){
           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
Line 3255  void cvevsij(double ***eij, double x[], Line 4903  void cvevsij(double ***eij, double x[],
         for(theta=1; theta <=npar; theta++)          for(theta=1; theta <=npar; theta++)
           trgradg[h][j][theta]=gradg[h][theta][j];            trgradg[h][j][theta]=gradg[h][theta][j];
           
                   
      for(ij=1;ij<=nlstate*nlstate;ij++)      for(ij=1;ij<=nlstate*nlstate;ij++)
       for(ji=1;ji<=nlstate*nlstate;ji++)        for(ji=1;ji<=nlstate*nlstate;ji++)
         varhe[ij][ji][(int)age] =0.;          varhe[ij][ji][(int)age] =0.;
                   
      printf("%d|",(int)age);fflush(stdout);      printf("%d|",(int)age);fflush(stdout);
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      for(h=0;h<=nhstepm-1;h++){      for(h=0;h<=nhstepm-1;h++){
       for(k=0;k<=nhstepm-1;k++){        for(k=0;k<=nhstepm-1;k++){
         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);          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]);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
Line 3271  void cvevsij(double ***eij, double x[], Line 4919  void cvevsij(double ***eij, double x[],
             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       }        }
     }      }
                   
     /* Computing expectancies */      /* Computing expectancies */
     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          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;            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]);*/            /* 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 );      fprintf(ficresstdeij,"%3.0f",age );
     for(i=1; i<=nlstate;i++){      for(i=1; i<=nlstate;i++){
       eip=0.;        eip=0.;
Line 3296  void cvevsij(double ***eij, double x[], Line 4944  void cvevsij(double ***eij, double x[],
       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     }      }
     fprintf(ficresstdeij,"\n");      fprintf(ficresstdeij,"\n");
                   
     fprintf(ficrescveij,"%3.0f",age );      fprintf(ficrescveij,"%3.0f",age );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
Line 3309  void cvevsij(double ***eij, double x[], Line 4957  void cvevsij(double ***eij, double x[],
           }            }
       }        }
     fprintf(ficrescveij,"\n");      fprintf(ficrescveij,"\n");
                      
   }    }
   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
Line 3319  void cvevsij(double ***eij, double x[], Line 4967  void cvevsij(double ***eij, double x[],
   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("\n");    printf("\n");
   fprintf(ficlog,"\n");    fprintf(ficlog,"\n");
           
   free_vector(xm,1,npar);    free_vector(xm,1,npar);
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(dnewm,1,nlstate*nlstate,1,npar);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
 }  }
   
 /************ Variance ******************/  
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])  
 {  
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   /* double **newm;*/  
   double **dnewm,**doldm;  
   double **dnewmp,**doldmp;  
   int i, j, nhstepm, hstepm, h, nstepm ;  
   int k;  
   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);  /************ Variance ******************/
   pstamp(ficresprobmorprev);   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 *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   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);     /* Variance of health expectancies */
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     fprintf(ficresprobmorprev," p.%-d SE",j);     /* double **newm;*/
     for(i=1; i<=nlstate;i++)     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);    
   }       /* int movingaverage(); */
   fprintf(ficresprobmorprev,"\n");     double **dnewm,**doldm;
   fprintf(ficgp,"\n# Routine varevsij");     double **dnewmp,**doldmp;
   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/     int i, j, nhstepm, hstepm, h, nstepm ;
   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");     int k;
   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);     double *xp;
 /*   } */     double **gp, **gm;  /* for var eij */
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     double ***gradg, ***trgradg; /*for var eij */
   pstamp(ficresvij);     double **gradgp, **trgradgp; /* for var p point j */
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");     double *gpp, *gmp; /* for var p point j */
   if(popbased==1)     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     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);     double ***p3mat;
   else     double age,agelim, hf;
     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");     /* double ***mobaverage; */
   fprintf(ficresvij,"# Age");     int theta;
   for(i=1; i<=nlstate;i++)     char digit[4];
     for(j=1; j<=nlstate;j++)     char digitp[25];
       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);  
   fprintf(ficresvij,"\n");     char fileresprobmorprev[FILENAMELENGTH];
   
   xp=vector(1,npar);     if(popbased==1){
   dnewm=matrix(1,nlstate,1,npar);       if(mobilav!=0)
   doldm=matrix(1,nlstate,1,nlstate);         strcpy(digitp,"-POPULBASED-MOBILAV_");
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);       else strcpy(digitp,"-POPULBASED-NOMOBIL_");
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     }
      else 
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);       strcpy(digitp,"-STABLBASED_");
   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++){     /* if (mobilav!=0) { */
       for(k=0;k<=nhstepm;k++){     /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);     /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);     /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
         for(i=1;i<=nlstate;i++)     /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
           for(j=1;j<=nlstate;j++)     /*   } */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;     /* } */
       }  
     }     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,fileresu);
      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(ficgp,"\nunset title \n");
      /* 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*/
       
     /* pptj */     if(estepm < stepm){
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);       printf ("Problem %d lower than %d\n",estepm, stepm);
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);     }
     for(j=nlstate+1;j<=nlstate+ndeath;j++)     else  hstepm=estepm;   
       for(i=nlstate+1;i<=nlstate+ndeath;i++)     /* For example we decided to compute the life expectancy with the smallest unit */
         varppt[j][i]=doldmp[j][i];     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     /* end ppptj */        nhstepm is the number of hstepm from age to agelim 
     /*  x centered again */        nstepm is the number of stepm from age to agelim. 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);          Look at function hpijx to understand why because of memory size limitations, 
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);        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
     if (popbased==1) {        means that if the survival funtion is printed every two years of age and if
       if(mobilav ==0){        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for(i=1; i<=nlstate;i++)        results. So we changed our mind and took the option of the best precision.
           prlim[i][i]=probs[(int)age][i][ij];     */
       }else{ /* mobilav */      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         for(i=1; i<=nlstate;i++)     agelim = AGESUP;
           prlim[i][i]=mobaverage[(int)age][i][ij];     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);
     /* This for computing probability of death (h=1 means       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        computed over hstepm (estepm) matrices product = hstepm*stepm months)        gp=matrix(0,nhstepm,1,nlstate);
        as a weighted average of prlim.       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);
          }
                           
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,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];
            }
          }
                           
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
          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];
            }
          }
          /* Next 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);
                           
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, 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];
            }
          }
                           
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, 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 */
                   
        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,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.
        */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        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"); */
      fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
      /* 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,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
      /*   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.svg\"> <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.svg\"> <br>\n", stepm,YEARM,digitp,digit);
     */      */
     for(j=nlstate+1;j<=nlstate+ndeath;j++){     /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
       for(i=1,gmp[j]=0.;i<= nlstate; i++)      fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
         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_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,nlstate);     free_matrix(doldm,1,nlstate,1,nlstate);
   free_matrix(dnewm,1,nlstate,1,npar);     free_matrix(dnewm,1,nlstate,1,npar);
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   fclose(ficresprobmorprev);     fclose(ficresprobmorprev);
   fflush(ficgp);     fflush(ficgp);
   fflush(fichtm);      fflush(fichtm); 
 }  /* end varevsij */   }  /* end varevsij */
   
 /************ Variance of prevlim ******************/  /************ 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[])   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 *ncvyearp, int ij, char strstart[])
 {  {
   /* Variance of prevalence limit */    /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
   double **dnewm,**doldm;    double **dnewm,**doldm;
Line 3642  void varprevlim(char fileres[], double * Line 5300  void varprevlim(char fileres[], double *
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
     double **mgm, **mgp;
   double age,agelim;    double age,agelim;
   int theta;    int theta;
       
Line 3664  void varprevlim(char fileres[], double * Line 5323  void varprevlim(char fileres[], double *
     if (stepm >= YEARM) hstepm=1;      if (stepm >= YEARM) hstepm=1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     gradg=matrix(1,npar,1,nlstate);      gradg=matrix(1,npar,1,nlstate);
       mgp=matrix(1,npar,1,nlstate);
       mgm=matrix(1,npar,1,nlstate);
     gp=vector(1,nlstate);      gp=vector(1,nlstate);
     gm=vector(1,nlstate);      gm=vector(1,nlstate);
   
Line 3671  void varprevlim(char fileres[], double * Line 5332  void varprevlim(char fileres[], double *
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(i=1; i<=npar; i++){ /* Computes gradient */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
       for(i=1;i<=nlstate;i++)          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         else
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         for(i=1;i<=nlstate;i++){
         gp[i] = prlim[i][i];          gp[i] = prlim[i][i];
               mgp[theta][i] = prlim[i][i];
         }
       for(i=1; i<=npar; i++) /* Computes gradient */        for(i=1; i<=npar; i++) /* Computes gradient */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
       for(i=1;i<=nlstate;i++)          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         else
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         for(i=1;i<=nlstate;i++){
         gm[i] = prlim[i][i];          gm[i] = prlim[i][i];
           mgm[theta][i] = prlim[i][i];
         }
       for(i=1;i<=nlstate;i++)        for(i=1;i<=nlstate;i++)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
     } /* End theta */      } /* End theta */
   
     trgradg =matrix(1,nlstate,1,npar);      trgradg =matrix(1,nlstate,1,npar);
Line 3690  void varprevlim(char fileres[], double * Line 5360  void varprevlim(char fileres[], double *
     for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
       for(theta=1; theta <=npar; theta++)        for(theta=1; theta <=npar; theta++)
         trgradg[j][theta]=gradg[theta][j];          trgradg[j][theta]=gradg[theta][j];
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\nmgm mgp %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf(" %d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\n gradg %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf("%d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf("%d %lf ",theta,gradg[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
   
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
       varpl[i][(int)age] =0.;        varpl[i][(int)age] =0.;
       if((int)age==79 ||(int)age== 80  ||(int)age== 81){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       }else{
       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++)      for(i=1;i<=nlstate;i++)
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
Line 3704  void varprevlim(char fileres[], double * Line 5397  void varprevlim(char fileres[], double *
     fprintf(ficresvpl,"\n");      fprintf(ficresvpl,"\n");
     free_vector(gp,1,nlstate);      free_vector(gp,1,nlstate);
     free_vector(gm,1,nlstate);      free_vector(gm,1,nlstate);
       free_matrix(mgm,1,npar,1,nlstate);
       free_matrix(mgp,1,npar,1,nlstate);
     free_matrix(gradg,1,npar,1,nlstate);      free_matrix(gradg,1,npar,1,nlstate);
     free_matrix(trgradg,1,nlstate,1,npar);      free_matrix(trgradg,1,nlstate,1,npar);
   } /* End age */    } /* End age */
Line 3716  void varprevlim(char fileres[], double * Line 5411  void varprevlim(char fileres[], double *
   
 /************ Variance of one-step probabilities  ******************/  /************ 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[])  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 i, j=0,  k1, l1, tj;
   int k2, l2, j1,  z1;     int k2, l2, j1,  z1;
   int k=0, l;     int k=0, l;
   int first=1, first1, first2;     int first=1, first1, first2;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double **dnewm,**doldm;     double **dnewm,**doldm;
   double *xp;     double *xp;
   double *gp, *gm;     double *gp, *gm;
   double **gradg, **trgradg;     double **gradg, **trgradg;
   double **mu;     double **mu;
   double age, cov[NCOVMAX+1];     double age, cov[NCOVMAX+1];
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int theta;     int theta;
   char fileresprob[FILENAMELENGTH];     char fileresprob[FILENAMELENGTH];
   char fileresprobcov[FILENAMELENGTH];     char fileresprobcov[FILENAMELENGTH];
   char fileresprobcor[FILENAMELENGTH];     char fileresprobcor[FILENAMELENGTH];
   double ***varpij;     double ***varpij;
   
   strcpy(fileresprob,"prob");      strcpy(fileresprob,"PROB_"); 
   strcat(fileresprob,fileres);     strcat(fileresprob,fileres);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);       printf("Problem with resultfile: %s\n", fileresprob);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }     }
   strcpy(fileresprobcov,"probcov");      strcpy(fileresprobcov,"PROBCOV_"); 
   strcat(fileresprobcov,fileres);     strcat(fileresprobcov,fileresu);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcov);       printf("Problem with resultfile: %s\n", fileresprobcov);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   }     }
   strcpy(fileresprobcor,"probcor");      strcpy(fileresprobcor,"PROBCOR_"); 
   strcat(fileresprobcor,fileres);     strcat(fileresprobcor,fileresu);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcor);       printf("Problem with resultfile: %s\n", fileresprobcor);
     fprintf(ficlog,"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);     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);     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);     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);     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);     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);     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   pstamp(ficresprob);     pstamp(ficresprob);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fprintf(ficresprob,"# Age");     fprintf(ficresprob,"# Age");
   pstamp(ficresprobcov);     pstamp(ficresprobcov);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   fprintf(ficresprobcov,"# Age");     fprintf(ficresprobcov,"# Age");
   pstamp(ficresprobcor);     pstamp(ficresprobcor);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   fprintf(ficresprobcor,"# Age");     fprintf(ficresprobcor,"# Age");
   
   
   for(i=1; i<=nlstate;i++)     for(i=1; i<=nlstate;i++)
     for(j=1; j<=(nlstate+ndeath);j++){       for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       fprintf(ficresprobcov," p%1d-%1d ",i,j);         fprintf(ficresprobcov," p%1d-%1d ",i,j);
       fprintf(ficresprobcor," p%1d-%1d ",i,j);         fprintf(ficresprobcor," p%1d-%1d ",i,j);
     }         }  
  /* fprintf(ficresprob,"\n");     /* fprintf(ficresprob,"\n");
   fprintf(ficresprobcov,"\n");        fprintf(ficresprobcov,"\n");
   fprintf(ficresprobcor,"\n");        fprintf(ficresprobcor,"\n");
  */     */
   xp=vector(1,npar);     xp=vector(1,npar);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   first=1;     first=1;
   fprintf(ficgp,"\n# Routine varprob");     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<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fprintf(fichtm,"\n");     fprintf(fichtm,"\n");
   
   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\     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);
   file %s<br>\n",optionfilehtmcov);     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
   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.\  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");   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. \     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 \  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 \  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>\  standard deviations wide on each axis. <br>\
Line 3804  standard deviations wide on each axis. < Line 5498  standard deviations wide on each axis. <
  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\   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");  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;     cov[1]=1;
   /* tj=cptcoveff; */     /* tj=cptcoveff; */
   tj = (int) pow(2,cptcoveff);     tj = (int) pow(2,cptcoveff);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   j1=0;     j1=0;
   for(j1=1; j1<=tj;j1++){     for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
     /*for(i1=1; i1<=ncodemax[t];i1++){ */       if  (cptcovn>0) {
     /*j1++;*/         fprintf(ficresprob, "\n#********** Variable "); 
       if  (cptcovn>0) {         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprob, "\n#********** Variable ");          fprintf(ficresprob, "**********\n#\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);         fprintf(ficresprobcov, "\n#********** Variable "); 
         fprintf(ficresprob, "**********\n#\n");         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprobcov, "\n#********** Variable ");          fprintf(ficresprobcov, "**********\n#\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                          
         fprintf(ficresprobcov, "**********\n#\n");         fprintf(ficgp, "\n#********** Variable "); 
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficgp, "\n#********** Variable ");          fprintf(ficgp, "**********\n#\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                          
         fprintf(ficgp, "**********\n#\n");                          
                  fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                          
         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(ficresprobcor, "\n#********** Variable ");    
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprobcor, "\n#********** Variable ");             fprintf(ficresprobcor, "**********\n#");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);         if(invalidvarcomb[j1]){
         fprintf(ficresprobcor, "**********\n#");               fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
       }           fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1); 
                  continue;
       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));         }
       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);       }
       gp=vector(1,(nlstate)*(nlstate+ndeath));       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       gm=vector(1,(nlstate)*(nlstate+ndeath));       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       for (age=bage; age<=fage; age ++){        gp=vector(1,(nlstate)*(nlstate+ndeath));
         cov[2]=age;       gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (k=1; k<=cptcovn;k++) {       for (age=bage; age<=fage; age ++){ 
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4         cov[2]=age;
                                                          * 1  1 1 1 1         if(nagesqr==1)
                                                          * 2  2 1 1 1           cov[3]= age*age;
                                                          * 3  1 2 1 1         for (k=1; k<=cptcovn;k++) {
                                                          */           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
           /* nbcode[1][1]=0 nbcode[1][2]=1;*/           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
         }                                                                      * 1  1 1 1 1
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];                                                                      * 2  2 1 1 1
         for (k=1; k<=cptcovprod;k++)                                                                      * 3  1 2 1 1
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];                                                                      */
                    /* nbcode[1][1]=0 nbcode[1][2]=1;*/
              }
         for(theta=1; theta <=npar; theta++){         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           for(i=1; i<=npar; i++)         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);         for (k=1; k<=cptcovprod;k++)
                      cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                          
                                     
           k=0;         for(theta=1; theta <=npar; theta++){
           for(i=1; i<= (nlstate); i++){           for(i=1; i<=npar; i++)
             for(j=1; j<=(nlstate+ndeath);j++){             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
               k=k+1;                                  
               gp[k]=pmmij[i][j];           pmij(pmmij,cov,ncovmodel,xp,nlstate);
             }                                  
           }           k=0;
                      for(i=1; i<= (nlstate); i++){
           for(i=1; i<=npar; i++)             for(j=1; j<=(nlstate+ndeath);j++){
             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);               k=k+1;
                    gp[k]=pmmij[i][j];
           pmij(pmmij,cov,ncovmodel,xp,nlstate);             }
           k=0;           }
           for(i=1; i<=(nlstate); i++){                                  
             for(j=1; j<=(nlstate+ndeath);j++){           for(i=1; i<=npar; i++)
               k=k+1;             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
               gm[k]=pmmij[i][j];                                  
             }           pmij(pmmij,cov,ncovmodel,xp,nlstate);
           }           k=0;
                 for(i=1; i<=(nlstate); i++){
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)              for(j=1; j<=(nlstate+ndeath);j++){
             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];                 k=k+1;
         }               gm[k]=pmmij[i][j];
              }
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)           }
           for(theta=1; theta <=npar; theta++)                                  
             trgradg[j][theta]=gradg[theta][j];           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                      gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
         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 */         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));           for(theta=1; theta <=npar; theta++)
                   /*v21=sqrt(1.-v11*v11); *//* error */             trgradg[j][theta]=gradg[theta][j];
                   v21=(lc1-v1)/cv12*v11;                          
                   v12=-v21;         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                   v22=v11;         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                   tnalp=v21/v11;                          
                   if(first1==1){         pmij(pmmij,cov,ncovmodel,x,nlstate);
                     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);         k=0;
                   }         for(i=1; i<=(nlstate); i++){
                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);           for(j=1; j<=(nlstate+ndeath);j++){
                   /*printf(fignu*/             k=k+1;
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */             mu[k][(int) age]=pmmij[i][j];
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */           }
                   if(first==1){         }
                     first=0;         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                     fprintf(ficgp,"\nset parametric;unset label");           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                     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);             varpij[i][j][(int)age] = doldm[i][j];
                     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>\         /*printf("\n%d ",(int)age);
  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                             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(ficresprob,"\n%d ",(int)age);
                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);         fprintf(ficresprobcov,"\n%d ",(int)age);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);         fprintf(ficresprobcor,"\n%d ",(int)age);
                     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",\         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   }else{           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                     first=0;           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);         }
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);         i=0;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);         for (k=1; k<=(nlstate);k++){
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\           for (l=1; l<=(nlstate+ndeath);l++){ 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\             i++;
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                   }/* if first */             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                 } /* age mod 5 */             for (j=1; j<=i;j++){
               } /* end loop age */               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
               first=1;               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
             } /*l12 */             }
           } /* k12 */           }
         } /*l1 */         }/* end of loop for state */
       }/* k1 */       } /* end of loop for age */
       /* } /* loop covariates */       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   }       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));      
   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);       /* Confidence intervalle of pij  */
   free_vector(xp,1,npar);       /*
   fclose(ficresprob);         fprintf(ficgp,"\nunset parametric;unset label");
   fclose(ficresprobcov);         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   fclose(ficresprobcor);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   fflush(ficgp);         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);
   fflush(fichtmcov);         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,"\n# Ellipsoids of confidence\n#\n");
                      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 svg size 640, 480");
                      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.svg\">                                                                                                                                           \
   %s_%d%1d%1d-%1d%1d.svg</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.svg\"> ",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.svg\"",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;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                first=1;
              } /*l12 */
            } /* k12 */
          } /*l1 */
        }/* k1 */
      }  /* loop on combination of covariates j1 */
      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 ***********/  /******************* Printing html file ***********/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   int popforecast, int estepm ,\                    int popforecast, int prevfcast, int backcast, int estepm , \
                   double jprev1, double mprev1,double anprev1, \                    double jprev1, double mprev1,double anprev1, double dateprev1, \
                   double jprev2, double mprev2,double anprev2){                    double jprev2, double mprev2,double anprev2, double dateprev2){
   int jj1, k1, i1, cpt;    int jj1, k1, i1, cpt;
   
    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \     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 \     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
 </ul>");  </ul>");
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \     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 ",     fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
      fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
      fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));             stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
      fprintf(fichtm,"\
    - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
    fprintf(fichtm,"\     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): \   - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
    <a href=\"%s\">%s</a> <br>\n",             subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));  
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Population projections by age and states: \   - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . 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</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));     <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
      if(prevfcast==1){
        fprintf(fichtm,"\
    - Prevalence projections by age and states:                            \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
      }
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");     fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
  m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  jj1=0;     jj1=0;
  for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
    for(i1=1; i1<=ncodemax[k1];i1++){  
        /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)          for (cpt=1; cpt<=cptcoveff;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][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\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
          if(invalidvarcomb[k1]){
            fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
            printf("\nCombination (%d) ignored because no cases \n",k1); 
            continue;
          }
      }       }
        /* aij, bij */
        fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
   <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
      /* Pij */       /* 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> \       fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
 <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);       <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);     
      /* Quasi-incidences */       /* Quasi-incidences */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\       fprintf(fichtm,"<br>\n- I<sub>ij</sub> 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> \   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
 <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);    incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
        /* Period (stable) prevalence in each health state */  divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
   <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); 
        /* Survival functions (period) in state j */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
        }
        /* State specific survival functions (period) */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
    Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
    <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
        }
        /* Period (stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- 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.svg\">%s_%d-%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
        }
        if(backcast==1){
          /* Period (stable) back prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>\n- Convergence to period (stable) back 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.svg\">%s_%d-%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
          }
        }
        if(prevfcast==1){
          /* Projection of prevalence up to period (stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         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> \           fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up 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.svg\">%s%d_%d.svg</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);  <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
        }         }
        }
            
      for(cpt=1; cpt<=nlstate;cpt++) {       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> \         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) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</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);  <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
      }       }
    } /* end i1 */       /* } /\* end i1 *\/ */
  }/* End k1 */     }/* End k1 */
  fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
   
   
  fprintf(fichtm,"\     fprintf(fichtm,"\
 \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);   - 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 if optimization has been done (mle != 0).<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," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",     fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));             subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));             subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
   
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));             subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
  fprintf(fichtm,"\     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): \   - 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>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));             estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
  fprintf(fichtm,"\     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) 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>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
  fprintf(fichtm,"\     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",   - 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"));             estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
  fprintf(fichtm,"\     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",   - 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"));             estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));             subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
   
 /*  if(popforecast==1) fprintf(fichtm,"\n */  /*  if(popforecast==1) fprintf(fichtm,"\n */
 /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
Line 4148  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 5905  fprintf(fichtm," \n<ul><li><b>Graphs</b>
 /*      <br>",fileres,fileres,fileres,fileres); */  /*      <br>",fileres,fileres,fileres,fileres); */
 /*  else  */  /*  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); */  /*    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);     fflush(fichtm);
  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");     fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
  m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  jj1=0;     jj1=0;
  for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
    for(i1=1; i1<=ncodemax[k1];i1++){       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)          for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   
          if(invalidvarcomb[k1]){
            fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
            continue;
          }
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \         fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\  prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
 <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);    <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);  
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       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) \  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\  true period expectancies (those weighted with period prevalences are also\
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences: %s%d.png<br>\   observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
 <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);  <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
    } /* end i1 */       /* } /\* end i1 *\/ */
  }/* End k1 */     }/* End k1 */
  fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
  fflush(fichtm);     fflush(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
     char gplotcondition[132];
   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int lv=0, vlv=0, kl=0;
   int ng=0;    int ng=0;
     int vpopbased;
     int ioffset; /* variable offset for columns */
   
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
 /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
Line 4194  void printinggnuplot(char fileres[], cha Line 5961  void printinggnuplot(char fileres[], cha
   
   /*#ifdef windows */    /*#ifdef windows */
   fprintf(ficgp,"cd \"%s\" \n",pathc);    fprintf(ficgp,"cd \"%s\" \n",pathc);
     /*#endif */    /*#endif */
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
   
     /* Contribution to likelihood */
     /* Plot the probability implied in the likelihood */
     fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
     /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
     fprintf(ficgp,"\nset ter pngcairo size 640, 480");
   /* nice for mle=4 plot by number of matrix products.
      replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
   /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
     /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
     fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
     fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
     for (i=1; i<= nlstate ; i ++) {
       fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
       fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
       fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
       for (j=2; j<= nlstate+ndeath ; j ++) {
         fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
       }
       fprintf(ficgp,";\nset out; unset ylabel;\n"); 
     }
     /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */                
     /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
     /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
     fprintf(ficgp,"\nset out;unset log\n");
     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
   
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
  /* 1eme*/    /* 1eme*/
   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");    for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
   for (cpt=1; cpt<= nlstate ; cpt ++) {      for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */        /* 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# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);        for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
      fprintf(ficgp,"set xlabel \"Age\" \n\          lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
 set ylabel \"Probability\" \n\          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
 set ter png small size 320, 240\n\          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
      for (i=1; i<= nlstate ; i ++) {          /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
        else        fprintf(ficgp," \%%*lf (\%%*lf)");        }
      }        fprintf(ficgp,"\n#\n");
      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);        if(invalidvarcomb[k1]){
      for (i=1; i<= nlstate ; i ++) {          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          continue;
        else fprintf(ficgp," \%%*lf (\%%*lf)");        }
      }   
      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
      for (i=1; i<= nlstate ; i ++) {        fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficgp,"set xlabel \"Age\" \n\
        else fprintf(ficgp," \%%*lf (\%%*lf)");  set ylabel \"Probability\" \n   \
      }    set ter svg size 640, 480\n     \
      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"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(fileresu,"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*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); 
         for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }  
         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
           fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
           if(cptcoveff ==0){
             fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );
           }else{
             kl=0;
             for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
               vlv= nbcode[Tvaraff[k]][lv];
               kl++;
               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
               if(k==cptcoveff){
                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                         6+(cpt-1),  cpt );
               }else{
                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                 kl++;
               }
             } /* end covariate */
           } /* end if no covariate */
         } /* end if backcast */
         fprintf(ficgp,"\nset out \n");
       } /* k1 */
     } /* cpt */
   /*2 eme*/    /*2 eme*/
   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");  
   for (k1=1; k1<= m ; k1 ++) {     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);      fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
           for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
     for (i=1; i<= nlstate+1 ; i ++) {        lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
       k=2*i;        /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);        /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
       for (j=1; j<= nlstate+1 ; j ++) {        /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        vlv= nbcode[Tvaraff[k]][lv];
         else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }         }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      fprintf(ficgp,"\n#\n");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      if(invalidvarcomb[k1]){
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);        fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
       for (j=1; j<= nlstate+1 ; j ++) {        continue;
         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,");  
     }      }
   }                          
         fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
         if(vpopbased==0)
           fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
         else
           fprintf(ficgp,"\nreplot ");
         for (i=1; i<= nlstate+1 ; i ++) {
           k=2*i;
           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
           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 lt %d, \\\n",i);
           else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
           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==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
           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,\\\n");
         } /* state */
       } /* vpopbased */
       fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
     } /* k1 */
           
           
   /*3eme*/    /*3eme*/
     
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
   
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
         fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         }
         fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;
         }
                           
       /*       k=2+nlstate*(2*cpt-2); */        /*       k=2+nlstate*(2*cpt-2); */
       k=2+(nlstate+1)*(cpt-1);        k=2+(nlstate+1)*(cpt-1);
       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
       fprintf(ficgp,"set ter png small size 320, 240\n\        fprintf(ficgp,"set ter svg size 640, 480\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);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"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);        /*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) ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          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);          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) ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                                           
       */        */
       for (i=1; i< nlstate ; i ++) {        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(fileresu,"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%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);        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
     }      }
   }    }
       
   /* CV preval stable (period) */    /* 4eme */
     /* Survival functions (period) from state i in state j by initial state i */
   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */    for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
   
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
       k=3;        fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
 set ter png small size 320, 240\n\          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
 unset log y\n\          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         }
         fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;
         }
                           
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\n                                                                                                                                                                                     \
   unset log y\n                                                                                                                                                                                                                                           \
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3;
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){
         if(i==1)          if(i==1){
           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
         else          }else{
           fprintf(ficgp,", '' ");            fprintf(ficgp,", '' ");
           }
         l=(nlstate+ndeath)*(i-1)+1;          l=(nlstate+ndeath)*(i-1)+1;
         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
         for (j=1; j<= (nlstate-1) ; j ++)          for (j=2; j<= nlstate+ndeath ; j ++)
           fprintf(ficgp,"+$%d",k+l+j);            fprintf(ficgp,"+$%d",k+l+j-1);
         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);          fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,"\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
             
   /* 5eme */
     /* Survival functions (period) from state i in state j by final state j */
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
                           
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                                   lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                                   /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                   /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                   /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                   vlv= nbcode[Tvaraff[k]][lv];
                                   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         }
         fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
                                   fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                   continue;
         }
                           
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\n                                                                                                                                                                                     \
   unset log y\n                                                                                                                                                                                                                                           \
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3;
         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
                                   if(j==1)
                                           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
                                   else
                                           fprintf(ficgp,", '' ");
                                   l=(nlstate+ndeath)*(cpt-1) +j;
                                   fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
                                   /* for (i=2; i<= nlstate+ndeath ; i ++) */
                                   /*   fprintf(ficgp,"+$%d",k+l+i-1); */
                                   fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
         } /* nlstate */
         fprintf(ficgp,", '' ");
         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
                                   l=(nlstate+ndeath)*(cpt-1) +j;
                                   if(j < nlstate)
                                           fprintf(ficgp,"$%d +",k+l);
                                   else
                                           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
         }
         fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/ 
     } /* end covariate */  
           
   /* 6eme */
     /* CV preval stable (period) for each covariate */
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                           
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                                   lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                                   /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                   /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                   /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                   vlv= nbcode[Tvaraff[k]][lv];
                                   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         }
         fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
                                   fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                   continue;
         }
                           
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter svg size 640, 480\n                                                                                                                                                                              \
   unset log y\n                                                                                                                                                                                                                                    \
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3; /* Offset */
         for (i=1; i<= nlstate ; i ++){
                                   if(i==1)
                                           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
                                   else
                                           fprintf(ficgp,", '' ");
                                   l=(nlstate+ndeath)*(i-1)+1;
                                   fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
                                   for (j=2; j<= nlstate ; j ++)
                                           fprintf(ficgp,"+$%d",k+l+j-1);
                                   fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/ 
     } /* end covariate */  
           
           
   /* 7eme */
     if(backcast == 1){
       /* CV back preval stable (period) for each covariate */
       for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                                   fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
                                   for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                                           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                                           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                           vlv= nbcode[Tvaraff[k]][lv];
                                           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                                   }
                                   fprintf(ficgp,"\n#\n");
                                   if(invalidvarcomb[k1]){
                                           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                           continue;
                                   }
                                   
                                   fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
                                   fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter svg size 640, 480\n                                                                                                                                                                                     \
   unset log y\n                                                                                                                                                                                                                                           \
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
                                   k=3; /* Offset */
                                   for (i=1; i<= nlstate ; i ++){
                                           if(i==1)
                                                   fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
                                           else
                                                   fprintf(ficgp,", '' ");
                                           /* l=(nlstate+ndeath)*(i-1)+1; */
                                           l=(nlstate+ndeath)*(cpt-1)+1;
                                           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
                                           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
                                           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
                                           /* for (j=2; j<= nlstate ; j ++) */
                                           /*      fprintf(ficgp,"+$%d",k+l+j-1); */
                                           /*      /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
                                           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
                                   } /* nlstate */
                                   fprintf(ficgp,"\nset out\n");
         } /* end cpt state*/ 
       } /* end covariate */  
     } /* End if backcast */
     
     /* 8eme */
     if(prevfcast==1){
       /* Projection from cross-sectional to stable (period) for each covariate */
       
       for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                                   fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
                                   for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
                                           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                                           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                           vlv= nbcode[Tvaraff[k]][lv];
                                           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                                   }
                                   fprintf(ficgp,"\n#\n");
                                   if(invalidvarcomb[k1]){
                                           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                           continue;
                                   }
                                   
                                   fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
                                   fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
                                   fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
   set ter svg size 640, 480\n                                                                                                                                                                                     \
   unset log y\n                                                                                                                                                                                                                                           \
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
                                   for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
                                           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                                           /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                                           if(i==1){
                                                   fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
                                           }else{
                                                   fprintf(ficgp,",\\\n '' ");
                                           }
                                           if(cptcoveff ==0){ /* No covariate */
                                                   ioffset=2; /* Age is in 2 */
                                                   /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                                                   /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                                                   /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                                                   /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                                                   fprintf(ficgp," u %d:(", ioffset); 
                                                   if(i==nlstate+1)
                                                           fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",                    \
                                                                                           ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                                                   else
                                                           fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",                    \
                                                                                           ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                                           }else{ /* more than 2 covariates */
                                                   if(cptcoveff ==1){
                                                           ioffset=4; /* Age is in 4 */
                                                   }else{
                                                           ioffset=6; /* Age is in 6 */
                                                           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                                           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
                                                   }   
                                                   fprintf(ficgp," u %d:(",ioffset); 
                                                   kl=0;
                                                   strcpy(gplotcondition,"(");
                                                   for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                                                           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                                                           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                                           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                                           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                                           vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                                                           kl++;
                                                           sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                                                           kl++;
                                                           if(k <cptcoveff && cptcoveff>1)
                                                                   sprintf(gplotcondition+strlen(gplotcondition)," && ");
                                                   }
                                                   strcpy(gplotcondition+strlen(gplotcondition),")");
                                                   /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                                                   /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                                                   /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                                                   /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                                                   if(i==nlstate+1){
                                                           fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
                                                                                           ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                                                   }else{
                                                           fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                                                                                           ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                                                   }
                                           } /* end if covariate */
                                   } /* nlstate */
                                   fprintf(ficgp,"\nset out\n");
         } /* end cpt state*/
       } /* end covariate */
     } /* End if prevfcast */
           
           
   /* proba elementaires */    /* proba elementaires */
     fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
   for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficgp,"# initial state %d\n",i);
     for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
       if (k != i) {        if (k != i) {
         for(j=1; j <=ncovmodel; j++){                                  fprintf(ficgp,"#   current state %d\n",k);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                                  for(j=1; j <=ncovmodel; j++){
           jk++;                                           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
           fprintf(ficgp,"\n");                                          jk++; 
         }                                  }
                                   fprintf(ficgp,"\n");
       }        }
     }      }
    }    }
     fprintf(ficgp,"##############\n#\n");
           
   /*goto avoid;*/    /*goto avoid;*/
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
      for(jk=1; jk <=m; jk++) {    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);     fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
        if (ng==2)    fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
        else    fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
          fprintf(ficgp,"\nset title \"Probability\"\n");    fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
        i=1;    fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
        for(k2=1; k2<=nlstate; k2++) {    fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
          k3=i;    fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
          for(k=1; k<=(nlstate+ndeath); k++) {    fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
            if (k != k2){    fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
              if(ng==2)    fprintf(ficgp,"#\n");
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
              else      fprintf(ficgp,"# ng=%d\n",ng);
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
              ij=1;/* To be checked else nbcode[0][0] wrong */      for(jk=1; jk <=m; jk++) {
              for(j=3; j <=ncovmodel; j++) {        fprintf(ficgp,"#    jk=%d\n",jk);
                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */        fprintf(ficgp,"\nset ter svg size 640, 480 ");
                /*        ij++; */        if (ng==1){
                /* } */          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
                /* else */          fprintf(ficgp,"\nunset log y");
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        }else if (ng==2){
              }          fprintf(ficgp,"\nset ylabel \"Probability\"\n");
              fprintf(ficgp,")/(1");          fprintf(ficgp,"\nset log y");
         }else if (ng==3){
           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           fprintf(ficgp,"\nset log y");
         }else
           fprintf(ficgp,"\nunset title ");
         fprintf(ficgp,"\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){
               switch( ng) {
               case 1:
                 if(nagesqr==0)
                   fprintf(ficgp," p%d+p%d*x",i,i+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                 break;
               case 2: /* ng=2 */
                 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);
                 break;
               case 3:
                 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);
                 break;
               }
               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,j-2)]);
                     /* 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)]); /* Valgrind bug nbcode */
               }
             }else{
               i=i-ncovmodel;
               if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
                 fprintf(ficgp," (1.");
             }
              
             if(ng != 1){
               fprintf(ficgp,")/(1");
                             
              for(k1=1; k1 <=nlstate; k1++){                 for(k1=1; k1 <=nlstate; k1++){ 
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                if(nagesqr==0)
                ij=1;                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                for(j=3; j <=ncovmodel; j++){                else /* nagesqr =1 */
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */                  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);
                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */                 
                  /*   ij++; */                ij=1;
                  /* } */                for(j=3; j <=ncovmodel-nagesqr; j++){
                  /* else */                  if(ij <=cptcovage) { /* Bug valgrind */
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                    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,j-2)]);
                fprintf(ficgp,")");                      /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
              }                      ij++;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);                    }
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                  }
              i=i+ncovmodel;                  else
            }                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
          } /* end k */                }
        } /* end k2 */                fprintf(ficgp,")");
      } /* end jk */              }
    } /* end ng */              fprintf(ficgp,")");
  /* avoid: */              if(ng ==2)
    fflush(ficgp);                 fprintf(ficgp," t \"p%d%d\" ", k2,k);
               else /* ng= 3 */
                 fprintf(ficgp," t \"i%d%d\" ", k2,k);
             }else{ /* end ng <> 1 */
               if( k !=k2) /* logit p11 is hard to draw */
                 fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
             }
             if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
               fprintf(ficgp,",");
             if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
               fprintf(ficgp,",");
             i=i+ncovmodel;
           } /* end k */
         } /* end k2 */
         fprintf(ficgp,"\n set out\n");
       } /* end jk */
     } /* end ng */
     /* avoid: */
     fflush(ficgp); 
 }  /* end gnuplot */  }  /* end gnuplot */
   
   
 /*************** Moving average **************/  /*************** Moving average **************/
 int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){  /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
    int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
   int i, cpt, cptcod;     
   int modcovmax =1;     int i, cpt, cptcod;
   int mobilavrange, mob;     int modcovmax =1;
   double age;     int mobilavrange, mob;
      int iage=0;
   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose   
                            a covariate has 2 modalities */     double sum=0.;
   if (cptcovn<1) modcovmax=1; /* At least 1 pass */     double age;
      double *sumnewp, *sumnewm;
   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){     double *agemingood, *agemaxgood; /* Currently identical for all covariates */
     if(mobilav==1) mobilavrange=5; /* default */    
     else mobilavrange=mobilav;    
     for (age=bage; age<=fage; age++)     /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
       for (i=1; i<=nlstate;i++)     /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
         for (cptcod=1;cptcod<=modcovmax;cptcod++)  
           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];     sumnewp = vector(1,ncovcombmax);
     /* We keep the original values on the extreme ages bage, fage and for      sumnewm = vector(1,ncovcombmax);
        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2     agemingood = vector(1,ncovcombmax);  
        we use a 5 terms etc. until the borders are no more concerned.      agemaxgood = vector(1,ncovcombmax);
     */   
     for (mob=3;mob <=mobilavrange;mob=mob+2){     for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){       sumnewm[cptcod]=0.;
         for (i=1; i<=nlstate;i++){       sumnewp[cptcod]=0.;
           for (cptcod=1;cptcod<=modcovmax;cptcod++){       agemingood[cptcod]=0;
             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];       agemaxgood[cptcod]=0;
               for (cpt=1;cpt<=(mob-1)/2;cpt++){     }
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];     if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];    
               }     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;       if(mobilav==1) mobilavrange=5; /* default */
           }       else mobilavrange=mobilav;
         }       for (age=bage; age<=fage; age++)
       }/* end age */         for (i=1; i<=nlstate;i++)
     }/* end mob */           for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
   }else return -1;             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   return 0;       /* We keep the original values on the extreme ages bage, fage and for 
 }/* End movingaverage */          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<=ncovcombmax;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;
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
        /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
        if(invalidvarcomb[cptcod]){
          printf("\nCombination (%d) ignored because no cases \n",cptcod); 
          continue;
        }
   
        agemingood[cptcod]=fage-(mob-1)/2;
        for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
            agemingood[cptcod]=age;
          }else{ /* bad */
            for (i=1; i<=nlstate;i++){
              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
            } /* i */
          } /* end bad */
        }/* age */
        sum=0.;
        for (i=1; i<=nlstate;i++){
          sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
        }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
          /* for (i=1; i<=nlstate;i++){ */
          /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
          /* } /\* i *\/ */
        } /* end bad */
        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
        /* From youngest, finding the oldest wrong */
        agemaxgood[cptcod]=bage+(mob-1)/2;
        for (age=bage+(mob-1)/2; age<=fage; age++){
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
            agemaxgood[cptcod]=age;
          }else{ /* bad */
            for (i=1; i<=nlstate;i++){
              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
            } /* i */
          } /* end bad */
        }/* age */
        sum=0.;
        for (i=1; i<=nlstate;i++){
          sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
        }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
          /* for (i=1; i<=nlstate;i++){ */
          /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
          /* } /\* i *\/ */
        } /* end bad */
                   
        for (age=bage; age<=fage; age++){
          printf("%d %d ", cptcod, (int)age);
          sumnewp[cptcod]=0.;
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewp[cptcod]+=probs[(int)age][i][cptcod];
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
          }
          /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
        }
        /* printf("\n"); */
        /* } */
        /* brutal averaging */
        for (i=1; i<=nlstate;i++){
          for (age=1; age<=bage; age++){
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
            /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
          }        
          for (age=fage; age<=AGESUP; age++){
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
            /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
          }
        } /* end i status */
        for (i=nlstate+1; i<=nlstate+ndeath;i++){
          for (age=1; age<=AGESUP; age++){
            /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
            mobaverage[(int)age][i][cptcod]=0.;
          }
        }
      }/* end cptcod */
      free_vector(sumnewm,1, ncovcombmax);
      free_vector(sumnewp,1, ncovcombmax);
      free_vector(agemaxgood,1, ncovcombmax);
      free_vector(agemingood,1, ncovcombmax);
      return 0;
    }/* End movingaverage */
    
   
 /************** Forecasting ******************/  /************** Forecasting ******************/
 prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){  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     /* proj1, year, month, day of starting projection 
      agemin, agemax range of age       agemin, agemax range of age
      dateprev1 dateprev2 range of dates during which prevalence is computed       dateprev1 dateprev2 range of dates during which prevalence is computed
Line 4430  prevforecast(char fileres[], double anpr Line 6743  prevforecast(char fileres[], double anpr
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    /* double ***mobaverage; */
   char fileresf[FILENAMELENGTH];    char fileresf[FILENAMELENGTH];
   
   agelim=AGESUP;    agelim=AGESUP;
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, 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.
     */
     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
     /*          firstpass, lastpass,  stepm,  weightopt, model); */
     
   strcpy(fileresf,"f");     strcpy(fileresf,"F_"); 
   strcat(fileresf,fileres);    strcat(fileresf,fileresu);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    if((ficresf=fopen(fileresf,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", fileresf);      printf("Problem with forecast resultfile: %s\n", fileresf);
     fprintf(ficlog,"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);    printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    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;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (stepm<=12) stepsize=1;    if (stepm<=12) stepsize=1;
Line 4484  prevforecast(char fileres[], double anpr Line 6795  prevforecast(char fileres[], double anpr
   for(cptcov=1, k=0;cptcov<=i1;cptcov++){    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficresf,"\n#******");        fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                  fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
       fprintf(ficresf,"******\n");        fprintf(ficresf," yearproj age");
       fprintf(ficresf,"# Covariate valuofcovar yearproj age");  
       for(j=1; j<=nlstate+ndeath;j++){         for(j=1; j<=nlstate+ndeath;j++){ 
         for(i=1; i<=nlstate;i++)                                                for(i=1; i<=nlstate;i++)              
           fprintf(ficresf," p%d%d",i,j);            fprintf(ficresf," p%d%d",i,j);
         fprintf(ficresf," p.%d",j);                                  fprintf(ficresf," wp.%d",j);
       }        }
       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
         fprintf(ficresf,"\n");                                  fprintf(ficresf,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);                                     fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
                                   for (agec=fage; agec>=(ageminpar-1); agec--){ 
         for (agec=fage; agec>=(ageminpar-1); agec--){                                           nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);                                           nhstepm = nhstepm/hstepm; 
           nhstepm = nhstepm/hstepm;                                           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                          oldm=oldms;savm=savms;
           oldm=oldms;savm=savms;                                          hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);                                            
                                                   for (h=0; h<=nhstepm; h++){
           for (h=0; h<=nhstepm; h++){                                                  if (h*hstepm/YEARM*stepm ==yearp) {
             if (h*hstepm/YEARM*stepm ==yearp) {  
               fprintf(ficresf,"\n");                fprintf(ficresf,"\n");
               for(j=1;j<=cptcoveff;j++)                 for(j=1;j<=cptcoveff;j++) 
                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);                                                          fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
             }                                                   } 
             for(j=1; j<=nlstate+ndeath;j++) {                                                  for(j=1; j<=nlstate+ndeath;j++) {
               ppij=0.;                                                          ppij=0.;
               for(i=1; i<=nlstate;i++) {                                                          for(i=1; i<=nlstate;i++) {
                 if (mobilav==1)                                                                   if (mobilav==1) 
                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];                                                                          ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                 else {                                                                  else {
                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];                                                                          ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                 }                                                                  }
                 if (h*hstepm/YEARM*stepm== yearp) {                                                                  if (h*hstepm/YEARM*stepm== yearp) {
                   fprintf(ficresf," %.3f", p3mat[i][j][h]);                                                                          fprintf(ficresf," %.3f", p3mat[i][j][h]);
                 }                                                                  }
               } /* end i */                                                          } /* end i */
               if (h*hstepm/YEARM*stepm==yearp) {                                                          if (h*hstepm/YEARM*stepm==yearp) {
                 fprintf(ficresf," %.3f", ppij);                                                                  fprintf(ficresf," %.3f", ppij);
               }                                                          }
             }/* end j */                                                  }/* end j */
           } /* end h */                                          } /* end h */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */                                  } /* end agec */
       } /* end yearp */        } /* end yearp */
     } /* end cptcod */      } /* end cptcod */
   } /* end  cptcov */    } /* end  cptcov */
                  
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   
   fclose(ficresf);    fclose(ficresf);
     printf("End of Computing forecasting \n");
     fprintf(ficlog,"End of Computing forecasting\n");
   
 }  }
   
   /* /\************** Back Forecasting ******************\/ */
   /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
   /*   /\* back1, year, month, day of starting backection  */
   /*      agemin, agemax range of age */
   /*      dateprev1 dateprev2 range of dates during which prevalence is computed */
   /*      anback2 year of en of backection (same day and month as back1). */
   /*   *\/ */
   /*   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 fileresfb[FILENAMELENGTH]; */
           
   /*   agelim=AGESUP; */
   /*   /\* 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. */
   /*   *\/ */
   /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
   /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */
   /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
           
   /*   strcpy(fileresfb,"FB_");  */
   /*   strcat(fileresfb,fileresu); */
   /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
   /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */
   /*     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
   /*   } */
   /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
   /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
           
   /*   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(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */
     
   /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\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(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
   /*       for(j=1;j<=cptcoveff;j++) { */
   /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
   /*       } */
   /*       fprintf(ficresfb," yearbproj age"); */
   /*       for(j=1; j<=nlstate+ndeath;j++){  */
   /*                              for(i=1; i<=nlstate;i++)               */
   /*           fprintf(ficresfb," p%d%d",i,j); */
   /*                              fprintf(ficresfb," p.%d",j); */
   /*       } */
   /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */
   /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */
   /*                              fprintf(ficresfb,"\n"); */
   /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+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; */
   /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */
   /*                                      for (h=0; h<=nhstepm; h++){ */
   /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */
   /*               fprintf(ficresfb,"\n"); */
   /*               for(j=1;j<=cptcoveff;j++)  */
   /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
   /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+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(ficresfb," %.3f", p3mat[i][j][h]); */
   /*                                                              } */
   /*                                                      } /\* end i *\/ */
   /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */
   /*                                                              fprintf(ficresfb," %.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(ficresfb); */
   /*   printf("End of Computing Back forecasting \n"); */
   /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */
           
   /* } */
   
 /************** Forecasting *****not tested NB*************/  /************** Forecasting *****not tested NB*************/
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  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 cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   int *popage;    int *popage;
   double calagedatem, agelim, kk1, kk2;    double calagedatem, agelim, kk1, kk2;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat,***tabpop,***tabpopprev;    double ***p3mat,***tabpop,***tabpopprev;
   double ***mobaverage;    /* double ***mobaverage; */
   char filerespop[FILENAMELENGTH];    char filerespop[FILENAMELENGTH];
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
Line 4560  populforecast(char fileres[], double anp Line 7000  populforecast(char fileres[], double anp
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       
       
   strcpy(filerespop,"pop");     strcpy(filerespop,"POP_"); 
   strcat(filerespop,fileres);    strcat(filerespop,fileresu);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", filerespop);      printf("Problem with forecast resultfile: %s\n", filerespop);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
Line 4571  populforecast(char fileres[], double anp Line 7011  populforecast(char fileres[], double anp
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   if (mobilav!=0) {    /* if (mobilav!=0) { */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){    /*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ */
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);    /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
       printf(" Error in movingaverage mobilav=%d\n",mobilav);    /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
     }    /*   } */
   }    /* } */
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (stepm<=12) stepsize=1;    if (stepm<=12) stepsize=1;
Line 4586  populforecast(char fileres[], double anp Line 7026  populforecast(char fileres[], double anp
       
   hstepm=1;    hstepm=1;
   hstepm=hstepm/stepm;     hstepm=hstepm/stepm; 
             
   if (popforecast==1) {    if (popforecast==1) {
     if((ficpop=fopen(popfile,"r"))==NULL) {      if((ficpop=fopen(popfile,"r"))==NULL) {
       printf("Problem with population file : %s\n",popfile);exit(0);        printf("Problem with population file : %s\n",popfile);exit(0);
Line 4598  populforecast(char fileres[], double anp Line 7038  populforecast(char fileres[], double anp
           
     i=1;         i=1;   
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
          
     imx=i;      imx=i;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   }    }
     
   for(cptcov=1,k=0;cptcov<=i2;cptcov++){    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficrespop,"\n#******");        fprintf(ficrespop,"\n#******");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
       fprintf(ficrespop,"******\n");        fprintf(ficrespop,"******\n");
       fprintf(ficrespop,"# Age");        fprintf(ficrespop,"# Age");
Line 4618  populforecast(char fileres[], double anp Line 7058  populforecast(char fileres[], double anp
       for (cpt=0; cpt<=0;cpt++) {         for (cpt=0; cpt<=0;cpt++) { 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,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--){           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           nhstepm = nhstepm/hstepm;             nhstepm = nhstepm/hstepm; 
                       
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;            oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                     
           for (h=0; h<=nhstepm; h++){            for (h=0; h<=nhstepm; h++){
             if (h==(int) (calagedatem+YEARM*cpt)) {              if (h==(int) (calagedatem+YEARM*cpt)) {
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
Line 4641  populforecast(char fileres[], double anp Line 7081  populforecast(char fileres[], double anp
               }                }
               if (h==(int)(calagedatem+12*cpt)){                if (h==(int)(calagedatem+12*cpt)){
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                   /*fprintf(ficrespop," %.3f", kk1);                  /*fprintf(ficrespop," %.3f", kk1);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/                    if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
               }                }
             }              }
             for(i=1; i<=nlstate;i++){              for(i=1; i<=nlstate;i++){
               kk1=0.;                kk1=0.;
                 for(j=1; j<=nlstate;j++){                for(j=1; j<=nlstate;j++){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                   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)];                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++)               if (h==(int)(calagedatem+12*cpt))
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);                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);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }          }
       }        }
          
   /******/        /******/
         
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,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--){           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
Line 4686  populforecast(char fileres[], double anp Line 7127  populforecast(char fileres[], double anp
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }          }
       }        }
    }       } 
   }    }
      
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
     
   if (popforecast==1) {    if (popforecast==1) {
     free_ivector(popage,0,AGESUP);      free_ivector(popage,0,AGESUP);
     free_vector(popeffectif,0,AGESUP);      free_vector(popeffectif,0,AGESUP);
Line 4700  populforecast(char fileres[], double anp Line 7141  populforecast(char fileres[], double anp
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficrespop);    fclose(ficrespop);
 } /* End of popforecast */  } /* End of popforecast */
    
 int fileappend(FILE *fichier, char *optionfich)  int fileappend(FILE *fichier, char *optionfich)
 {  {
   if((fichier=fopen(optionfich,"a"))==NULL) {    if((fichier=fopen(optionfich,"a"))==NULL) {
Line 4841  double gompertz(double x[]) Line 7282  double gompertz(double x[])
   double A,B,L=0.0,sump=0.,num=0.;    double A,B,L=0.0,sump=0.,num=0.;
   int i,n=0; /* n is the size of the sample */    int i,n=0; /* n is the size of the sample */
   
   for (i=0;i<=imx-1 ; i++) {    for (i=1;i<=imx ; i++) {
     sump=sump+weight[i];      sump=sump+weight[i];
     /*    sump=sump+1;*/      /*    sump=sump+1;*/
     num=num+1;      num=num+1;
Line 4914  double gompertz_f(const gsl_vector *v, v Line 7355  double gompertz_f(const gsl_vector *v, v
 #endif  #endif
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
 void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \  void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,  double p[],double **matcov,double agemortsup){                    int imx,  double p[],double **matcov,double agemortsup){
   int i,k;    int i,k;
Line 4923  void printinghtmlmort(char fileres[], ch Line 7364  void printinghtmlmort(char fileres[], ch
   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);    fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
   for (i=1;i<=2;i++)     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," 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,"<br><br><img src=\"graphmort.svg\">");
   fprintf(fichtm,"</ul>");    fprintf(fichtm,"</ul>");
   
 fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");  fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
Line 4938  fprintf(fichtm,"<ul><li><h4>Life table</ Line 7379  fprintf(fichtm,"<ul><li><h4>Life table</
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   
Line 4952  void printinggnuplotmort(char fileres[], Line 7393  void printinggnuplotmort(char fileres[],
   
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
   fprintf(ficgp,"set out \"graphmort.png\"\n ");     fprintf(ficgp,"set out \"graphmort.svg\"\n "); 
   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \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 ter svg size 640, 480\n set log y\n"); 
   /* fprintf(ficgp, "set size 0.65,0.65\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);    fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
Line 4966  int readdata(char datafile[], int firsto Line 7407  int readdata(char datafile[], int firsto
   /*-------- data file ----------*/    /*-------- data file ----------*/
   FILE *fic;    FILE *fic;
   char dummy[]="                         ";    char dummy[]="                         ";
   int i=0, j=0, n=0;    int i=0, j=0, n=0, iv=0;
     int lstra;
   int linei, month, year,iout;    int linei, month, year,iout;
   char line[MAXLINE], linetmp[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char stra[MAXLINE], strb[MAXLINE];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
   int lstra;  
   
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem while opening datafile: %s\n", datafile);return 1;      printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;      fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
   }    }
   
   i=1;    i=1;
Line 4998  int readdata(char datafile[], int firsto Line 7440  int readdata(char datafile[], int firsto
     }      }
     trimbb(linetmp,line); /* Trims multiple blanks in line */      trimbb(linetmp,line); /* Trims multiple blanks in line */
     strcpy(line, linetmp);      strcpy(line, linetmp);
         
       /* Loops on waves */
     for (j=maxwav;j>=1;j--){      for (j=maxwav;j>=1;j--){
         for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
           cutv(stra, strb, line, ' '); 
           if(strb[0]=='.') { /* Missing value */
             lval=-1;
             cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
             if(isalpha(strb[1])) { /* .m or .d Really Missing value */
               printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
               fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
               return 1;
             }
           }else{
             errno=0;
             /* what_kind_of_number(strb); */
             dval=strtod(strb,&endptr); 
             /* if( strb[0]=='\0' || (*endptr != '\0')){ */
             /* if(strb != endptr && *endptr == '\0') */
             /*    dval=dlval; */
             /* 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 the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
               fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
               return 1;
             }
             cotqvar[j][iv][i]=dval; 
           }
           strcpy(line,stra);
         }/* end loop ntqv */
         
         for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
           cutv(stra, strb, line, ' '); 
           if(strb[0]=='.') { /* Missing value */
             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 the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
               fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);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;
           }
           cotvar[j][iv][i]=(double)(lval);
           strcpy(line,stra);
         }/* end loop ntv */
         
         /* Statuses  at wave */
       cutv(stra, strb, line, ' ');         cutv(stra, strb, line, ' '); 
       if(strb[0]=='.') { /* Missing status */        if(strb[0]=='.') { /* Missing value */
         lval=-1;          lval=-1;
       }else{        }else{
         errno=0;          errno=0;
         lval=strtol(strb,&endptr,10);           lval=strtol(strb,&endptr,10); 
       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/          /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){          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);            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);            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;            return 1;
         }          }
       }        }
         
       s[j][i]=lval;        s[j][i]=lval;
               
         /* Date of Interview */
       strcpy(line,stra);        strcpy(line,stra);
       cutv(stra, strb,line,' ');        cutv(stra, strb,line,' ');
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){        if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }        }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){        else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;          month=99;
         year=9999;          year=9999;
       }else{        }else{
Line 5031  int readdata(char datafile[], int firsto Line 7543  int readdata(char datafile[], int firsto
       anint[j][i]= (double) year;         anint[j][i]= (double) year; 
       mint[j][i]= (double)month;         mint[j][i]= (double)month; 
       strcpy(line,stra);        strcpy(line,stra);
     } /* ENd Waves */      } /* End loop on waves */
           
       /* Date of death */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
     else  if(iout=sscanf(strb,"%s.",dummy) != 0){      else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
       month=99;        month=99;
       year=9999;        year=9999;
     }else{      }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);        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);        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;        return 1;
     }      }
     andc[i]=(double) year;       andc[i]=(double) year; 
     moisdc[i]=(double) month;       moisdc[i]=(double) month; 
     strcpy(line,stra);      strcpy(line,stra);
           
       /* Date of birth */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
     else  if(iout=sscanf(strb,"%s.", dummy) != 0){      else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
       month=99;        month=99;
       year=9999;        year=9999;
     }else{      }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);        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);        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;        return 1;
     }      }
     if (year==9999) {      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);        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);        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;        return 1;
         
     }      }
     annais[i]=(double)(year);      annais[i]=(double)(year);
     moisnais[i]=(double)(month);       moisnais[i]=(double)(month); 
     strcpy(line,stra);      strcpy(line,stra);
           
       /* Sample weight */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     errno=0;      errno=0;
     dval=strtod(strb,&endptr);       dval=strtod(strb,&endptr); 
Line 5081  int readdata(char datafile[], int firsto Line 7596  int readdata(char datafile[], int firsto
     weight[i]=dval;       weight[i]=dval; 
     strcpy(line,stra);      strcpy(line,stra);
           
       for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing value */
           lval=-1;
         }else{
           errno=0;
           /* what_kind_of_number(strb); */
           dval=strtod(strb,&endptr);
           /* if(strb != endptr && *endptr == '\0') */
           /*   dval=dlval; */
           /* 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 the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
             return 1;
           }
           coqvar[iv][i]=dval; 
           covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */ 
         }
         strcpy(line,stra);
       }/* end loop nqv */
       
       /* Covariate values */
     for (j=ncovcol;j>=1;j--){      for (j=ncovcol;j>=1;j--){
       cutv(stra, strb,line,' ');         cutv(stra, strb,line,' '); 
       if(strb[0]=='.') { /* Missing status */        if(strb[0]=='.') { /* Missing covariate value */
         lval=-1;          lval=-1;
       }else{        }else{
         errno=0;          errno=0;
Line 5098  int readdata(char datafile[], int firsto Line 7636  int readdata(char datafile[], int firsto
         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \          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 \   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 the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
  For example, for multinomial values like 1, 2 and 3,\n \   For example, for multinomial values like 1, 2 and 3,\n                 \
  build V1=0 V2=0 for the reference value (1),\n \   build V1=0 V2=0 for the reference value (1),\n                         \
         V1=1 V2=0 for (2) \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 \   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 \   output of IMaCh is often meaningless.\n                                \
  Exiting.\n",lval,linei, i,line,j);   Exiting.\n",lval,linei, i,line,j);
         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \          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 \   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 the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
  For example, for multinomial values like 1, 2 and 3,\n \   For example, for multinomial values like 1, 2 and 3,\n                 \
  build V1=0 V2=0 for the reference value (1),\n \   build V1=0 V2=0 for the reference value (1),\n                         \
         V1=1 V2=0 for (2) \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 \   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 \   output of IMaCh is often meaningless.\n                                \
  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);   Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
         return 1;          return 1;
       }        }
Line 5119  int readdata(char datafile[], int firsto Line 7657  int readdata(char datafile[], int firsto
       strcpy(line,stra);        strcpy(line,stra);
     }        }  
     lstra=strlen(stra);      lstra=strlen(stra);
            
     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */      if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
       stratrunc = &(stra[lstra-9]);        stratrunc = &(stra[lstra-9]);
       num[i]=atol(stratrunc);        num[i]=atol(stratrunc);
Line 5131  int readdata(char datafile[], int firsto Line 7669  int readdata(char datafile[], int firsto
           
     i=i+1;      i=i+1;
   } /* End loop reading  data */    } /* End loop reading  data */
     
   *imax=i-1; /* Number of individuals */    *imax=i-1; /* Number of individuals */
   fclose(fic);    fclose(fic);
      
   return (0);    return (0);
   /* endread: */    /* endread: */
     printf("Exiting readdata: ");    printf("Exiting readdata: ");
     fclose(fic);    fclose(fic);
     return (1);    return (1);
   
   
   
 }  }
   
 void removespace(char *str) {  void removespace(char *str) {
   char *p1 = str, *p2 = str;    char *p1 = str, *p2 = str;
   do    do
     while (*p2 == ' ')      while (*p2 == ' ')
       p2++;        p2++;
   while (*p1++ = *p2++);    while (*p1++ == *p2++);
 }  }
   
 int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:  int decodemodel ( char model[], int lastobs)
    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age   /**< This routine decode the model and returns:
    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8          * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
    * - cptcovn or number of covariates k of the models excluding age*products =6          * - nagesqr = 1 if age*age in the model, otherwise 0.
    * - cptcovage number of covariates with age*products =2          * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
    * - cptcovs number of simple covariates          * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
    * - 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          * - cptcovage number of covariates with age*products =2
    *     which is a new column after the 9 (ncovcol) variables.           * - cptcovs number of simple covariates
    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual          * - 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
    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage          *     which is a new column after the 9 (ncovcol) variables. 
    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.          * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .          * - 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 i, j, k, ks;
   int  j1, k1, k2;    int  j1, k1, k2;
   char modelsav[80];    char modelsav[80];
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
     char *strpt;
   
   /*removespace(model);*/    /*removespace(model);*/
   if (strlen(model) >1){ /* If there is at least 1 covariate */    if (strlen(model) >1){ /* If there is at least 1 covariate */
     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;      j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
     j=nbocc(model,'+'); /**< j=Number of '+' */  
     j1=nbocc(model,'*'); /**< j1=Number of '*' */  
     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */  
     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/  
                   /* including age products which are counted in cptcovage.  
                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */  
     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */  
     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */  
     strcpy(modelsav,model);   
     if (strstr(model,"AGE") !=0){      if (strstr(model,"AGE") !=0){
       printf("Error. AGE must be in lower case 'age' model=%s ",model);        printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);        fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
       return 1;        return 1;
     }      }
     if (strstr(model,"v") !=0){      if (strstr(model,"v") !=0){
Line 5193  int decodemodel ( char model[], int last Line 7723  int decodemodel ( char model[], int last
       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);        fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
       return 1;        return 1;
     }      }
           strcpy(modelsav,model); 
     /*   Design      if ((strpt=strstr(model,"age*age")) !=0){
      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight        printf(" strpt=%s, model=%s\n",strpt, model);
      *  <          ncovcol=8                >        if(strpt != model){
      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8          printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
      *   k=  1    2      3       4     5       6      7        8   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8   corresponding column of parameters.\n",model);
      *  covar[k,i], value of kth covariate if not including age for individual i:          fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8   corresponding column of parameters.\n",model); fflush(ficlog);
      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and           return 1;
      *  Tage[++cptcovage]=k        }
      *       if products, new covar are created after ncovcol with k1        nagesqr=1;
      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11        if (strstr(model,"+age*age") !=0)
      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product          substrchaine(modelsav, model, "+age*age");
      *  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        else if (strstr(model,"age*age+") !=0)
      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];          substrchaine(modelsav, model, "age*age+");
      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted        else 
      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11          substrchaine(modelsav, model, "age*age");
      *  <          ncovcol=8                >      }else
      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2        nagesqr=0;
      *          k=  1    2      3       4     5       6      7        8    9   10   11  12      if (strlen(modelsav) >1){
      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8        j=nbocc(modelsav,'+'); /**< j=Number of '+' */
      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}        j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
      * p Tprod[1]@2={                         6, 5}        cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
      *p Tvard[1][1]@4= {7, 8, 5, 6}        cptcovt= j+1; /* Number of total covariates in the model, not including
      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8                          * cst, age and age*age 
      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];                       * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
      *How to reorganize?        /* including age products which are counted in cptcovage.
      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age         * but the covariates which are products must be treated 
      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}         * separately: ncovn=4- 2=2 (V1+V3). */
      *       {2,   1,     4,      8,    5,      6,     3,       7}        cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
      * Struct []        cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
      */        
         
     /* This loop fills the array Tvar from the string 'model'.*/        /*   Design
     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */         *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */         *  <          ncovcol=8                >
     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */         * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */         *   k=  1    2      3       4     5       6      7        8
     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */         *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
     /*  k=1 Tvar[1]=2 (from V2) */         *  covar[k,i], value of kth covariate if not including age for individual i:
     /*  k=5 Tvar[5] */         *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
     /* for (k=1; k<=cptcovn;k++) { */         *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */         *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
     /*  } */         *  Tage[++cptcovage]=k
     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */         *       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
      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */         *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
     for(k=cptcovt; k>=1;k--) /**< Number of covariates */         *  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 not including constant and age, neither age*age*/
         Tvar[k]=0;          Tvar[k]=0;
     cptcovage=0;        cptcovage=0;
     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */                                            modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */          if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
       /*scanf("%d",i);*/          /*scanf("%d",i);*/
       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */          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 */            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 */            if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
           /* covar is not filled and then is empty */              /* covar is not filled and then is empty */
           cptcovprod--;              cptcovprod--;
           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */              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 */              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 */              Typevar[k]=1;  /* 1 for age product */
           Tage[cptcovage]=k;  /* Tage[1] = 4 */              cptcovage++; /* Sums the number of covariates which include age as a product */
           /*printf("stre=%s ", stre);*/              Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
         } else if (strcmp(strd,"age")==0) { /* or age*Vn */              /*printf("stre=%s ", stre);*/
           cptcovprod--;            } else if (strcmp(strd,"age")==0) { /* or age*Vn */
           cutl(stre,strb,strc,'V');              cptcovprod--;
           Tvar[k]=atoi(stre);              cutl(stre,strb,strc,'V');
           cptcovage++;              Tvar[k]=atoi(stre);
           Tage[cptcovage]=k;              Typevar[k]=1;  /* 1 for age product */
         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/              cptcovage++;
           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */              Tage[cptcovage]=k;
           cptcovn++;            } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
           cptcovprodnoage++;k1++;              /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/              cptcovn++;
           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but              cptcovprodnoage++;k1++;
                                   because this model-covariate is a construction we invent a new column              cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
                                   ncovcol + k1              Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2                                     because this model-covariate is a construction we invent a new column
                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */                                     which is after existing variables ncovcol+nqv+ntv+nqtv + k1
           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/              Typevar[k]=2;  /* 2 for double fixed dummy covariates */
           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/              cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
           k2=k2+2;              Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */              Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */              Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
           for (i=1; i<=lastobs;i++){              k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
             /* Computes the new covariate which is a product of              /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */              /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];              /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
           }              /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
         } /* End age is not in the model */              for (i=1; i<=lastobs;i++){
       } /* End if model includes a product */                /* Computes the new covariate which is a product of
       else { /* no more sum */                   covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
        /*  scanf("%d",i);*/              }
         cutl(strd,strc,strb,'V');            } /* End age is not in the model */
         ks++; /**< Number of simple covariates */          } /* End if model includes a product */
         cptcovn++;          else { /* no more sum */
         Tvar[k]=atoi(strd);            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
       }            /*  scanf("%d",i);*/
       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */             cutl(strd,strc,strb,'V');
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            ks++; /**< Number of simple covariates*/
         scanf("%d",i);*/            cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
     } /* end of loop + */            Tvar[k]=atoi(strd);
   } /* end model */            Typevar[k]=0;  /* 0 for simple covariates */
           }
           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.    /*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*/      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("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
   printf("cptcovprod=%d ", cptcovprod);       printf("cptcovprod=%d ", cptcovprod);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);       fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
        scanf("%d ",i);*/
   scanf("%d ",i);*/  
   
   /* Decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
      of variable (dummy vs quantitative, fixed vs time varying) is behind */
   /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1  = 5 possible variables data: 2 fixed 3, varying
      model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
      k =           1    2   3     4       5       6      7      8        9
      Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5
      Typevar[k]=   0    0   0     2       1       0      2      1        1
      Fixed[Tvar[k]]1    1   1     1       2       0      1      2        3
      Dummy[Tvar[k]]1    0   0     0       2       1      1      2        3
   */  
   /* Dispatching between quantitative and time varying covariates */
     /* If Tvar[k] >ncovcol it is a product */
     /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
           /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
     for(k=1, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
       if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */
         Fixed[Tvar[k]]= 0;
         Dummy[Tvar[k]]= 0;
         ncoveff++;
       }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/
         Fixed[Tvar[k]]= 0;
         Dummy[Tvar[k]]= 1;
         nqfveff++;  /* Only simple fixed quantitative variable */
       }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){
         Fixed[Tvar[k]]= 1;
         Dummy[Tvar[k]]= 0;
         ntveff++; /* Only simple time varying dummy variable */
       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
         if( Typevar[k]==0){
           Fixed[Tvar[k]]= 1;
           Dummy[Tvar[k]]= 1;
           nqtveff++;/* Only simple time varying quantitative variable */
         }
       }else if (Typevar[k] == 2) {
         for(k1=1; k1 <= cptcovprodnoage; k1++){
           if(Tvard[k1][1] <=ncovcol){
             if(Tvard[k1][2] <=ncovcol){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 0;
             }else if(Tvard[k1][2] <=ncovcol+nqv){
               Fixed[Tvar[k]]= 0;
               Dummy[Tvar[k]]= 1;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 0;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 1;
             } 
           }else if(Tvard[k1][1] <=ncovcol+nqv){
             if(Tvard[k1][2] <=ncovcol){
               Fixed[Tvar[k]]= 0;
               Dummy[Tvar[k]]= 1;
             }else if(Tvard[k1][2] <=ncovcol+nqv){
               Fixed[Tvar[k]]= 0;
               Dummy[Tvar[k]]= 1;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 1;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 1;
             } 
           }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
             if(Tvard[k1][2] <=ncovcol){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 1;
             }else if(Tvard[k1][2] <=ncovcol+nqv){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 1;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 0;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 1;
             } 
           }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
             if(Tvard[k1][2] <=ncovcol){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 1;
             }else if(Tvard[k1][2] <=ncovcol+nqv){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 1;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 1;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
               Fixed[Tvar[k]]= 1;
               Dummy[Tvar[k]]= 1;
             } 
           }else{
             printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
             fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
           }
         } /* end k1 */
       }else{
         printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
         fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
       }
       printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[Tvar[k]],Dummy[Tvar[k]]);
       fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[Tvar[k]],Dummy[Tvar[k]]);
     }
     printf("Model=%s\n\
   Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
   Fixed[Tvar[k]] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product \n\
   Dummy[Tvar[k]] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
   
     printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
     fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
   return (0); /* with covar[new additional covariate if product] and Tage if age */     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
   /*endread:*/    /*endread:*/
     printf("Exiting decodemodel: ");    printf("Exiting decodemodel: ");
     return (1);    return (1);
 }  }
   
 calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
 {  {
   int i, m;    int i, m;
     int firstone=0;
     
   for (i=1; i<=imx; i++) {    for (i=1; i<=imx; i++) {
     for(m=2; (m<= maxwav); m++) {      for(m=2; (m<= maxwav); m++) {
       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
         anint[m][i]=9999;          anint[m][i]=9999;
         s[m][i]=-1;          if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
             s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
         *nberr++;          *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\n",(int)moisdc[i],(int)andc[i],num[i],i);          if(firstone == 0){
         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);            firstone=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 can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
           }
           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 can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
         s[m][i]=-1;          s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
         *nberr++;          (*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]);           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]);           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 */          s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
Line 5349  calandcheckages(int imx, int maxwav, dou Line 8034  calandcheckages(int imx, int maxwav, dou
   for (i=1; i<=imx; i++)  {    for (i=1; i<=imx; i++)  {
     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
     for(m=firstpass; (m<= lastpass); m++){      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] >0  || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
         if (s[m][i] >= nlstate+1) {          if (s[m][i] >= nlstate+1) {
           if(agedc[i]>0)            if(agedc[i]>0){
             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)              if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
               agev[m][i]=agedc[i];                agev[m][i]=agedc[i];
           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/                /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
             else {              }else {
               if ((int)andc[i]!=9999){                if ((int)andc[i]!=9999){
                 nbwarn++;                  nbwarn++;
                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);                  printf("Warning negative age at death: %ld line:%d\n",num[i],i);
Line 5363  calandcheckages(int imx, int maxwav, dou Line 8048  calandcheckages(int imx, int maxwav, dou
                 agev[m][i]=-1;                  agev[m][i]=-1;
               }                }
             }              }
         }            } /* agedc > 0 */
           } /* end if */
         else if(s[m][i] !=9){ /* Standard case, age in fractional          else if(s[m][i] !=9){ /* Standard case, age in fractional
                                  years but with the precision of a month */                                   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]);            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
Line 5379  calandcheckages(int imx, int maxwav, dou Line 8065  calandcheckages(int imx, int maxwav, dou
           }            }
           /*agev[m][i]=anint[m][i]-annais[i];*/            /*agev[m][i]=anint[m][i]-annais[i];*/
           /*     agev[m][i] = age[i]+2*m;*/            /*     agev[m][i] = age[i]+2*m;*/
         }          } /* en if 9*/
         else { /* =9 */          else { /* =9 */
             /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
           agev[m][i]=1;            agev[m][i]=1;
           s[m][i]=-1;            s[m][i]=-1;
         }          }
       }        }
       else /*= 0 Unknown */        else if(s[m][i]==0) /*= 0 Unknown */
         agev[m][i]=1;          agev[m][i]=1;
     }        else{
               printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
           fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
           agev[m][i]=0;
         }
       } /* End for lastpass */
   }    }
       
   for (i=1; i<=imx; i++)  {    for (i=1; i<=imx; i++)  {
     for(m=firstpass; (m<=lastpass); m++){      for(m=firstpass; (m<=lastpass); m++){
       if (s[m][i] > (nlstate+ndeath)) {        if (s[m][i] > (nlstate+ndeath)) {
         *nberr++;          (*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);               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);               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;          return 1;
Line 5418  calandcheckages(int imx, int maxwav, dou Line 8110  calandcheckages(int imx, int maxwav, dou
     return (1);      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, double ftolpl, int *ncvyearp){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     /* double ftolpl = 1.e-10; */
     double age, agebase, agelim;
     double tot;
   
     strcpy(filerespl,"PL_");
     strcat(filerespl,fileresu);
     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. Precision given by ftolpl=%g \n", ftolpl);
     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,ncoveff);
     if (cptcovn < 1){i1=1;}
   
     for(k=1; k<=i1;k++){
     /* 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,"#******");
       printf("#******");
       fprintf(ficlog,"#******");
       for(j=1;j<=nqfveff;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");
                   if(invalidvarcomb[k]){
                                                   printf("\nCombination (%d) ignored because no cases \n",k); 
                                                   fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k); 
                                                   fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k); 
                                                   continue;
                   }
   
       fprintf(ficrespl,"#Age ");
       for(j=1;j<=nqfveff;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,"Total Years_to_converge\n");
           
       for (age=agebase; age<=agelim; age++){
         /* for (age=agebase; age<=agebase; age++){ */
         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
         fprintf(ficrespl,"%.0f ",age );
         for(j=1;j<=nqfveff;j++)
                                                           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         tot=0.;
         for(i=1; i<=nlstate;i++){
                                                           tot +=  prlim[i][i];
                                                           fprintf(ficrespl," %.5f", prlim[i][i]);
         }
         fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
       } /* Age */
       /* was end of cptcod */
     } /* cptcov */
     return 0;
   }
   
   int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
           /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
           
           /* Computes the back prevalence limit  for any combination      of covariate values 
      * at any age between ageminpar and agemaxpar
            */
     int i, j, k, i1 ;
     /* double ftolpl = 1.e-10; */
     double age, agebase, agelim;
     double tot;
     /* double ***mobaverage; */
     /* double      **dnewm, **doldm, **dsavm;  /\* for use *\/ */
   
     strcpy(fileresplb,"PLB_");
     strcat(fileresplb,fileresu);
     if((ficresplb=fopen(fileresplb,"w"))==NULL) {
       printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
       fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
     }
     printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
     fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
     pstamp(ficresplb);
     fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
     fprintf(ficresplb,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
     fprintf(ficresplb,"\n");
     
     
     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
     
     agebase=ageminpar;
     agelim=agemaxpar;
     
     
     i1=pow(2,nqfveff);
     if (cptcovn < 1){i1=1;}
   
           for(k=1; k<=i1;k++){ 
     /* 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(ficresplb,"#******");
       printf("#******");
       fprintf(ficlog,"#******");
       for(j=1;j<=nqfveff;j++) {
         fprintf(ficresplb," 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(ficresplb,"******\n");
       printf("******\n");
       fprintf(ficlog,"******\n");
                   if(invalidvarcomb[k]){
                                                   printf("\nCombination (%d) ignored because no cases \n",k); 
                                                   fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k); 
                                                   fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k); 
                                                   continue;
                   }
       
       fprintf(ficresplb,"#Age ");
       for(j=1;j<=nqfveff;j++) {
         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
       fprintf(ficresplb,"Total Years_to_converge\n");
       
       
       for (age=agebase; age<=agelim; age++){
         /* for (age=agebase; age<=agebase; age++){ */
         if(mobilavproj > 0){
           /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
           /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
                                   bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
         }else if (mobilavproj == 0){
                                   printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
                                   fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
                                   exit(1);
         }else{
                                   /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
                                   bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
         }
         fprintf(ficresplb,"%.0f ",age );
         for(j=1;j<=nqfveff;j++)
                                   fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         tot=0.;
         for(i=1; i<=nlstate;i++){
                                   tot +=  bprlim[i][i];
                                   fprintf(ficresplb," %.5f", bprlim[i][i]);
         }
         fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
       } /* Age */
       /* was end of cptcod */
     } /* cptcov */
     
     /* hBijx(p, bage, fage); */
     /* fclose(ficrespijb); */
     
     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,fileresu);
       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,nqfveff);
                   /* 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,nqfveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=nqfveff;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;
   }
    
    int hBijx(double *p, int bage, int fage, double ***prevacurrent){
       /*------------- h Bij x at various ages ------------*/
   
     int stepsize;
     /* int agelim; */
           int ageminl;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
           
     double agedeb;
     double ***p3mat;
           
     strcpy(filerespijb,"PIJB_");  strcat(filerespijb,fileresu);
     if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
       printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
       fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
     }
     printf("Computing pij back: result on file '%s' \n", filerespijb);
     fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
     
     /* agelim=AGESUP; */
     ageminl=30;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
     
     /* hstepm=1;   aff par mois*/
     pstamp(ficrespijb);
     fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
     i1= pow(2,nqfveff);
     /* 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,nqfveff); k++){
       fprintf(ficrespijb,"\n#****** ");
       for(j=1;j<=nqfveff;j++)
         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       fprintf(ficrespijb,"******\n");
       if(invalidvarcomb[k]){
         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
         continue;
       }
       
       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
         
         /*          nhstepm=nhstepm*YEARM; aff par mois*/
         
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         /* oldm=oldms;savm=savms; */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
         fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
         for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespijb," %1d-%1d",i,j);
         fprintf(ficrespijb,"\n");
         for (h=0; h<=nhstepm; h++){
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
           /* fprintf(ficrespijb,"%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(ficrespijb," %.5f", p3mat[i][j][h]);
           fprintf(ficrespijb,"\n");
         }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespijb,"\n");
       }
       /*}*/
     }
     return 0;
    } /*  hBijx */
   
   
 /***********************************************/  /***********************************************/
 /**************** Main Program *****************/  /**************** Main Program *****************/
Line 5434  int main(int argc, char *argv[]) Line 8656  int main(int argc, char *argv[])
 #endif  #endif
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    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 i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
     int ncvyear=0; /* Number of years needed for the period prevalence to converge */
   int jj, ll, li, lj, lk;    int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
     int num_filled;
   int itimes;    int itimes;
   int NDIM=2;    int NDIM=2;
   int vpopbased=0;    int vpopbased=0;
Line 5445  int main(int argc, char *argv[]) Line 8668  int main(int argc, char *argv[])
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */    /* FILE *ficgp;*/ /*Gnuplot File */
   struct stat info;    struct stat info;
   double agedeb;    double agedeb=0.;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
     double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
     double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
   
   double fret;    double fret;
   double dum; /* Dummy variable */    double dum=0.; /* Dummy variable */
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    /* double ***mobaverage; */
   
   char line[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
     char model[MAXLINE], modeltemp[MAXLINE];
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
   int c,  h , cpt;    int c,  h , cpt, c2;
   int jl;    int jl=0;
   int i1, j1, jk, stepsize;    int i1, j1, jk, stepsize=0;
     int count=0;
   
   int *tab;     int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int backcast=0;
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm, nhstepm;    int hstepm=0, nhstepm=0;
   int agemortsup;    int agemortsup;
   float  sumlpop=0.;    float  sumlpop=0.;
   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;    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 jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
   double bage=0, fage=110, age, agelim, agebase;    double bage=0, fage=110., age, agelim=0., agebase=0.;
   double ftolpl=FTOL;    double ftolpl=FTOL;
   double **prlim;    double **prlim;
     double **bprlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters */
   double  *p;    double  *p;
   double **matcov; /* Matrix of covariance */    double **matcov; /* Matrix of covariance */
     double **hess; /* Hessian matrix */
   double ***delti3; /* Scale */    double ***delti3; /* Scale */
   double *delti; /* Scale */    double *delti; /* Scale */
   double ***eij, ***vareij;    double ***eij, ***vareij;
Line 5483  int main(int argc, char *argv[]) Line 8715  int main(int argc, char *argv[])
   double *epj, vepp;    double *epj, vepp;
   
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
   
   double **ximort;    double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
   int *dcwave;    int *dcwave;
Line 5526  int main(int argc, char *argv[]) Line 8760  int main(int argc, char *argv[])
   
   nberr=0; /* Number of errors and warnings */    nberr=0; /* Number of errors and warnings */
   nbwarn=0;    nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
   getcwd(pathcd, size);    getcwd(pathcd, size);
   #endif
   printf("\n%s\n%s",version,fullversion);    syscompilerinfo(0);
     printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
   if(argc <=1){    if(argc <=1){
     printf("\nEnter the parameter file name: ");      printf("\nEnter the parameter file name: ");
     fgets(pathr,FILENAMELENGTH,stdin);      if(!fgets(pathr,FILENAMELENGTH,stdin)){
         printf("ERROR Empty parameter file name\n");
         goto end;
       }
     i=strlen(pathr);      i=strlen(pathr);
     if(pathr[i-1]=='\n')      if(pathr[i-1]=='\n')
       pathr[i-1]='\0';        pathr[i-1]='\0';
     i=strlen(pathr);      i=strlen(pathr);
     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */      if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
       pathr[i-1]='\0';        pathr[i-1]='\0';
    for (tok = pathr; tok != NULL; ){      }
       i=strlen(pathr);
       if( i==0 ){
         printf("ERROR Empty parameter file name\n");
         goto end;
       }
       for (tok = pathr; tok != NULL; ){
       printf("Pathr |%s|\n",pathr);        printf("Pathr |%s|\n",pathr);
       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');        while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
       printf("val= |%s| pathr=%s\n",val,pathr);        printf("val= |%s| pathr=%s\n",val,pathr);
Line 5562  int main(int argc, char *argv[]) Line 8809  int main(int argc, char *argv[])
   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */    /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",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 */    chdir(path); /* Can be a relative path */
   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */    if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
     printf("Current directory %s!\n",pathcd);  #endif
     printf("Current directory %s!\n",pathcd);
   strcpy(command,"mkdir ");    strcpy(command,"mkdir ");
   strcat(command,optionfilefiname);    strcat(command,optionfilefiname);
   if((outcmd=system(command)) != 0){    if((outcmd=system(command)) != 0){
     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);      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); */      /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
     /* fclose(ficlog); */      /* fclose(ficlog); */
 /*     exit(1); */  /*     exit(1); */
Line 5579  int main(int argc, char *argv[]) Line 8831  int main(int argc, char *argv[])
   
   /*-------- arguments in the command line --------*/    /*-------- arguments in the command line --------*/
   
   /* Log file */    /* Main Log file */
   strcat(filelog, optionfilefiname);    strcat(filelog, optionfilefiname);
   strcat(filelog,".log");    /* */    strcat(filelog,".log");    /* */
   if((ficlog=fopen(filelog,"w"))==NULL)    {    if((ficlog=fopen(filelog,"w"))==NULL)    {
Line 5587  int main(int argc, char *argv[]) Line 8839  int main(int argc, char *argv[])
     goto end;      goto end;
   }    }
   fprintf(ficlog,"Log filename:%s\n",filelog);    fprintf(ficlog,"Log filename:%s\n",filelog);
   fprintf(ficlog,"\n%s\n%s",version,fullversion);    fprintf(ficlog,"Version %s %s",version,fullversion);
   fprintf(ficlog,"\nEnter the parameter file name: \n");    fprintf(ficlog,"\nEnter the parameter file name: \n");
   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\    fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
  path=%s \n\   path=%s \n\
Line 5595  int main(int argc, char *argv[]) Line 8847  int main(int argc, char *argv[])
  optionfilext=%s\n\   optionfilext=%s\n\
  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);   optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo(1);
   
   printf("Local time (at start):%s",strstart);    printf("Local time (at start):%s",strstart);
   fprintf(ficlog,"Local time (at start): %s",strstart);    fprintf(ficlog,"Local time (at start): %s",strstart);
   fflush(ficlog);    fflush(ficlog);
Line 5604  int main(int argc, char *argv[]) Line 8858  int main(int argc, char *argv[])
   /* */    /* */
   strcpy(fileres,"r");    strcpy(fileres,"r");
   strcat(fileres, optionfilefiname);    strcat(fileres, optionfilefiname);
     strcat(fileresu, optionfilefiname); /* Without r in front */
   strcat(fileres,".txt");    /* Other files have txt extension */    strcat(fileres,".txt");    /* Other files have txt extension */
     strcat(fileresu,".txt");    /* Other files have txt extension */
   
   /*---------arguments file --------*/    /* Main ---------arguments file --------*/
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));      printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
Line 5619  int main(int argc, char *argv[]) Line 8875  int main(int argc, char *argv[])
   
   
   strcpy(filereso,"o");    strcpy(filereso,"o");
   strcat(filereso,fileres);    strcat(filereso,fileresu);
   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
     printf("Problem with Output resultfile: %s\n", filereso);      printf("Problem with Output resultfile: %s\n", filereso);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
Line 5629  int main(int argc, char *argv[]) Line 8885  int main(int argc, char *argv[])
   
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
   numlinepar=0;    numlinepar=0;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      /* First parameter line */
     fgets(line, MAXLINE, ficpar);    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++;      numlinepar++;
     fputs(line,stdout);      printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
     fputs(line,ficparo);  
     fputs(line,ficlog);  
   }    }
   ungetc(c,ficpar);    /* Second parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      /* If line starts with a # it is a comment */
   numlinepar++;      if (line[0] == '#') {
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);        numlinepar++;
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);        fputs(line,stdout);
   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);        fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                           &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
       if (num_filled != 11) {
         printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
         printf("but line=%s\n",line);
       }
       printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
     }
     /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
     /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
     /* 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]", model)) !=EOF){
       if (num_filled == 0)
               model[0]='\0';
       else 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); */
       printf("model=1+age+%s\n",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); */
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
   fflush(ficlog);    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){    while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
     numlinepar++;      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);      fputs(line, stdout);
     //puts(line);      //puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
Line 5658  int main(int argc, char *argv[]) Line 8992  int main(int argc, char *argv[])
   
         
   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */    covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
     cotvar=ma3x(1,maxwav,1,ntv,1,n);  /**< Time varying covariate */
     cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/    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+v3+v2*v4+v5*age makes cptcovn = 5
      v1+v2*age+v2*v3 makes cptcovn = 3       v1+v2*age+v2*v3 makes cptcovn = 3
   */    */
   if (strlen(model)>1)     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*/      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    else
     ncovmodel=2;      ncovmodel=2; /* Constant and age */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */    nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
   npar= nforce*ncovmodel; /* Number of parameters like aij*/    npar= nforce*ncovmodel; /* Number of parameters like aij*/
   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){    if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
Line 5681  int main(int argc, char *argv[]) Line 9017  int main(int argc, char *argv[])
   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
   if(mle==-1){ /* Print a wizard for help writing covariance matrix */    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      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);       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     fclose (ficparo);      fclose (ficparo);
     fclose (ficlog);      fclose (ficlog);
     goto end;      goto end;
     exit(0);      exit(0);
   }    }  else if(mle==-5) { /* Main Wizard */
   else if(mle==-3) {  
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      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);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
   }      hess=matrix(1,npar,1,npar);
   else{    }  else{ /* Begin of mle != -1 or -5 */
     /* Read guessed parameters */      /* Read guessed parameters */
     /* Reads comments: lines beginning with '#' */      /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
Line 5711  int main(int argc, char *argv[]) Line 9046  int main(int argc, char *argv[])
           
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       j=0;                          j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){        for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;                                  if(jj==i) continue;
         j++;                                  j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);                                  fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){                                  if ((i1 != i) || (j1 != jj)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \                                          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 \  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);  run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
           exit(1);                                          exit(1);
         }                                  }
         fprintf(ficparo,"%1d%1d",i1,j1);                                  fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)                                  if(mle==1)
           printf("%1d%1d",i,j);                                          printf("%1d%1d",i,jj);
         fprintf(ficlog,"%1d%1d",i,j);                                  fprintf(ficlog,"%1d%1d",i,jj);
         for(k=1; k<=ncovmodel;k++){                                  for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);                                          fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){                                          if(mle==1){
             printf(" %lf",param[i][j][k]);                                                  printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);                                                  fprintf(ficlog," %lf",param[i][j][k]);
           }                                          }
           else                                          else
             fprintf(ficlog," %lf",param[i][j][k]);                                                  fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);                                          fprintf(ficparo," %lf",param[i][j][k]);
         }                                  }
         fscanf(ficpar,"\n");                                  fscanf(ficpar,"\n");
         numlinepar++;                                  numlinepar++;
         if(mle==1)                                  if(mle==1)
           printf("\n");                                          printf("\n");
         fprintf(ficlog,"\n");                                  fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");                                  fprintf(ficparo,"\n");
       }        }
     }        }  
     fflush(ficlog);      fflush(ficlog);
Line 5762  run imach with mle=-1 to get a correct t Line 9097  run imach with mle=-1 to get a correct t
   
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){        for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);                                  fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ( (i1-i) * (j1-j) != 0){                                  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);                                          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);                                          exit(1);
         }                                  }
         printf("%1d%1d",i,j);                                  printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);                                  fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);                                  fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){                                  for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);                                          fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);                                          printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);                                          fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);                                          fprintf(ficlog," %le",delti3[i][j][k]);
         }                                  }
         fscanf(ficpar,"\n");                                  fscanf(ficpar,"\n");
         numlinepar++;                                  numlinepar++;
         printf("\n");                                  printf("\n");
         fprintf(ficparo,"\n");                                  fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");                                  fprintf(ficlog,"\n");
       }        }
     }      }
     fflush(ficlog);      fflush(ficlog);
                   
     /* Reads covariance matrix */      /* Reads covariance matrix */
     delti=delti3[1][1];      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 */      /* 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 '#' */      /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
Line 5801  run imach with mle=-1 to get a correct t Line 9136  run imach with mle=-1 to get a correct t
       fputs(line,ficlog);        fputs(line,ficlog);
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
                     
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
       hess=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++)      for(i=1; i <=npar; i++)
       for(j=1; j <=npar; j++) matcov[i][j]=0.;        for(j=1; j <=npar; j++) matcov[i][j]=0.;
                         
       /* Scans npar lines */
     for(i=1; i <=npar; i++){      for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",str);        count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
       if(mle==1)        if(count != 3){
         printf("%s",str);          printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
       fprintf(ficlog,"%s",str);  This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
       fprintf(ficparo,"%s",str);  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%d",i1,j1,jk);
         }
         fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
         fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
       for(j=1; j <=i; j++){        for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);          fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){          if(mle==1){
Line 5823  run imach with mle=-1 to get a correct t Line 9170  run imach with mle=-1 to get a correct t
       fscanf(ficpar,"\n");        fscanf(ficpar,"\n");
       numlinepar++;        numlinepar++;
       if(mle==1)        if(mle==1)
         printf("\n");                                  printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");        fprintf(ficparo,"\n");
     }      }
       /* End of read covariance matrix npar lines */
     for(i=1; i <=npar; i++)      for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)        for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];          matcov[i][j]=matcov[j][i];
Line 5843  run imach with mle=-1 to get a correct t Line 9191  run imach with mle=-1 to get a correct t
     strcat(rfileres,".");    /* */      strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */      strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {      if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        printf("Problem writing new parameter file: %s\n", rfileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;        fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
     }      }
     fprintf(ficres,"#%s\n",version);      fprintf(ficres,"#%s\n",version);
   }    /* End of mle != -3 */    }    /* End of mle != -3 */
     
     /*  Main data
      */
   n= lastobs;    n= lastobs;
   num=lvector(1,n);    num=lvector(1,n);
   moisnais=vector(1,n);    moisnais=vector(1,n);
   annais=vector(1,n);    annais=vector(1,n);
   moisdc=vector(1,n);    moisdc=vector(1,n);
   andc=vector(1,n);    andc=vector(1,n);
     weight=vector(1,n);
   agedc=vector(1,n);    agedc=vector(1,n);
   cod=ivector(1,n);    cod=ivector(1,n);
   weight=vector(1,n);    for(i=1;i<=n;i++){
   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                  num[i]=0;
                   moisnais[i]=0;
                   annais[i]=0;
                   moisdc[i]=0;
                   andc[i]=0;
                   agedc[i]=0;
                   cod[i]=0;
                   weight[i]=1.0; /* Equal weights, 1 by default */
           }
   mint=matrix(1,maxwav,1,n);    mint=matrix(1,maxwav,1,n);
   anint=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 */     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
   tab=ivector(1,NCOVMAX);    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 */    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 */    /* Reads data from file datafile */
   if (readdata(datafile, firstobs, lastobs, &imx)==1)    if (readdata(datafile, firstobs, lastobs, &imx)==1)
Line 5878  run imach with mle=-1 to get a correct t Line 9237  run imach with mle=-1 to get a correct t
         k=1 Tvar[1]=2 (from V2)          k=1 Tvar[1]=2 (from V2)
     */      */
   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */    Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
     Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
     Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).     /*  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,         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.        Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
Line 5900  run imach with mle=-1 to get a correct t Line 9262  run imach with mle=-1 to get a correct t
                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                       */                          */  
   
   if(decodemodel(model, lastobs) == 1)  /* Main decodemodel */
   
   
     if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
     goto end;      goto end;
   
   if((double)(lastobs-imx)/(double)imx > 1.10){    if((double)(lastobs-imx)/(double)imx > 1.10){
Line 5925  run imach with mle=-1 to get a correct t Line 9290  run imach with mle=-1 to get a correct t
   free_vector(annais,1,n);    free_vector(annais,1,n);
   /* free_matrix(mint,1,maxwav,1,n);    /* free_matrix(mint,1,maxwav,1,n);
      free_matrix(anint,1,maxwav,1,n);*/       free_matrix(anint,1,maxwav,1,n);*/
   free_vector(moisdc,1,n);    /* free_vector(moisdc,1,n); */
   free_vector(andc,1,n);    /* free_vector(andc,1,n); */
   /* */    /* */
       
   wav=ivector(1,imx);    wav=ivector(1,imx);
   dh=imatrix(1,lastpass-firstpass+1,1,imx);    /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
   bh=imatrix(1,lastpass-firstpass+1,1,imx);    /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
   mw=imatrix(1,lastpass-firstpass+1,1,imx);    /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
     dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
     bh=imatrix(1,lastpass-firstpass+2,1,imx);
     mw=imatrix(1,lastpass-firstpass+2,1,imx);
         
   /* Concatenates waves */    /* Concatenates waves */
     /* 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 number of (mi=1 to wav[i]) effective wave out of mi 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.
     */
   
   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    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 */    free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
   ncodemax[1]=1;    ncodemax[1]=1;
   Ndum =ivector(-1,NCOVMAX);      Ndum =ivector(-1,NCOVMAX);  
   if (ncovmodel > 2)    cptcoveff=0;
     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */    if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
       tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
           }
           
           ncovcombmax=pow(2,cptcoveff);
           invalidvarcomb=ivector(1, ncovcombmax); 
           for(i=1;i<ncovcombmax;i++)
                   invalidvarcomb[i]=0;
   
     /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] which 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).*/
     /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j, 
      * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded 
      * (currently 0 or 1) in the data.
      * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of 
      * corresponding modality (h,j).
      */
   
   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */  
   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/  
   h=0;    h=0;
   
   
   /*if (cptcovn > 0) */    /*if (cptcovn > 0) */
         
    
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
     
   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */  
     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */   
       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/  
         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */   
           h++;  
           if (h>m)   
             h=1;  
           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1            /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
            *     h     1     2     3     4             * For k=4 covariates, h goes from 1 to m=2**k
              * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
              * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
              *     h\k   1     2     3     4
            *______________________________               *______________________________  
            *     1 i=1 1 i=1 1 i=1 1 i=1 1             *     1 i=1 1 i=1 1 i=1 1 i=1 1
            *     2     2     1     1     1             *     2     2     1     1     1
Line 5974  run imach with mle=-1 to get a correct t Line 9362  run imach with mle=-1 to get a correct t
            *     6     2     1     2     1             *     6     2     1     2     1
            *     7 i=4 1     2     2     1             *     7 i=4 1     2     2     1
            *     8     2     2     2     1             *     8     2     2     2     1
            *     9 i=5 1 i=3 1 i=2 1     1             *     9 i=5 1 i=3 1 i=2 1     2
            *    10     2     1     1     1             *    10     2     1     1     2
            *    11 i=6 1     2     1     1             *    11 i=6 1     2     1     2
            *    12     2     2     1     1             *    12     2     2     1     2
            *    13 i=7 1 i=4 1     2     1                 *    13 i=7 1 i=4 1     2     2    
            *    14     2     1     2     1             *    14     2     1     2     2
            *    15 i=8 1     2     2     1             *    15 i=8 1     2     2     2
            *    16     2     2     2     1             *    16     2     2     2     2
            */             */
           codtab[h][k]=j;    /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
           /*codtab[h][Tvar[k]]=j;*/       /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
           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]]);       * and the value of each covariate?
         }        * V1=1, V2=1, V3=2, V4=1 ?
       }       * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
     }       * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
   }        * In order to get the real value in the data, we use nbcode
   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);        * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
      codtab[1][2]=1;codtab[2][2]=2; */       * We are keeping this crazy system in order to be able (in the future?) 
   /* for(i=1; i <=m ;i++){        * to have more than 2 values (0 or 1) for a covariate.
      for(k=1; k <=cptcovn; k++){       * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);       * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
      }       *              bbbbbbbb
      printf("\n");       *              76543210     
      }       *   h-1        00000101 (6-1=5)
      scanf("%d",i);*/       *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
        *           &
        *     1        00000001 (1)
        *              00000000        = 1 & ((h-1) >> (k-1))
        *          +1= 00000001 =1 
        *
        * h=14, k=3 => h'=h-1=13, k'=k-1=2
        *          h'      1101 =2^3+2^2+0x2^1+2^0
        *    >>k'            11
        *          &   00000001
        *            = 00000001
        *      +1    = 00000010=2    =  codtabm(14,3)   
        * Reverse h=6 and m=16?
        * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
        * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
        * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1 
        * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
        * V3=decodtabm(14,3,2**4)=2
        *          h'=13   1101 =2^3+2^2+0x2^1+2^0
        *(h-1) >> (j-1)    0011 =13 >> 2
        *          &1 000000001
        *           = 000000001
        *         +1= 000000010 =2
        *                  2211
        *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
        *                  V3=2
                    * codtabm and decodtabm are identical
        */
   
   
  free_ivector(Ndum,-1,NCOVMAX);   free_ivector(Ndum,-1,NCOVMAX);
   
   
           
   /*------------ gnuplot -------------*/    /* Initialisation of ----------- gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
   if(mle==-3)    if(mle==-3)
     strcat(optionfilegnuplot,"-mort");      strcat(optionfilegnuplot,"-MORT_");
   strcat(optionfilegnuplot,".gp");    strcat(optionfilegnuplot,".gp");
   
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
     printf("Problem with file %s",optionfilegnuplot);      printf("Problem with file %s",optionfilegnuplot);
   }    }
   else{    else{
     fprintf(ficgp,"\n# %s\n", version);       fprintf(ficgp,"\n# IMaCh-%s\n", version); 
     fprintf(ficgp,"# %s\n", optionfilegnuplot);       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
     //fprintf(ficgp,"set missing 'NaNq'\n");      //fprintf(ficgp,"set missing 'NaNq'\n");
     fprintf(ficgp,"set datafile missing 'NaNq'\n");      fprintf(ficgp,"set datafile missing 'NaNq'\n");
   }    }
   /*  fclose(ficgp);*/    /*  fclose(ficgp);*/
   /*--------- index.htm --------*/  
   
     /* Initialisation of --------- index.htm --------*/
   
   strcpy(optionfilehtm,optionfilefiname); /* Main html file */    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
   if(mle==-3)    if(mle==-3)
     strcat(optionfilehtm,"-mort");      strcat(optionfilehtm,"-MORT_");
   strcat(optionfilehtm,".htm");    strcat(optionfilehtm,".htm");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
     printf("Problem with %s \n",optionfilehtm);      printf("Problem with %s \n",optionfilehtm);
Line 6039  run imach with mle=-1 to get a correct t Line 9457  run imach with mle=-1 to get a correct t
   else{    else{
   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \    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\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);            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> \    fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   <font size=\"2\">IMaCh-%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
 \n\  \n\
 <hr  size=\"2\" color=\"#EC5E5E\">\  <hr  size=\"2\" color=\"#EC5E5E\">\
  <ul><li><h4>Parameter files</h4>\n\   <ul><li><h4>Parameter files</h4>\n\
Line 6062  Title=%s <br>Datafile=%s Firstpass=%d La Line 9482  Title=%s <br>Datafile=%s Firstpass=%d La
   
   strcpy(pathr,path);    strcpy(pathr,path);
   strcat(pathr,optionfilefiname);    strcat(pathr,optionfilefiname);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
   chdir(optionfilefiname); /* Move to directory named optionfile */    chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
       
   /* Calculates basic frequencies. Computes observed prevalence at single age    /* Calculates basic frequencies. Computes observed prevalence at single age 
                    and for any valid combination of covariates
      and prints on file fileres'p'. */       and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart,    \
                                                           firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 6074  Youngest age at first (selected) pass %. Line 9501  Youngest age at first (selected) pass %.
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
           imx,agemin,agemax,jmin,jmax,jmean);            imx,agemin,agemax,jmin,jmax,jmean);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= 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 */          newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= 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 */          oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
   /* For Powell, parameters are in a vector p[] starting at p[1]    /* 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] */       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) */    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     /* For mortality only */
   if (mle==-3){    if (mle==-3){
     ximort=matrix(1,NDIM,1,NDIM);       ximort=matrix(1,NDIM,1,NDIM); 
 /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */                  for(i=1;i<=NDIM;i++)
                           for(j=1;j<=NDIM;j++)
                                   ximort[i][j]=0.;
       /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);      cens=ivector(1,n);
     ageexmed=vector(1,n);      ageexmed=vector(1,n);
     agecens=vector(1,n);      agecens=vector(1,n);
     dcwave=ivector(1,n);      dcwave=ivector(1,n);
                    
     for (i=1; i<=imx; i++){      for (i=1; i<=imx; i++){
       dcwave[i]=-1;        dcwave[i]=-1;
       for (m=firstpass; m<=lastpass; m++)        for (m=firstpass; m<=lastpass; m++)
Line 6103  Interval (in months) between two waves: Line 9532  Interval (in months) between two waves:
           break;            break;
         }          }
     }      }
       
     for (i=1; i<=imx; i++) {      for (i=1; i<=imx; i++) {
       if (wav[i]>0){        if (wav[i]>0){
         ageexmed[i]=agev[mw[1][i]][i];          ageexmed[i]=agev[mw[1][i]][i];
         j=wav[i];          j=wav[i];
         agecens[i]=1.;           agecens[i]=1.; 
           
         if (ageexmed[i]> 1 && wav[i] > 0){          if (ageexmed[i]> 1 && wav[i] > 0){
           agecens[i]=agev[mw[j][i]][i];            agecens[i]=agev[mw[j][i]][i];
           cens[i]= 1;            cens[i]= 1;
Line 6135  Interval (in months) between two waves: Line 9564  Interval (in months) between two waves:
 #else  #else
     printf("Powell\n");  fprintf(ficlog,"Powell\n");      printf("Powell\n");  fprintf(ficlog,"Powell\n");
 #endif  #endif
     strcpy(filerespow,"pow-mort");       strcpy(filerespow,"POW-MORT_"); 
     strcat(filerespow,fileres);      strcat(filerespow,fileresu);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {      if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);        printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
Line 6178  Interval (in months) between two waves: Line 9607  Interval (in months) between two waves:
       
     /* Initialize method and iterate */      /* Initialize method and iterate */
     /*     p[1]=0.0268; p[NDIM]=0.083; */      /*     p[1]=0.0268; p[NDIM]=0.083; */
 /*     gsl_vector_set(x, 0, 0.0268); */      /*     gsl_vector_set(x, 0, 0.0268); */
 /*     gsl_vector_set(x, 1, 0.083); */      /*     gsl_vector_set(x, 1, 0.083); */
     gsl_vector_set(x, 0, p[1]);      gsl_vector_set(x, 0, p[1]);
     gsl_vector_set(x, 1, p[2]);      gsl_vector_set(x, 1, p[2]);
   
Line 6232  Interval (in months) between two waves: Line 9661  Interval (in months) between two waves:
 #endif    #endif  
     fclose(ficrespow);      fclose(ficrespow);
           
     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);       hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); 
   
     for(i=1; i <=NDIM; i++)      for(i=1; i <=NDIM; i++)
       for(j=i+1;j<=NDIM;j++)        for(j=i+1;j<=NDIM;j++)
         matcov[i][j]=matcov[j][i];                                  matcov[i][j]=matcov[j][i];
           
     printf("\nCovariance matrix\n ");      printf("\nCovariance matrix\n ");
       fprintf(ficlog,"\nCovariance matrix\n ");
     for(i=1; i <=NDIM; i++) {      for(i=1; i <=NDIM; i++) {
       for(j=1;j<=NDIM;j++){         for(j=1;j<=NDIM;j++){ 
         printf("%f ",matcov[i][j]);                                  printf("%f ",matcov[i][j]);
                                   fprintf(ficlog,"%f ",matcov[i][j]);
       }        }
       printf("\n ");        printf("\n ");  fprintf(ficlog,"\n ");
     }      }
           
     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);      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++)       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]));        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);      lsurv=vector(1,AGESUP);
     lpop=vector(1,AGESUP);      lpop=vector(1,AGESUP);
     tpop=vector(1,AGESUP);      tpop=vector(1,AGESUP);
Line 6281  Interval (in months) between two waves: Line 9713  Interval (in months) between two waves:
           
           
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);                  ageminpar=50;
                       agemaxpar=100;
     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \      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{
                           printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
                           fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
         printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
                   }
       printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                      stepm, weightopt,\                       stepm, weightopt,\
                      model,imx,p,matcov,agemortsup);                       model,imx,p,matcov,agemortsup);
           
     free_vector(lsurv,1,AGESUP);      free_vector(lsurv,1,AGESUP);
     free_vector(lpop,1,AGESUP);      free_vector(lpop,1,AGESUP);
     free_vector(tpop,1,AGESUP);      free_vector(tpop,1,AGESUP);
 #ifdef GSL      free_matrix(ximort,1,NDIM,1,NDIM);
     free_ivector(cens,1,n);      free_ivector(cens,1,n);
     free_vector(agecens,1,n);      free_vector(agecens,1,n);
     free_ivector(dcwave,1,n);      free_ivector(dcwave,1,n);
     free_matrix(ximort,1,NDIM,1,NDIM);  #ifdef GSL
 #endif  #endif
   } /* Endof if mle==-3 */    } /* Endof if mle==-3 mortality only */
       /* Standard  */
   else{ /* For mle >=1 */    else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
     globpr=0;/* debug */      globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
       /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      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);      printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
     globpr=1; /* to print the contributions */      if(mle>=1){ /* Could be 1 or 2, Real Maximization */
         /* mlikeli uses func not funcone */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
         globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
         /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
         likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       }
       globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      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);      printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */  
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }  
           
     /*--------- results files --------------*/      /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);      fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
           
           
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
Line 6329  Interval (in months) between two waves: Line 9780  Interval (in months) between two waves:
           fprintf(ficlog,"%d%d ",i,k);            fprintf(ficlog,"%d%d ",i,k);
           fprintf(ficres,"%1d%1d ",i,k);            fprintf(ficres,"%1d%1d ",i,k);
           for(j=1; j <=ncovmodel; j++){            for(j=1; j <=ncovmodel; j++){
             printf("%lf ",p[jk]);              printf("%12.7f ",p[jk]);
             fprintf(ficlog,"%lf ",p[jk]);              fprintf(ficlog,"%12.7f ",p[jk]);
             fprintf(ficres,"%lf ",p[jk]);              fprintf(ficres,"%12.7f ",p[jk]);
             jk++;               jk++; 
           }            }
           printf("\n");            printf("\n");
Line 6340  Interval (in months) between two waves: Line 9791  Interval (in months) between two waves:
         }          }
       }        }
     }      }
     if(mle!=0){      if(mle != 0){
       /* Computing hessian and covariance matrix */        /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
       ftolhess=ftol; /* Usually correct */        ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);        hesscov(matcov, hess, 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");
             }
           }
         }
       } /* end of hesscov and Wald tests */
       
       /*  */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");      printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
Line 6368  Interval (in months) between two waves: Line 9838  Interval (in months) between two waves:
     }      }
           
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      fprintf(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)      if(mle >= 1) /* To big for the screen */
       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");        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");      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\ */      /* # 121 Var(a12)\n\ */
Line 6431  Interval (in months) between two waves: Line 9901  Interval (in months) between two waves:
                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);                          fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                       }else{                        }else{
                         if(mle>=1)                          if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]);                             printf(" %.7e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]);                           fprintf(ficlog," %.7e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]);                           fprintf(ficres," %.7e",matcov[jj][ll]); 
                       }                        }
                     }                      }
                   }                    }
Line 6452  Interval (in months) between two waves: Line 9922  Interval (in months) between two waves:
           
     fflush(ficlog);      fflush(ficlog);
     fflush(ficres);      fflush(ficres);
           while(fgets(line, MAXLINE, ficpar)) {
     while((c=getc(ficpar))=='#' && c!= EOF){        /* If line starts with a # it is a comment */
       ungetc(c,ficpar);        if (line[0] == '#') {
       fgets(line, MAXLINE, ficpar);          numlinepar++;
       fputs(line,stdout);          fputs(line,stdout);
       fputs(line,ficparo);          fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
     }      }
     ungetc(c,ficpar);      
       /* while((c=getc(ficpar))=='#' && c!= EOF){ */
       /*   ungetc(c,ficpar); */
       /*   fgets(line, MAXLINE, ficpar); */
       /*   fputs(line,stdout); */
       /*   fputs(line,ficparo); */
       /* } */
       /* ungetc(c,ficpar); */
           
     estepm=0;      estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
         
         if (num_filled != 6) {
           printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
           fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
           goto end;
         }
         printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
       }
       /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
       /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
       
       /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
     if (estepm==0 || estepm < stepm) estepm=stepm;      if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {      if (fage <= 2) {
       bage = ageminpar;        bage = ageminpar;
Line 6470  Interval (in months) between two waves: Line 9963  Interval (in months) between two waves:
     }      }
           
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      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(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
     fprintf(ficparo,"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, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
                       
       /* Other stuffs, more or less useful */    
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
Line 6500  Interval (in months) between two waves: Line 9994  Interval (in months) between two waves:
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
           
     fscanf(ficpar,"pop_based=%d\n",&popbased);      fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficlog,"pop_based=%d\n",popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);         fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);         fprintf(ficres,"pop_based=%d\n",popbased);   
           
Line 6518  Interval (in months) between two waves: Line 10013  Interval (in months) between two waves:
     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);      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.*/      /* day and month of proj2 are not used but only year anproj2.*/
           
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
       fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
       fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
       fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,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); */                  /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
           
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);      if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
                               printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);                          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\
    /*------------ free_vector  -------------*/  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
    /*  chdir(path); */      }else{
          printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
     free_ivector(wav,1,imx);      }
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);                   model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                      jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
                   
       /*------------ free_vector  -------------*/
       /*  chdir(path); */
                   
       /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
       /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
       /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
       /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
     free_lvector(num,1,n);      free_lvector(num,1,n);
     free_vector(agedc,1,n);      free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/      /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);      fclose(ficparo);
     fclose(ficres);      fclose(ficres);
                   
                   
       /* Other results (useful)*/
                   
                   
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
 #include "prevlim.h"  /* Use ficrespl, ficlog */      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
     fclose(ficrespl);      fclose(ficrespl);
   
 #ifdef FREEEXIT2  
 #include "freeexit2.h"  
 #endif  
   
     /*------------- h Pij x at various ages ------------*/      /*------------- h Pij x at various ages ------------*/
 #include "hpijx.h"      /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
     fclose(ficrespij);      fclose(ficrespij);
   
   /*-------------- Variance of one-step probabilities---*/      /* ncovcombmax=  pow(2,cptcoveff); */
       /*-------------- Variance of one-step probabilities---*/
     k=1;      k=1;
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       /* Prevalence for each covariates in probs[age][status][cov] */
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
     for(i=1;i<=AGESUP;i++)      for(i=1;i<=AGESUP;i++)
       for(j=1;j<=NCOVMAX;j++)        for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
         for(k=1;k<=NCOVMAX;k++)          for(k=1;k<=ncovcombmax;k++)
           probs[i][j][k]=0.;            probs[i][j][k]=0.;
       prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       if (mobilav!=0 ||mobilavproj !=0 ) {
         mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
                           for(i=1;i<=AGESUP;i++)
                                   for(j=1;j<=nlstate;j++)
                                           for(k=1;k<=ncovcombmax;k++)
                                                   mobaverages[i][j][k]=0.;
         mobaverage=mobaverages;
         if (mobilav!=0) {
                                   if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
                                           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                                           printf(" Error in movingaverage mobilav=%d\n",mobilav);
                                   }
         }
         /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
         /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
         else if (mobilavproj !=0) {
                                   if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
                                           fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
                                           printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
                                   }
         }
       }/* end if moving average */
                   
     /*---------- Forecasting ------------------*/      /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){      if(prevfcast==1){
       /*    if(stepm ==1){*/        /*    if(stepm ==1){*/
       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        prevforecast(fileresu, 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); */  
       /*      } */  
     }      }
         if(backcast==1){
         ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */        ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
         ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
     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",\        /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);  
     */        bprlim=matrix(1,nlstate,1,nlstate);
         back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
     if (mobilav!=0) {        fclose(ficresplb);
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){        hBijx(p, bage, fage, mobaverage);
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);        fclose(ficrespijb);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);        free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
       }  
         /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
            bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
         free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
         free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
         free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
     }      }
       
    
       /* ------ Other prevalence ratios------------ */
   
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+2,1,imx);   
                   
                   
     /*---------- Health expectancies, no variances ------------*/      /*---------- Health expectancies, no variances ------------*/
                   
     strcpy(filerese,"e");      strcpy(filerese,"E_");
     strcat(filerese,fileres);      strcat(filerese,fileresu);
     if((ficreseij=fopen(filerese,"w"))==NULL) {      if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"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);      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){                  
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/  
             
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                  fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }        }
         fprintf(ficreseij,"******\n");        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);        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);      fclose(ficreseij);
       printf("done evsij\n");fflush(stdout);
       fprintf(ficlog,"done evsij\n");fflush(ficlog);
                   
     /*---------- Health expectancies and variances ------------*/      /*---------- Health expectancies and variances ------------*/
                   
                   
     strcpy(filerest,"t");      strcpy(filerest,"T_");
     strcat(filerest,fileres);      strcat(filerest,fileresu);
     if((ficrest=fopen(filerest,"w"))==NULL) {      if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"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);       printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
     fprintf(ficlog,"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); fflush(ficlog);
                   
   
       strcpy(fileresstde,"STDE_");
     strcpy(fileresstde,"stde");      strcat(fileresstde,fileresu);
     strcat(fileresstde,fileres);  
     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        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);        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);      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);      fprintf(ficlog,"  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
     strcpy(filerescve,"cve");      strcpy(filerescve,"CVE_");
     strcat(filerescve,fileres);      strcat(filerescve,fileresu);
     if((ficrescveij=fopen(filerescve,"w"))==NULL) {      if((ficrescveij=fopen(filerescve,"w"))==NULL) {
       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        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);        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);      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);      fprintf(ficlog,"    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
     strcpy(fileresv,"v");      strcpy(fileresv,"V_");
     strcat(fileresv,fileres);      strcat(fileresv,fileresu);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {      if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"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);      printf("      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
   
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                       
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrest,"\n#****** ");        fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                  fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficrest,"******\n");        fprintf(ficrest,"******\n");
         
         fprintf(ficresstdeij,"\n#****** ");        fprintf(ficresstdeij,"\n#****** ");
         fprintf(ficrescveij,"\n#****** ");        fprintf(ficrescveij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                  fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                  fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }        }
         fprintf(ficresstdeij,"******\n");        fprintf(ficresstdeij,"******\n");
         fprintf(ficrescveij,"******\n");        fprintf(ficrescveij,"******\n");
         
         fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                  fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
         
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);          printf(" cvevsij %d, ",k);
         /*        fprintf(ficlog, " cvevsij %d, ",k);
          */        cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
         /* goto endfree; */        printf(" end cvevsij \n ");
          fprintf(ficlog, " end cvevsij \n ");
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        
         pstamp(ficrest);        /*
          */
         /* goto endfree; */
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        
           oldm=oldms;savm=savms; /* Segmentation fault */        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           cptcod= 0; /* To be deleted */        pstamp(ficrest);
           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)        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==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);                                  oldm=oldms;savm=savms; /* ZZ Segmentation fault */
           else                                  cptcod= 0; /* To be deleted */
             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");                                  printf("varevsij %d \n",vpopbased);
           fprintf(ficrest,"# Age e.. (std) ");                                  fprintf(ficlog, "varevsij %d \n",vpopbased);
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                                  varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
           fprintf(ficrest,"\n");                                  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)
           epj=vector(1,nlstate+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);
           for(age=bage; age <=fage ;age++){                                  else
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                                          fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             if (vpopbased==1) {                                  fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
               if(mobilav ==0){                                  for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
                 for(i=1; i<=nlstate;i++)                                  fprintf(ficrest,"\n");
                   prlim[i][i]=probs[(int)age][i][k];                                  /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
               }else{ /* mobilav */                                   epj=vector(1,nlstate+1);
                 for(i=1; i<=nlstate;i++)                                  printf("Computing age specific period (stable) prevalences in each health state \n");
                   prlim[i][i]=mobaverage[(int)age][i][k];                                  fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
               }                                  for(age=bage; age <=fage ;age++){
             }                                          prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
                                                   if (vpopbased==1) {
             fprintf(ficrest," %4.0f",age);                                                  if(mobilav ==0){
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                                                          for(i=1; i<=nlstate;i++)
               for(i=1, epj[j]=0.;i <=nlstate;i++) {                                                                  prlim[i][i]=probs[(int)age][i][k];
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];                                                  }else{ /* mobilav */ 
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                                                          for(i=1; i<=nlstate;i++)
               }                                                                  prlim[i][i]=mobaverage[(int)age][i][k];
               epj[nlstate+1] +=epj[j];                                                  }
             }                                          }
             
             for(i=1, vepp=0.;i <=nlstate;i++)                                          fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
               for(j=1;j <=nlstate;j++)                                          /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
                 vepp += vareij[i][j][(int)age];                                          /* printf(" age %4.0f ",age); */
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));                                          for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(j=1;j <=nlstate;j++){                                                  for(i=1, epj[j]=0.;i <=nlstate;i++) {
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                                                          epj[j] += prlim[i][i]*eij[i][j][(int)age];
             }                                                          /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             fprintf(ficrest,"\n");                                                          /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
           }                                                  }
         }                                                  epj[nlstate+1] +=epj[j];
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                                          }
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                                          /* printf(" age %4.0f \n",age); */
         free_vector(epj,1,nlstate+1);            
                                           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");
                                   }
         } /* End vpopbased */
         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);
         printf("done \n");fflush(stdout);
         fprintf(ficlog,"done\n");fflush(ficlog);
         
       /*}*/        /*}*/
     }      } /* End k */
     free_vector(weight,1,n);      free_vector(weight,1,n);
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,1,n);      free_imatrix(s,1,maxwav+1,1,n);
Line 6764  Interval (in months) between two waves: Line 10326  Interval (in months) between two waves:
     fclose(ficrescveij);      fclose(ficrescveij);
     fclose(ficresvij);      fclose(ficresvij);
     fclose(ficrest);      fclose(ficrest);
       printf("done Health expectancies\n");fflush(stdout);
       fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
     fclose(ficpar);      fclose(ficpar);
       
     /*------- Variance of period (stable) prevalence------*/         /*------- Variance of period (stable) prevalence------*/   
   
     strcpy(fileresvpl,"vpl");      strcpy(fileresvpl,"VPL_");
     strcat(fileresvpl,fileres);      strcat(fileresvpl,fileresu);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);        printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
       exit(0);        exit(0);
     }      }
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);      printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
       fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
   
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                       
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficresvpl,"\n#****** ");          fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)                           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                  fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresvpl,"******\n");                          fprintf(ficresvpl,"******\n");
               
         varpl=matrix(1,nlstate,(int) bage, (int) fage);                          varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;                          oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);                          varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                          free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       /*}*/        /*}*/
     }      }
                   
     fclose(ficresvpl);      fclose(ficresvpl);
       printf("done variance-covariance of period prevalence\n");fflush(stdout);
       fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
   
     /*---------- End : free ----------------*/      /*---------- End : free ----------------*/
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (mobilav!=0 ||mobilavproj !=0)
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
   }  /* mle==-3 arrives here for freeing */      free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
  /* endfree:*/  
     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
     free_matrix(oldms, 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(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
       free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
       free_matrix(coqvar,1,maxwav,1,n);
     free_matrix(covar,0,NCOVMAX,1,n);      free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);      free_matrix(matcov,1,npar,1,npar);
       free_matrix(hess,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/      /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);      free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
     free_ivector(ncodemax,1,NCOVMAX);      free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(ncodemaxwundef,1,NCOVMAX);
       free_ivector(Dummy,-1,NCOVMAX);
       free_ivector(Fixed,-1,NCOVMAX);
       free_ivector(Typevar,-1,NCOVMAX);
     free_ivector(Tvar,1,NCOVMAX);      free_ivector(Tvar,1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);      free_ivector(Tprod,1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);      free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(invalidvarcomb,1,ncovcombmax);
     free_ivector(Tage,1,NCOVMAX);      free_ivector(Tage,1,NCOVMAX);
   
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);      free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     free_imatrix(codtab,1,100,1,10);      /* free_imatrix(codtab,1,100,1,10); */
   fflush(fichtm);    fflush(fichtm);
   fflush(ficgp);    fflush(ficgp);
       
   
   if((nberr >0) || (nbwarn>0)){    if((nberr >0) || (nbwarn>0)){
     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);      printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);      fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
   }else{    }else{
     printf("End of Imach\n");      printf("End of Imach\n");
     fprintf(ficlog,"End of Imach\n");      fprintf(ficlog,"End of Imach\n");
Line 6856  Interval (in months) between two waves: Line 10433  Interval (in months) between two waves:
   
   
    printf("Before Current directory %s!\n",pathcd);     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)     if(chdir(pathcd) != 0)
     printf("Can't move to directory %s!\n",path);             printf("Can't move to directory %s!\n", path);
   if(getcwd(pathcd,MAXLINE) > 0)     if (getcwd(pathcd, MAXLINE) > 0)
   #endif 
     printf("Current directory %s!\n",pathcd);      printf("Current directory %s!\n",pathcd);
   /*strcat(plotcmd,CHARSEPARATOR);*/    /*strcat(plotcmd,CHARSEPARATOR);*/
   sprintf(plotcmd,"gnuplot");    sprintf(plotcmd,"gnuplot");
Line 6913  Interval (in months) between two waves: Line 10496  Interval (in months) between two waves:
   }    }
   end:    end:
   while (z[0] != 'q') {    while (z[0] != 'q') {
     printf("\nType  q for exiting: ");      printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);      scanf("%s",z);
   }    }
 }  }

Removed from v.1.166  
changed lines
  Added in v.1.226


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