Diff for /imach/src/imach.c between versions 1.219 and 1.308

version 1.219, 2016/02/15 00:48:12 version 1.308, 2021/03/31 13:11:57
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.308  2021/03/31 13:11:57  brouard
     Summary: Version 0.99r23
   
   
     * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
   
     Revision 1.307  2021/03/08 18:11:32  brouard
     Summary: 0.99r22 fixed bug on result:
   
     Revision 1.306  2021/02/20 15:44:02  brouard
     Summary: Version 0.99r21
   
     * imach.c (Module): Fix bug on quitting after result lines!
     (Module): Version 0.99r21
   
     Revision 1.305  2021/02/20 15:28:30  brouard
     * imach.c (Module): Fix bug on quitting after result lines!
   
     Revision 1.304  2021/02/12 11:34:20  brouard
     * imach.c (Module): The use of a Windows BOM (huge) file is now an error
   
     Revision 1.303  2021/02/11 19:50:15  brouard
     *  (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
   
     Revision 1.302  2020/02/22 21:00:05  brouard
     *  (Module): imach.c Update mle=-3 (for computing Life expectancy
     and life table from the data without any state)
   
     Revision 1.301  2019/06/04 13:51:20  brouard
     Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
   
     Revision 1.300  2019/05/22 19:09:45  brouard
     Summary: version 0.99r19 of May 2019
   
     Revision 1.299  2019/05/22 18:37:08  brouard
     Summary: Cleaned 0.99r19
   
     Revision 1.298  2019/05/22 18:19:56  brouard
     *** empty log message ***
   
     Revision 1.297  2019/05/22 17:56:10  brouard
     Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
   
     Revision 1.296  2019/05/20 13:03:18  brouard
     Summary: Projection syntax simplified
   
   
     We can now start projections, forward or backward, from the mean date
     of inteviews up to or down to a number of years of projection:
     prevforecast=1 yearsfproj=15.3 mobil_average=0
     or
     prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
     or
     prevbackcast=1 yearsbproj=12.3 mobil_average=1
     or
     prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
   
     Revision 1.295  2019/05/18 09:52:50  brouard
     Summary: doxygen tex bug
   
     Revision 1.294  2019/05/16 14:54:33  brouard
     Summary: There was some wrong lines added
   
     Revision 1.293  2019/05/09 15:17:34  brouard
     *** empty log message ***
   
     Revision 1.292  2019/05/09 14:17:20  brouard
     Summary: Some updates
   
     Revision 1.291  2019/05/09 13:44:18  brouard
     Summary: Before ncovmax
   
     Revision 1.290  2019/05/09 13:39:37  brouard
     Summary: 0.99r18 unlimited number of individuals
   
     The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.
   
     Revision 1.289  2018/12/13 09:16:26  brouard
     Summary: Bug for young ages (<-30) will be in r17
   
     Revision 1.288  2018/05/02 20:58:27  brouard
     Summary: Some bugs fixed
   
     Revision 1.287  2018/05/01 17:57:25  brouard
     Summary: Bug fixed by providing frequencies only for non missing covariates
   
     Revision 1.286  2018/04/27 14:27:04  brouard
     Summary: some minor bugs
   
     Revision 1.285  2018/04/21 21:02:16  brouard
     Summary: Some bugs fixed, valgrind tested
   
     Revision 1.284  2018/04/20 05:22:13  brouard
     Summary: Computing mean and stdeviation of fixed quantitative variables
   
     Revision 1.283  2018/04/19 14:49:16  brouard
     Summary: Some minor bugs fixed
   
     Revision 1.282  2018/02/27 22:50:02  brouard
     *** empty log message ***
   
     Revision 1.281  2018/02/27 19:25:23  brouard
     Summary: Adding second argument for quitting
   
     Revision 1.280  2018/02/21 07:58:13  brouard
     Summary: 0.99r15
   
     New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
   
     Revision 1.279  2017/07/20 13:35:01  brouard
     Summary: temporary working
   
     Revision 1.278  2017/07/19 14:09:02  brouard
     Summary: Bug for mobil_average=0 and prevforecast fixed(?)
   
     Revision 1.277  2017/07/17 08:53:49  brouard
     Summary: BOM files can be read now
   
     Revision 1.276  2017/06/30 15:48:31  brouard
     Summary: Graphs improvements
   
     Revision 1.275  2017/06/30 13:39:33  brouard
     Summary: Saito's color
   
     Revision 1.274  2017/06/29 09:47:08  brouard
     Summary: Version 0.99r14
   
     Revision 1.273  2017/06/27 11:06:02  brouard
     Summary: More documentation on projections
   
     Revision 1.272  2017/06/27 10:22:40  brouard
     Summary: Color of backprojection changed from 6 to 5(yellow)
   
     Revision 1.271  2017/06/27 10:17:50  brouard
     Summary: Some bug with rint
   
     Revision 1.270  2017/05/24 05:45:29  brouard
     *** empty log message ***
   
     Revision 1.269  2017/05/23 08:39:25  brouard
     Summary: Code into subroutine, cleanings
   
     Revision 1.268  2017/05/18 20:09:32  brouard
     Summary: backprojection and confidence intervals of backprevalence
   
     Revision 1.267  2017/05/13 10:25:05  brouard
     Summary: temporary save for backprojection
   
     Revision 1.266  2017/05/13 07:26:12  brouard
     Summary: Version 0.99r13 (improvements and bugs fixed)
   
     Revision 1.265  2017/04/26 16:22:11  brouard
     Summary: imach 0.99r13 Some bugs fixed
   
     Revision 1.264  2017/04/26 06:01:29  brouard
     Summary: Labels in graphs
   
     Revision 1.263  2017/04/24 15:23:15  brouard
     Summary: to save
   
     Revision 1.262  2017/04/18 16:48:12  brouard
     *** empty log message ***
   
     Revision 1.261  2017/04/05 10:14:09  brouard
     Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
   
     Revision 1.260  2017/04/04 17:46:59  brouard
     Summary: Gnuplot indexations fixed (humm)
   
     Revision 1.259  2017/04/04 13:01:16  brouard
     Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
   
     Revision 1.258  2017/04/03 10:17:47  brouard
     Summary: Version 0.99r12
   
     Some cleanings, conformed with updated documentation.
   
     Revision 1.257  2017/03/29 16:53:30  brouard
     Summary: Temp
   
     Revision 1.256  2017/03/27 05:50:23  brouard
     Summary: Temporary
   
     Revision 1.255  2017/03/08 16:02:28  brouard
     Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
   
     Revision 1.254  2017/03/08 07:13:00  brouard
     Summary: Fixing data parameter line
   
     Revision 1.253  2016/12/15 11:59:41  brouard
     Summary: 0.99 in progress
   
     Revision 1.252  2016/09/15 21:15:37  brouard
     *** empty log message ***
   
     Revision 1.251  2016/09/15 15:01:13  brouard
     Summary: not working
   
     Revision 1.250  2016/09/08 16:07:27  brouard
     Summary: continue
   
     Revision 1.249  2016/09/07 17:14:18  brouard
     Summary: Starting values from frequencies
   
     Revision 1.248  2016/09/07 14:10:18  brouard
     *** empty log message ***
   
     Revision 1.247  2016/09/02 11:11:21  brouard
     *** empty log message ***
   
     Revision 1.246  2016/09/02 08:49:22  brouard
     *** empty log message ***
   
     Revision 1.245  2016/09/02 07:25:01  brouard
     *** empty log message ***
   
     Revision 1.244  2016/09/02 07:17:34  brouard
     *** empty log message ***
   
     Revision 1.243  2016/09/02 06:45:35  brouard
     *** empty log message ***
   
     Revision 1.242  2016/08/30 15:01:20  brouard
     Summary: Fixing a lots
   
     Revision 1.241  2016/08/29 17:17:25  brouard
     Summary: gnuplot problem in Back projection to fix
   
     Revision 1.240  2016/08/29 07:53:18  brouard
     Summary: Better
   
     Revision 1.239  2016/08/26 15:51:03  brouard
     Summary: Improvement in Powell output in order to copy and paste
   
     Author:
   
     Revision 1.238  2016/08/26 14:23:35  brouard
     Summary: Starting tests of 0.99
   
     Revision 1.237  2016/08/26 09:20:19  brouard
     Summary: to valgrind
   
     Revision 1.236  2016/08/25 10:50:18  brouard
     *** empty log message ***
   
     Revision 1.235  2016/08/25 06:59:23  brouard
     *** empty log message ***
   
     Revision 1.234  2016/08/23 16:51:20  brouard
     *** empty log message ***
   
     Revision 1.233  2016/08/23 07:40:50  brouard
     Summary: not working
   
     Revision 1.232  2016/08/22 14:20:21  brouard
     Summary: not working
   
     Revision 1.231  2016/08/22 07:17:15  brouard
     Summary: not working
   
     Revision 1.230  2016/08/22 06:55:53  brouard
     Summary: Not working
   
     Revision 1.229  2016/07/23 09:45:53  brouard
     Summary: Completing for func too
   
     Revision 1.228  2016/07/22 17:45:30  brouard
     Summary: Fixing some arrays, still debugging
   
     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    Revision 1.219  2016/02/15 00:48:12  brouard
   *** empty log message ***    *** empty log message ***
   
Line 36 Line 323
   Author: Nicolas Brouard    Author: Nicolas Brouard
   
   Revision 1.210  2015/11/18 17:41:20  brouard    Revision 1.210  2015/11/18 17:41:20  brouard
   Summary: Start working on projected prevalences    Summary: Start working on projected prevalences  Revision 1.209  2015/11/17 22:12:03  brouard
   
   Revision 1.209  2015/11/17 22:12:03  brouard  
   Summary: Adding ftolpl parameter    Summary: Adding ftolpl parameter
   Author: N Brouard    Author: N Brouard
   
Line 621 Line 906
   
   Short summary of the programme:    Short summary of the programme:
       
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies or State-specific
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    (if states aren't health statuses) Expectancies from
   first survey ("cross") where individuals from different ages are    cross-longitudinal data. Cross-longitudinal data consist in: 
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    -1- a first survey ("cross") where individuals from different ages
   second wave of interviews ("longitudinal") which measure each change    are interviewed on their health status or degree of disability (in
   (if any) in individual health status.  Health expectancies are    the case of a health survey which is our main interest)
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    -2- at least a second wave of interviews ("longitudinal") which
   Maximum Likelihood of the parameters involved in the model.  The    measure each change (if any) in individual health status.  Health
   simplest model is the multinomial logistic model where pij is the    expectancies are computed from the time spent in each health state
   probability to be observed in state j at the second wave    according to a model. More health states you consider, more time is
   conditional to be observed in state i at the first wave. Therefore    necessary to reach the Maximum Likelihood of the parameters involved
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    in the model.  The simplest model is the multinomial logistic model
   'age' is age and 'sex' is a covariate. If you want to have a more    where pij is the probability to be observed in state j at the second
   complex model than "constant and age", you should modify the program    wave conditional to be observed in state i at the first
   where the markup *Covariates have to be included here again* invites    wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
   you to do it.  More covariates you add, slower the    etc , where 'age' is age and 'sex' is a covariate. If you want to
     have a more complex model than "constant and age", you should modify
     the program where the markup *Covariates have to be included here
     again* invites you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
Line 660 Line 948
   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 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   - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
     at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,     double agemaxpar, double ftolpl, int *ncvyearp, double
    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);     dateprev1,double dateprev2, int firstpass, int lastpass, int
  - hBijx Back Probability to be in state i at age x-h being in j at x     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      Computes for any combination of covariates k and any age between bage and fage 
    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;
          - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
      - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
      Computes the transition matrix starting at age 'age' over       Computes the transition matrix starting at age 'age' 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. Returns p3mat[i][j][h] after calling        nhstepm*hstepm matrices. 
      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);       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.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
Line 736  Back prevalence and projections: Line 1055  Back prevalence and projections:
 /* #define DEBUGLINMIN */  /* #define DEBUGLINMIN */
 /* #define DEBUGHESS */  /* #define DEBUGHESS */
 #define DEBUGHESSIJ  #define DEBUGHESSIJ
 /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan)*\/ */  /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
 #define POWELL /* Instead of NLOPT */  #define POWELL /* Instead of NLOPT */
 #define POWELLF1F3 /* Skip test */  #define POWELLNOF3INFF1TEST /* Skip test */
 /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
 /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
   
Line 746  Back prevalence and projections: Line 1065  Back prevalence and projections:
 #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>
Line 791  typedef struct { Line 1111  typedef struct {
 /* #include <libintl.h> */  /* #include <libintl.h> */
 /* #define _(String) gettext (String) */  /* #define _(String) gettext (String) */
   
 #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */  #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   
 #define GNUPLOTPROGRAM "gnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
Line 806  typedef struct { Line 1126  typedef struct {
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #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))+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<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
 #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1   #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 
 #define MAXN 20000  /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
 #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 AGESUP 150 */
   #define AGESUP 200
   #define AGEINF 0
 #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */  #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 AGEOVERFLOW 1.e20
Line 832  typedef struct { Line 1154  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";  char copyright[]="March 2021,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021, INED 2000-2021";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 841  int nagesqr=0, nforce=0; /* nagesqr=1 if Line 1163  int nagesqr=0, nforce=0; /* nagesqr=1 if
 /* 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 ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
   int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
   int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
   int nsd=0; /**< Total number of single dummy variables (output) */
   int nsq=0; /**< Total number of single quantitative variables (output) */
   int ncoveff=0; /* Total number of effective fixed dummy 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 nobs=10;  /* Number of observations in the data lastobs-firstobs */
 int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */  int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
 int npar=NPARMAX;  int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
 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 865  int **dh; /* dh[mi][i] is number of step Line 1199  int **dh; /* dh[mi][i] is number of step
 int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
            * wave mi and wave mi+1 is not an exact multiple of stepm. */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 int countcallfunc=0;  /* Count the number of calls to func */  int countcallfunc=0;  /* Count the number of calls to func */
   int selected(int kvar); /* Is covariate kvar selected for printing results */
   
 double jmean=1; /* Mean space between 2 waves */  double jmean=1; /* Mean space between 2 waves */
 double **matprod2(); /* test */  double **matprod2(); /* test */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
Line 892  FILE *ficrescveij; Line 1228  FILE *ficrescveij;
 char filerescve[FILENAMELENGTH];  char filerescve[FILENAMELENGTH];
 FILE  *ficresvij;  FILE  *ficresvij;
 char fileresv[FILENAMELENGTH];  char fileresv[FILENAMELENGTH];
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];  
 char title[MAXLINE];  char title[MAXLINE];
   char model[MAXLINE]; /**< The model line */
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[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]; 
Line 932  double dval; Line 1268  double dval;
 #define FTOL 1.0e-10  #define FTOL 1.0e-10
   
 #define NRANSI   #define NRANSI 
 #define ITMAX 200   #define ITMAX 200
   #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */ 
   
 #define TOL 2.0e-4   #define TOL 2.0e-4 
   
Line 982  double **pmmij, ***probs; /* Global poin Line 1319  double **pmmij, ***probs; /* Global poin
 double ***mobaverage, ***mobaverages; /* New global variable */  double ***mobaverage, ***mobaverages; /* New global variable */
 double *ageexmed,*agecens;  double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
     double anprojd, mprojd, jprojd; /* For eventual projections */
     double anprojf, mprojf, jprojf;
   
     double anbackd, mbackd, jbackd; /* For eventual backprojections */
     double anbackf, mbackf, jbackf;
     double jintmean,mintmean,aintmean;  
 double *weight;  double *weight;
 int **s; /* Status */  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]*age; */                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
   double **coqvar; /* Fixed quantitative covariate nqv */
   double ***cotvar; /* Time varying covariate ntv */
   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 */
   /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   /*k          1  2   3   4     5    6    7     8    9 */
   /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */
   /* Tndvar[k]    1   2   3               4          5 */
   /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */
   /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */
   /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */
   /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */
   /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */
   /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */
   /* Tprod[i]=k           4               7            */
   /* Tage[i]=k                  5               8      */
   /* */
   /* Type                    */
   /* V         1  2  3  4  5 */
   /*           F  F  V  V  V */
   /*           D  Q  D  D  Q */
   /*                         */
   int *TvarsD;
   int *TvarsDind;
   int *TvarsQ;
   int *TvarsQind;
   
   #define MAXRESULTLINES 10
   int nresult=0;
   int parameterline=0; /* # of the parameter (type) line */
   int TKresult[MAXRESULTLINES];
   int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
   int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
   int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
   double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
   double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
   int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
   
   /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
   int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
   int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
   int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
   int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
   int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
   int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
   
   int *Tvarsel; /**< Selected covariates for output */
   double *Tvalsel; /**< Selected modality value of covariate for output */
   int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
   int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ 
   int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
   int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
   int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
 int *Tage;  int *Tage;
   int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */ 
   int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
   int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/ 
   int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1  */
 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;
   int *Tprod;/**< Gives the k position of the k1 product */
   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
   int *Tposprod; /**< Gives the k1 product from the k position */
      /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
      /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
   int cptcovprod, *Tvaraff, *invalidvarcomb;
 double *lsurv, *lpop, *tpop;  double *lsurv, *lpop, *tpop;
   
   #define FD 1; /* Fixed dummy covariate */
   #define FQ 2; /* Fixed quantitative covariate */
   #define FP 3; /* Fixed product covariate */
   #define FPDD 7; /* Fixed product dummy*dummy covariate */
   #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
   #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
   #define VD 10; /* Varying dummy covariate */
   #define VQ 11; /* Varying quantitative covariate */
   #define VP 12; /* Varying product covariate */
   #define VPDD 13; /* Varying product dummy*dummy covariate */
   #define VPDQ 14; /* Varying product dummy*quantitative covariate */
   #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
   #define APFD 16; /* Age product * fixed dummy covariate */
   #define APFQ 17; /* Age product * fixed quantitative covariate */
   #define APVD 18; /* Age product * varying dummy covariate */
   #define APVQ 19; /* Age product * varying quantitative covariate */
   
   #define FTYPE 1; /* Fixed covariate */
   #define VTYPE 2; /* Varying covariate (loop in wave) */
   #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
   
   struct kmodel{
           int maintype; /* main type */
           int subtype; /* subtype */
   };
   struct kmodel modell[NCOVMAX];
   
 double ftol=FTOL; /**< Tolerance for computing Max Likelihood */  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
 double ftolhess; /**< Tolerance for computing hessian */  double ftolhess; /**< Tolerance for computing hessian */
   
Line 1192  int nbocc(char *s, char occ) Line 1631  int nbocc(char *s, char occ)
   i=0;    i=0;
   lg=strlen(s);    lg=strlen(s);
   for(i=0; i<= lg; i++) {    for(i=0; i<= lg; i++) {
   if  (s[i] == occ ) j++;      if  (s[i] == occ ) j++;
   }    }
   return j;    return j;
 }  }
Line 1536  double brent(double ax, double bx, doubl Line 1975  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 1555  double brent(double ax, double bx, doubl Line 1994  double brent(double ax, double bx, doubl
     } 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; 
       }         } 
     }       } 
   }     } 
Line 1602  values at the three points, fa, fb , and Line 2041  values at the three points, fa, fb , and
   *cx=(*bx)+GOLD*(*bx-*ax);     *cx=(*bx)+GOLD*(*bx-*ax); 
   *fc=(*func)(*cx);     *fc=(*func)(*cx); 
 #ifdef DEBUG  #ifdef DEBUG
   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);    printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);    fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
 #endif  #endif
   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */    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 abscissa 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 abscissa where function should be evaluated */      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
Line 1618  values at the three points, fa, fb , and Line 2057  values at the three points, fa, fb , and
       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 */        /* 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),        /* 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) */          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
Line 1652  values at the three points, fa, fb , and Line 2091  values at the three points, fa, fb , and
 /*      fu = *fc; */  /*      fu = *fc; */
 /*      *fc =dum; */  /*      *fc =dum; */
 /*       } */  /*       } */
 #ifdef DEBUG  #ifdef DEBUGMNBRAK
       printf("mnbrak34  fu < or >= fc \n");                   double A, fparabu; 
       fprintf(ficlog, "mnbrak34 fu < fc\n");       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  #endif
       dum=u; /* Shifting c and u */        dum=u; /* Shifting c and u */
       u = *cx;        u = *cx;
Line 1665  values at the three points, fa, fb , and Line 2107  values at the three points, fa, fb , and
 #endif  #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  #ifdef DEBUG
       printf("mnbrak2  u after c but before ulim\n");        printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");        fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
 #endif  #endif
       fu=(*func)(u);         fu=(*func)(u); 
       if (fu < *fc) {         if (fu < *fc) { 
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2  u after c but before ulim AND fu < fc\n");                                  printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");                            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  #endif
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))   
         SHFT(*fb,*fc,fu,(*func)(u))   
       }         } 
     } 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  #ifdef DEBUG
       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");        printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");        fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
 #endif  #endif
       u=ulim;         u=ulim; 
       fu=(*func)(u);         fu=(*func)(u); 
     } else { /* u could be left to b (if r > q parabola has a maximum) */      } else { /* u could be left to b (if r > q parabola has a maximum) */
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");        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, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");        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  #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 */      } /* end tests */
     SHFT(*ax,*bx,*cx,u)       SHFT(*ax,*bx,*cx,u) 
     SHFT(*fa,*fb,*fc,fu)       SHFT(*fa,*fb,*fc,fu) 
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);        printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
       fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);        fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
 #endif  #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) */    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
 }   } 
Line 1711  int ncom; Line 2160  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 1755  void linmin(double p[], double xi[], int Line 2208  void linmin(double p[], double xi[], int
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
 #else  #else
     if (fx != fx){      if (fx != fx){
         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */                          xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
         printf("|");                          printf("|");
         fprintf(ficlog,"|");                          fprintf(ficlog,"|");
 #ifdef DEBUGLINMIN  #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);                          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  #endif
     }      }
   }while(fx != fx);    }while(fx != fx && xxs > 1.e-5);
 #endif  #endif
       
 #ifdef DEBUGLINMIN  #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);    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);    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  #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),*/    *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]) */    /* 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]) */    /* fmin = f(p[j] + xmin * xi[j]) */
   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */    /* 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]; */    /* 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  #endif
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
   printf("linmin end ");    printf("linmin end ");
Line 1826  such that failure to decrease by more th Line 2292  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 [])); 
   int i,ibig,j;   #else 
    void linmin(double p[], double xi[], int n, double *fret,
                double (*func)(double []),int *flat); 
   #endif
    int i,ibig,j,jk,k; 
   double del,t,*pt,*ptt,*xit;    double del,t,*pt,*ptt,*xit;
   double directest;    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 1857  void powell(double p[], double **xi, int Line 2339  void powell(double p[], double **xi, int
     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]);  
       fprintf(ficlog," %d %.12lf",i, p[i]);  
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
     }      }
       fprintf(ficrespow,"\n");fflush(ficrespow);
       printf("\n#model=  1      +     age ");
       fprintf(ficlog,"\n#model=  1      +     age ");
       if(nagesqr==1){
           printf("  + age*age  ");
           fprintf(ficlog,"  + age*age  ");
       }
       for(j=1;j <=ncovmodel-2;j++){
         if(Typevar[j]==0) {
           printf("  +      V%d  ",Tvar[j]);
           fprintf(ficlog,"  +      V%d  ",Tvar[j]);
         }else if(Typevar[j]==1) {
           printf("  +    V%d*age ",Tvar[j]);
           fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
         }else if(Typevar[j]==2) {
           printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         }
       }
     printf("\n");      printf("\n");
   /*     printf("12   47.0114589    0.0154322   33.2424412    0.3279905    2.3731903  */
   /* 13  -21.5392400    0.1118147    1.2680506    1.2973408   -1.0663662  */
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
     fprintf(ficrespow,"\n");fflush(ficrespow);      for(i=1,jk=1; i <=nlstate; i++){
     if(*iter <=3){        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 ",p[jk]);
               fprintf(ficlog,"%12.7f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
           }
         }
       }
       if(*iter <=3 && *iter >1){
       tml = *localtime(&rcurr_time);        tml = *localtime(&rcurr_time);
       strcpy(strcurr,asctime(&tml));        strcpy(strcurr,asctime(&tml));
       rforecast_time=rcurr_time;         rforecast_time=rcurr_time; 
Line 1879  void powell(double p[], double **xi, int Line 2394  void powell(double p[], double **xi, int
         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);
       }        }
Line 1893  void powell(double p[], double **xi, int Line 2408  void powell(double p[], double **xi, int
 #endif  #endif
       printf("%d",i);fflush(stdout); /* print direction (parameter) i */        printf("%d",i);fflush(stdout); /* print direction (parameter) i */
       fprintf(ficlog,"%d",i);fflush(ficlog);        fprintf(ficlog,"%d",i);fflush(ficlog);
   #ifdef LINMINORIGINAL
       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                                     /* Outputs are fret(new point p) p is updated and xit rescaled */  #else
         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 */        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 */                                  /* 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. */                                  /* 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 */                                  /* Unless the n directions are conjugate some gain in the determinant may be obtained */
         /* with the new direction. */                                  /* with the new direction. */
         del=fabs(fptt-(*fret));                                   del=fabs(fptt-(*fret)); 
         ibig=i;                                   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");
Line 1922  void powell(double p[], double **xi, int Line 2442  void powell(double p[], double **xi, int
     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */       /* 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  */      /* 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) */      /* New value of last point Pn is not computed, P(n-1) */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */        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? *\/ */
       if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */        /* 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 */        /* 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 */        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
Line 1930  void powell(double p[], double **xi, int Line 2459  void powell(double p[], double **xi, int
       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */        /* 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 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 */        /* 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 */        /* 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 */        /* 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 */        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
Line 1958  void powell(double p[], double **xi, int Line 2487  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 */       } /* enough precision */ 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */      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); /* f_3 */      fptt=(*func)(ptt); /* f_3 */
 #ifdef POWELLF1F3  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
                   if (*iter <=4) {
   #else
   #endif
   #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
 #else  #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  #endif
Line 1981  void powell(double p[], double **xi, int Line 2517  void powell(double p[], double **xi, int
       /* 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 */
       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
         /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
         /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
       /* 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 */
         /* 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  #ifdef NRCORIGINAL
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
 #else  #else
Line 2004  void powell(double p[], double **xi, int Line 2548  void powell(double p[], double **xi, int
       if (t < 0.0) { /* Then we use it for new direction */        if (t < 0.0) { /* Then we use it for new direction */
 #else  #else
       if (directest*t < 0.0) { /* Contradiction between both tests */        if (directest*t < 0.0) { /* Contradiction between both tests */
         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("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("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         fprintf(ficlog,"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);          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,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);          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 */        if (directest < 0.0) { /* Then we use it for new direction */
 #endif  #endif
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
         printf("Before linmin in direction P%d-P0\n",n);          printf("Before linmin in direction P%d-P0\n",n);
         for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) {
           printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[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]);            fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
           if(j % ncovmodel == 0){            if(j % ncovmodel == 0){
Line 2022  void powell(double p[], double **xi, int Line 2566  void powell(double p[], double **xi, int
           }            }
         }          }
 #endif  #endif
   #ifdef LINMINORIGINAL
         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/          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  #ifdef DEBUGLINMIN
         for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);            printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
Line 2037  void powell(double p[], double **xi, int Line 2587  void powell(double p[], double **xi, int
           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */            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 */            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: ",flatd);
             fprintf(ficlog,"%d flat directions :",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);          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);          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 or directest negative */        } /* end of t or directest negative */
 #ifdef POWELLF1F3  #ifdef POWELLNOF3INFF1TEST
   #else
         } /* 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  #else
     } /* end if (fptt < fp)  */  
 #endif  #endif
   } /* loop iteration */                   } /* 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 *ncvyear, int ij)    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
 {    {
   /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit      /**< Computes the prevalence limit in each live state at age x and for covariate combination ij 
      matrix by transitions matrix until convergence is reached with precision ftolpl */       *   (and selected quantitative values in nres)
   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */       *  by left multiplying the unit
   /* Wx is row vector: population in state 1, population in state 2, population dead */       *  matrix by transitions matrix until convergence is reached with precision ftolpl 
   /* or prevalence in state 1, prevalence in state 2, 0 */       * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I
   /* newm is the matrix after multiplications, its rows are identical at a factor */       * Wx is row vector: population in state 1, population in state 2, population dead
   /* Initial matrix pimij */       * or prevalence in state 1, prevalence in state 2, 0
        * newm is the matrix after multiplications, its rows are identical at a factor.
        * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
        * Output is prlim.
        * Initial matrix pimij 
        */
   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */    /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
   /*  0,                   0                  , 1} */    /*  0,                   0                  , 1} */
Line 2081  double **prevalim(double **prlim, int nl Line 2659  double **prevalim(double **prlim, int nl
   /* {0.51571254859325999, 0.4842874514067399, */    /* {0.51571254859325999, 0.4842874514067399, */
   /*  0.51326036147820708, 0.48673963852179264} */    /*  0.51326036147820708, 0.48673963852179264} */
   /* If we start from prlim again, prlim tends to a constant matrix */    /* 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, *meandiff, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
Line 2089  double **prevalim(double **prlim, int nl Line 2667  double **prevalim(double **prlim, int nl
   double **newm;    double **newm;
   double agefin, delaymax=200. ; /* 100 Max number of years to converge */    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
   int ncvloop=0;    int ncvloop=0;
     int first=0;
       
   min=vector(1,nlstate);    min=vector(1,nlstate);
   max=vector(1,nlstate);    max=vector(1,nlstate);
Line 2111  double **prevalim(double **prlim, int nl Line 2690  double **prevalim(double **prlim, int nl
     cov[2]=agefin;      cov[2]=agefin;
     if(nagesqr==1)      if(nagesqr==1)
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;k++) {      for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
                         /* Here comes the value of the covariate 'ij' */        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];        /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, 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])]); */      }
     }      for (k=1; k<=nsq;k++) { /* For single varying covariates only */
     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */                          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */        cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];        /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
     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])]; */      for (k=1; k<=cptcovage;k++){  /* For product with age */
       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];        if(Dummy[Tvar[Tage[k]]]){
               cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
         } else{
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
         }
         /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
       }
       for (k=1; k<=cptcovprod;k++){ /* For product without age */
         /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
         if(Dummy[Tvard[k][1]==0]){
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
           }else{
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
           }
         }else{
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
           }else{
             cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
           }
         }
       }
     /*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]);*/
Line 2164  double **prevalim(double **prlim, int nl Line 2764  double **prevalim(double **prlim, int nl
       free_vector(meandiff,1,nlstate);        free_vector(meandiff,1,nlstate);
       return prlim;        return prlim;
     }      }
   } /* age loop */    } /* agefin loop */
     /* After some age loop it doesn't converge */      /* 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\    if(!first){
 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);      first=1;
       printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
     }
     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
   
   /* 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); */    /* 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(min,1,nlstate);
   free_vector(max,1,nlstate);    free_vector(max,1,nlstate);
Line 2181  Earliest age to start was %d-%d=%d, ncvl Line 2785  Earliest age to start was %d-%d=%d, ncvl
   
  /* 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 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 **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)    double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
 {  {
   /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit    /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
      matrix by transitions matrix until convergence is reached with precision ftolpl */       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= 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 */    /* Wx is row vector: population in state 1, population in state 2, population dead */
Line 2204  Earliest age to start was %d-%d=%d, ncvl Line 2808  Earliest age to start was %d-%d=%d, ncvl
   /* If we start from prlim again, prlim tends to a constant matrix */    /* If we start from prlim again, prlim tends to a constant matrix */
   
   int i, ii,j,k;    int i, ii,j,k;
     int first=0;
   double *min, *max, *meandiff, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **bmij();    double **out, cov[NCOVMAX+1], **bmij();
Line 2218  Earliest age to start was %d-%d=%d, ncvl Line 2823  Earliest age to start was %d-%d=%d, ncvl
   max=vector(1,nlstate);    max=vector(1,nlstate);
   meandiff=vector(1,nlstate);    meandiff=vector(1,nlstate);
   
         dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;    dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
         oldm=oldms; savm=savms;    oldm=oldms; savm=savms;
     
         /* Starting with matrix unity */    /* 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);
     }      }
       
Line 2232  Earliest age to start was %d-%d=%d, ncvl Line 2837  Earliest age to start was %d-%d=%d, ncvl
   /* 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 */    /* 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+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 */    /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
     for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
     ncvloop++;      ncvloop++;
     newm=savm; /* oldm should be kept from previous iteration or unity at start */      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 */                  /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
Line 2240  Earliest age to start was %d-%d=%d, ncvl Line 2846  Earliest age to start was %d-%d=%d, ncvl
     cov[2]=agefin;      cov[2]=agefin;
     if(nagesqr==1)      if(nagesqr==1)
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;k++) {      for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[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])]); */        /* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
     }      }
     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */      /* for (k=1; k<=cptcovn;k++) { */
     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */      /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];      /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
     for (k=1; k<=cptcovprod;k++) /* Useless */      /*   /\* 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])]); *\/ */
       /* 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)];      for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                           /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
         /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
       }
       /* 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)]; */
       for (k=1; k<=cptcovage;k++){  /* For product with age */
         if(Dummy[Tvar[Tage[k]]]){
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
         } else{
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
         }
         /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
       }
       for (k=1; k<=cptcovprod;k++){ /* For product without age */
         /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
         if(Dummy[Tvard[k][1]==0]){
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
           }else{
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
           }
         }else{
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
           }else{
             cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
           }
         }
       }
           
     /*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]);*/
Line 2265  Earliest age to start was %d-%d=%d, ncvl Line 2903  Earliest age to start was %d-%d=%d, ncvl
     /* 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, 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, 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 */      out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
       /* if((int)age == 86 || (int)age == 87){ */
       /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
       /*   for(i=1; i<=nlstate+ndeath; i++) { */
       /*  printf("%d newm= ",i); */
       /*  for(j=1;j<=nlstate+ndeath;j++) { */
       /*    printf("%f ",newm[i][j]); */
       /*  } */
       /*  printf("oldm * "); */
       /*  for(j=1;j<=nlstate+ndeath;j++) { */
       /*    printf("%f ",oldm[i][j]); */
       /*  } */
       /*  printf(" bmmij "); */
       /*  for(j=1;j<=nlstate+ndeath;j++) { */
       /*    printf("%f ",pmmij[i][j]); */
       /*  } */
       /*  printf("\n"); */
       /*   } */
       /* } */
     savm=oldm;      savm=oldm;
     oldm=newm;      oldm=newm;
   
     for(j=1; j<=nlstate; j++){      for(j=1; j<=nlstate; j++){
       max[j]=0.;        max[j]=0.;
       min[j]=1.;        min[j]=1.;
     }      }
     for(j=1; j<=nlstate; j++){       for(j=1; j<=nlstate; j++){ 
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
                                 /* bprlim[i][j]= newm[i][j]/(1-sumnew); */          /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
                                 bprlim[i][j]= newm[i][j];          bprlim[i][j]= newm[i][j];
                                 max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */          max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
                                 min[i]=FMIN(min[i],bprlim[i][j]);          min[i]=FMIN(min[i],bprlim[i][j]);
       }        }
     }      }
                                   
Line 2285  Earliest age to start was %d-%d=%d, ncvl Line 2942  Earliest age to start was %d-%d=%d, ncvl
       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */        meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
       maxmax=FMAX(maxmax,meandiff[i]);        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); */        /* 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 */      } /* i loop */
     *ncvyear= -( (int)age- (int)agefin);      *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);*/      /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
     if(maxmax < ftolpl){      if(maxmax < ftolpl){
       printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);        /* 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(min,1,nlstate);
       free_vector(max,1,nlstate);        free_vector(max,1,nlstate);
       free_vector(meandiff,1,nlstate);        free_vector(meandiff,1,nlstate);
       return bprlim;        return bprlim;
     }      }
   } /* age loop */    } /* agefin loop */
     /* After some age loop it doesn't converge */      /* 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\    if(!first){
       first=1;
       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'. Others in log file only...\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);
     }
     fprintf(ficlog,"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);  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); */    /* 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(min,1,nlstate);
Line 2312  Oldest age to start was %d-%d=%d, ncvloo Line 2974  Oldest age to start was %d-%d=%d, ncvloo
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
   /* According to parameters values stored in x and the covariate's values stored in cov,    /* 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       computes the probability to be observed in state j (after stepm years) being in state i by appying the
      model to the ncovmodel covariates (including constant and age).       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]       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       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
Line 2321  double **pmij(double **ps, double *cov, Line 2983  double **pmij(double **ps, double *cov,
      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,       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.       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       Outputs ps[i][j] or probability to be observed in j being in i according to
      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
        Sum on j ps[i][j] should equal to 1.
   */    */
   double s1, lnpijopii;    double s1, lnpijopii;
   /*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++){  
                 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;  
                 }  
         }  
       
     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=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++){
         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */        ps[ii][jj]=0;
         /*   } */        ps[ii][ii]=1;
         /*   printf("\n "); */      }
         /* } */    }
         /* printf("\n ");printf("%lf ",cov[2]);*/  
         /*  
                 for(i=1; i<= npar; i++) printf("%f ",x[i]);    /* 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;*/                  goto end;*/
         return ps;    return ps; /* Pointer is unchanged since its call */
 }  }
   
 /*************** backward transition probabilities ***************/   /*************** backward transition probabilities ***************/ 
Line 2395  double **pmij(double **ps, double *cov, Line 3058  double **pmij(double **ps, double *cov,
 /* 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, double ***dnewm, double **doldm, double **dsavm, int ij ) */
  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, 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    /* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
          * and returns in **ps as well as **bmij.     * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
          */     */
   int i, ii, j,k;    int i, ii, j,k;
     
         double **out, **pmij();    double **out, **pmij();
         double sumnew=0.;    double sumnew=0.;
   double agefin;    double agefin;
     double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
         double **dnewm, **dsavm, **doldm;    double **dnewm, **dsavm, **doldm;
         double **bbmij;    double **bbmij;
     
   doldm=ddoldms; /* global pointers */    doldm=ddoldms; /* global pointers */
         dnewm=ddnewms;    dnewm=ddnewms;
         dsavm=ddsavms;    dsavm=ddsavms;
     
         agefin=cov[2];    agefin=cov[2];
         /* bmij *//* age is cov[2], ij is included in cov, but we need for    /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
                  the observed prevalence (with this covariate ij) */    /* bmij *//* age is cov[2], ij is included in cov, but we need for
         dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);       the observed prevalence (with this covariate ij) at beginning of transition */
         /* We do have the matrix Px in savm  and we need pij */    /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         for (j=1;j<=nlstate+ndeath;j++){  
                 sumnew=0.; /* w1 p11 + w2 p21 only on live states */    /* P_x */
                 for (ii=1;ii<=nlstate;ii++){    pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
                         sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];    /* outputs pmmij which is a stochastic matrix in row */
                 } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */  
                 for (ii=1;ii<=nlstate+ndeath;ii++){    /* Diag(w_x) */
                         if(sumnew >= 1.e-10){    /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
                                 /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */    sumnew=0.;
                                 /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */    /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
                                 /* }else if(agefin >= agemaxpar+stepm/YEARM){ */    for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
                                 /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */      /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
                                 /* }else */      sumnew+=prevacurrent[(int)agefin][ii][ij];
                                         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);    }
                         }else{    if(sumnew >0.01){  /* At least some value in the prevalence */
                                 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);      for (ii=1;ii<=nlstate+ndeath;ii++){
                         }        for (j=1;j<=nlstate+ndeath;j++)
                 } /*End ii */          doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
         } /* 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) */    }else{
         bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */      for (ii=1;ii<=nlstate+ndeath;ii++){
         /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */        for (j=1;j<=nlstate+ndeath;j++)
         /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */        doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
         /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */      }
         /* left Product of this matrix by diag matrix of prevalences (savm) */      /* if(sumnew <0.9){ */
         for (j=1;j<=nlstate+ndeath;j++){      /*   printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
                 for (ii=1;ii<=nlstate+ndeath;ii++){      /* } */
                         dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);    }
                 }    k3=0.0;  /* We put the last diagonal to 0 */
         } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */    for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
         ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */        doldm[ii][ii]= k3;
         /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */    }
         /* end bmij */    /* End doldm, At the end doldm is diag[(w_i)] */
         return ps;     
     /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
     bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
   
     /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
     /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
     for (j=1;j<=nlstate+ndeath;j++){
       sumnew=0.;
       for (ii=1;ii<=nlstate;ii++){
         /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
         sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
       } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
       for (ii=1;ii<=nlstate+ndeath;ii++){
           /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
           /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
           /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
           /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
           /* }else */
         dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
       } /*End ii */
     } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
   
     ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
     /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
     /* end bmij */
     return ps; /*pointer is unchanged */
 }  }
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
   
Line 2471  double **bpmij(double **ps, double *cov, Line 3159  double **bpmij(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;
                 }      }
         }    }
         /* Added for backcast */ /* Transposed matrix too */    /* Added for prevbcast */ /* Transposed matrix too */
         for(jj=1; jj<= nlstate+ndeath; jj++){    for(jj=1; jj<= nlstate+ndeath; jj++){
                 s1=0.;      s1=0.;
                 for(ii=1; ii<= nlstate+ndeath; ii++){      for(ii=1; ii<= nlstate+ndeath; ii++){
                         s1+=ps[ii][jj];        s1+=ps[ii][jj];
                 }      }
                 for(ii=1; ii<= nlstate; ii++){      for(ii=1; ii<= nlstate; ii++){
                         ps[ii][jj]=ps[ii][jj]/s1;        ps[ii][jj]=ps[ii][jj]/s1;
                 }      }
         }    }
         /* Transposition */    /* Transposition */
         for(jj=1; jj<= nlstate+ndeath; jj++){    for(jj=1; jj<= nlstate+ndeath; jj++){
                 for(ii=jj; ii<= nlstate+ndeath; ii++){      for(ii=jj; ii<= nlstate+ndeath; ii++){
                         s1=ps[ii][jj];        s1=ps[ii][jj];
                         ps[ii][jj]=ps[jj][ii];        ps[ii][jj]=ps[jj][ii];
                         ps[jj][ii]=s1;        ps[jj][ii]=s1;
                 }      }
         }    }
         /* for(ii=1; ii<= nlstate+ndeath; ii++){ */    /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
         /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */    /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
         /*   } */    /*   } */
         /*   printf("\n "); */    /*   printf("\n "); */
         /* } */    /* } */
         /* printf("\n ");printf("%lf ",cov[2]);*/    /* printf("\n ");printf("%lf ",cov[2]);*/
         /*    /*
                 for(i=1; i<= npar; i++) printf("%f ",x[i]);      for(i=1; i<= npar; i++) printf("%f ",x[i]);
                 goto end;*/      goto end;*/
         return ps;    return ps;
 }  }
   
   
Line 2571  double **matprod2(double **out, double * Line 3259  double **matprod2(double **out, double *
   
 /************* Higher Matrix Product ***************/  /************* Higher Matrix Product ***************/
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
 {  {
   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij 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
Line 2606  double ***hpxij(double ***po, int nhstep Line 3294  double ***hpxij(double ***po, int nhstep
       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;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1)
                                 cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++)         for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                                 cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
                         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */          /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
                                 /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */        }
                                 cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];        for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */          cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
                                 cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];          /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
                         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */        }
         for (k=1; k<=cptcovage;k++){
           if(Dummy[Tvar[Tage[k]]]){
             cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
           } else{
             cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
           }
           /* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
         }
         for (k=1; k<=cptcovprod;k++){ /*  */
           /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
         }
         /* for (k=1; k<=cptcovn;k++)  */
         /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
         /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
         /*        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,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)]; */
         
         
       /*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 */                          /* right multiplication of oldm by the current matrix */
Line 2643  double ***hpxij(double ***po, int nhstep Line 3349  double ***hpxij(double ***po, int nhstep
     }      }
     for(i=1; i<=nlstate+ndeath; i++)      for(i=1; i<=nlstate+ndeath; i++)
       for(j=1;j<=nlstate+ndeath;j++) {        for(j=1;j<=nlstate+ndeath;j++) {
                                 po[i][j][h]=newm[i][j];          po[i][j][h]=newm[i][j];
                                 /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       }        }
     /*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;
 }  }
   
 /************* Higher Back Matrix Product ***************/  /************* 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, 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 )  double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
 {  {
   /* Computes the transition matrix starting at age 'age' over    /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' 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 2664  double ***hpxij(double ***po, int nhstep Line 3370  double ***hpxij(double ***po, int nhstep
      (typically every 2 years instead of every month which is too big       (typically every 2 years instead of every month which is too big
      for the memory).       for the memory).
      Model is determined by parameters x and covariates have to be       Model is determined by parameters x and covariates have to be
      included manually here.       included manually here. Then we use a call to bmij(x and cov)
        The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
      */    */
   
   int i, j, d, h, k;    int i, j, d, h, k;
   double **out, cov[NCOVMAX+1];    double **out, cov[NCOVMAX+1], **bmij();
   double **newm;    double **newm, ***newmm;
   double agexact;    double agexact;
   double agebegin, ageend;    double agebegin, ageend;
         double **oldm, **savm;    double **oldm, **savm;
   
         oldm=oldms;savm=savms;    newmm=po; /* To be saved */
     oldm=oldms;savm=savms; /* Global pointers */
   /* 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++)
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
Line 2688  double ***hpxij(double ***po, int nhstep Line 3395  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.;
       agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */        agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-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;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1)
                                 cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++)        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,k)]; */
                         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[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+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
                                 /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */          /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
                                 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<=nsq;k++) { /* For single varying covariates only */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
                                 cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];          cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][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("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
                                 }
                                 for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
           if(Dummy[Tvar[Tage[k]]]){
             cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
           } else{
             cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
           }
           /* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
         }
         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)];
         }                 
       /*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]);*/
   
       /* Careful transposed matrix */        /* Careful transposed matrix */
                         /* age is in cov[2] */        /* age is in cov[2], prevacurrent at beginning of transition. */
       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
                         /*                                               1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */        /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\        out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
                                                                          1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);                     1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       /* if((int)age == 70){ */        /* if((int)age == 70){ */
       /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */        /*        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++) { */        /*        for(i=1; i<=nlstate+ndeath; i++) { */
Line 2732  double ***hpxij(double ***po, int nhstep Line 3450  double ***hpxij(double ***po, int nhstep
     }      }
     for(i=1; i<=nlstate+ndeath; i++)      for(i=1; i<=nlstate+ndeath; i++)
       for(j=1;j<=nlstate+ndeath;j++) {        for(j=1;j<=nlstate+ndeath;j++) {
                                 po[i][j][h]=newm[i][j];          po[i][j][h]=newm[i][j];
                                 /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/          /* if(h==nhstepm) */
           /*   printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
       }        }
     /*printf("h=%d ",h);*/      /* printf("h=%d %.1f ",h, agexact); */
   } /* end h */    } /* end h */
         /*     printf("\n H=%d \n",h); */    /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
   return po;    return po;
 }  }
   
Line 2766  double ***hpxij(double ***po, int nhstep Line 3485  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 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, quantitative time varying covariate */
   double bbh, survp;    double bbh, survp;
   long ipmx;    long ipmx;
   double agexact;    double agexact;
Line 2786  double func( double *x) Line 3506  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 ;
           cov[2+nagesqr+k]=covar[Tvar[k]][i];     /* Fixed */
         for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
           cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
       }        }
       /* 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(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
             /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
             cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][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);
Line 2811  double func( double *x) Line 3546  double func( double *x)
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;            cov[2]=agexact;
           if(nagesqr==1)            if(nagesqr==1)
             cov[3]= agexact*agexact;              cov[3]= agexact*agexact;  /* Should be changed here */
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
             if(!FixedV[Tvar[Tage[kk]]])
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* 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 */
             else
               cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][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));
           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 2829  double func( double *x) Line 3567  double func( double *x)
          * we keep into memory the bias bh[mi][i] and also the previous matrix product           * we keep into memory the bias bh[mi][i] and also the previous matrix product
          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
          * probability in order to take into account the bias as a fraction of the way           * probability in order to take into account the bias as a fraction of the way
          * from savm to out if bh is negative or even beyond if bh is positive. bh varies                                   * from savm to out if bh is negative or even beyond if bh is positive. bh varies
          * -stepm/2 to stepm/2 .                                   * -stepm/2 to stepm/2 .
          * For stepm=1 the results are the same as for previous versions of Imach.                                   * For stepm=1 the results are the same as for previous versions of Imach.
          * For stepm > 1 the results are less biased than in previous versions.                                    * For stepm > 1 the results are less biased than in previous versions. 
          */                                   */
         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];
         bbh=(double)bh[mi][i]/(double)stepm;           bbh=(double)bh[mi][i]/(double)stepm; 
Line 2848  double func( double *x) Line 3586  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.
           */            */
         /* 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 */  /* #ifdef INFINITYORIGINAL */
 /*          lli=log(out[s1][s2] - savm[s1][s2]); */  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
 /* #else */  /* #else */
Line 2893  double func( double *x) Line 3631  double func( double *x)
           /*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 2910  double func( double *x) Line 3648  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)){ */          /* if (lli < log(mytinydouble)){ */
Line 3071  double func( double *x) Line 3809  double func( double *x)
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
 double funcone( double *x)  double funcone( double *x)
 {  {
   /* Same as likeli but slower because of a lot of printf and if */    /* Same as func 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, quantitative time varying covariate */
   
   double bbh, survp;    double bbh, survp;
   double agexact;    double agexact;
   double agebegin, ageend;    double agebegin, ageend;
Line 3090  double funcone( double *x) Line 3831  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+nagesqr+k]=covar[Tvar[k]][i];      /* ioffset=2+nagesqr+cptcovage; */
     for(mi=1; mi<= wav[i]-1; mi++){      ioffset=2+nagesqr;
       /* Fixed */
       /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
       /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
   /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
   /*    cov[2+6]=covar[Tvar[6]][i];  */
   /*    cov[2+6]=covar[2][i]; V2  */
   /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
   /*    cov[2+7]=covar[Tvar[7]][i];  */
   /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
   /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
   /*    cov[2+9]=covar[Tvar[9]][i];  */
   /*    cov[2+9]=covar[1][i]; V1  */
       }
       /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
       /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
       /* } */
       /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
       /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
       /* } */
       
   
       for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
       /* Wave varying (but not age varying) */
         for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
         }
         /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
         /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
         /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
         /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
         /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
         /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
         /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
         /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
         /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
         /*        cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[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);
Line 3103  double funcone( double *x) Line 3884  double funcone( double *x)
       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */        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 */        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 */        for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
         /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][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.*/            and mw[mi+1][i]. dh depends on stepm.*/
         newm=savm;          newm=savm;
         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
         cov[2]=agexact;          cov[2]=agexact;
         if(nagesqr==1)          if(nagesqr==1)
           cov[3]= agexact*agexact;            cov[3]= agexact*agexact;
         for (kk=1; kk<=cptcovage;kk++) {          for (kk=1; kk<=cptcovage;kk++) {
           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;            if(!FixedV[Tvar[Tage[kk]]])
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             else
               cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][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 3126  double funcone( double *x) Line 3911  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){ */        /* if(s2==-1){ */
       /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */        /*        printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
       /*        /\* exit(1); *\/ */        /*        /\* exit(1); *\/ */
       /* } */        /* } */
       bbh=(double)bh[mi][i]/(double)stepm;         bbh=(double)bh[mi][i]/(double)stepm; 
Line 3156  double funcone( double *x) Line 3941  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 %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\          fprintf(ficresilk,"%09ld %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], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,                  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,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: 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;
           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         }          }
         fprintf(ficresilk," %10.6f\n", -llt);          fprintf(ficresilk," %10.6f\n", -llt);
       }        }
     } /* end of wave */          } /* end of wave */
   } /* end of individual */  } /* end of individual */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   if(globpr==0){ /* First time we count the contributions and weights */  if(globpr==0){ /* First time we count the contributions and weights */
     gipmx=ipmx;          gipmx=ipmx;
     gsw=sw;          gsw=sw;
   }  }
   return -l;  return -l;
 }  }
   
   
 /*************** function likelione ***********/  /*************** function likelione ***********/
 void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
 {  {
   /* This routine should help understanding what is done with     /* This routine should help understanding what is done with 
      the selection of individuals/waves and       the selection of individuals/waves and
Line 3204  void likelione(FILE *ficres,double p[], Line 3989  void likelione(FILE *ficres,double p[],
     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   }    }
   
   *fretone=(*funcone)(p);    *fretone=(*func)(p);
   if(*globpri !=0){    if(*globpri !=0){
     fclose(ficresilk);      fclose(ficresilk);
     if (mle ==0)      if (mle ==0)
Line 3212  void likelione(FILE *ficres,double p[], Line 3997  void likelione(FILE *ficres,double p[],
     else if(mle >=1)      else if(mle >=1)
       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);        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));      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));
           fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model); 
               
     for (k=1; k<= nlstate ; k++) {      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> \        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> \
Line 3514  double hessij( double x[], double **hess Line 4299  double hessij( double x[], double **hess
       kmax=kmax+10;        kmax=kmax+10;
     }      }
     if(kmax >=10 || firstime ==1){      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);        printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could 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);        fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could 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);        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);        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);
     }      }
Line 3604  void ludcmp(double **a, int n, int *indx Line 4389  void ludcmp(double **a, int n, int *indx
     big=0.0;       big=0.0; 
     for (j=1;j<=n;j++)       for (j=1;j<=n;j++) 
       if ((temp=fabs(a[i][j])) > big) big=temp;         if ((temp=fabs(a[i][j])) > big) big=temp; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");       if (big == 0.0){
         printf(" Singular Hessian matrix at row %d:\n",i);
         for (j=1;j<=n;j++) {
           printf(" a[%d][%d]=%f,",i,j,a[i][j]);
           fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
         }
         fflush(ficlog);
         fclose(ficlog);
         nrerror("Singular matrix in routine ludcmp"); 
       }
     vv[i]=1.0/big;       vv[i]=1.0/big; 
   }     } 
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
Line 3670  void pstamp(FILE *fichier) Line 4464  void pstamp(FILE *fichier)
   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }  }
   
   void date2dmy(double date,double *day, double *month, double *year){
     double yp=0., yp1=0., yp2=0.;
     
     yp1=modf(date,&yp);/* extracts integral of date in yp  and
                           fractional in yp1 */
     *year=yp;
     yp2=modf((yp1*12),&yp);
     *month=yp;
     yp1=modf((yp2*30.5),&yp);
     *day=yp;
     if(*day==0) *day=1;
     if(*month==0) *month=1;
   }
   
   
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \  void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
                   int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],\                    int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
 {  /* Some frequencies */  {  /* Some frequencies as well as proposing some starting values */
       
   int i, m, jk, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
     int iind=0, iage=0;
   int mi; /* Effective wave */    int mi; /* Effective wave */
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp, **prop;    double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */
   double pos,posprop, k2, dateintsum=0,k2cpt=0;    int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);
     double *meanq, *stdq, *idq;
     double **meanqt;
     double *pp, **prop, *posprop, *pospropt;
     double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
   char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];    char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
   double agebegin, ageend;    double agebegin, ageend;
           
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
     posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
     pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */    /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
     meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
     stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
     idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
     meanqt=matrix(1,lastpass,1,nqtveff);
   strcpy(fileresp,"P_");    strcpy(fileresp,"P_");
   strcat(fileresp,fileresu);    strcat(fileresp,fileresu);
   /*strcat(fileresphtm,fileresu);*/    /*strcat(fileresphtm,fileresu);*/
Line 3696  void  freqsummary(char fileres[], int ia Line 4517  void  freqsummary(char fileres[], int ia
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     exit(0);      exit(0);
   }    }
     
   strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));    strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
   if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {    if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
     printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));      printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
Line 3706  void  freqsummary(char fileres[], int ia Line 4527  void  freqsummary(char fileres[], int ia
   }    }
   else{    else{
     fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \      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\  <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",\  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);              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);    fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);
         
   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));    strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {    if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
     printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));      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));      fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
     fflush(ficlog);      fflush(ficlog);
     exit(70);       exit(70); 
   }    } else{
   else{  
     fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \      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\  <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",\  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);              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);    fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
     
   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);    y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
     x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
   j1=0;    j1=0;
       
   j=cptcoveff;    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
     j=cptcoveff;  /* Only dummy covariates of the model */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
     
     /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
        reference=low_education V1=0,V2=0
        med_educ                V1=1 V2=0, 
        high_educ               V1=0 V2=1
        Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
     */
     dateintsum=0;
     k2cpt=0;
   
   first=1;    if(cptcoveff == 0 )
       nl=1;  /* Constant and age model only */
     else
       nl=2;
   
   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */    /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
     /* Loop on nj=1 or 2 if dummy covariates j!=0
      *   Loop on j1(1 to 2**cptcoveff) covariate combination
      *     freq[s1][s2][iage] =0.
      *     Loop on iind
      *       ++freq[s1][s2][iage] weighted
      *     end iind
      *     if covariate and j!0
      *       headers Variable on one line
      *     endif cov j!=0
      *     header of frequency table by age
      *     Loop on age
      *       pp[s1]+=freq[s1][s2][iage] weighted
      *       pos+=freq[s1][s2][iage] weighted
      *       Loop on s1 initial state
      *         fprintf(ficresp
      *       end s1
      *     end age
      *     if j!=0 computes starting values
      *     end compute starting values
      *   end j1
      * end nl 
      */
     for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
       if(nj==1)
         j=0;  /* First pass for the constant */
       else{
         j=cptcoveff; /* Other passes for the covariate values */
       }
       first=1;
       for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
         posproptt=0.;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         scanf("%d", i);*/          scanf("%d", i);*/
       for (i=-5; i<=nlstate+ndeath; i++)          for (i=-5; i<=nlstate+ndeath; i++)  
         for (jk=-5; jk<=nlstate+ndeath; jk++)            for (s2=-5; s2<=nlstate+ndeath; s2++)  
           for(m=iagemin; m <= iagemax+3; m++)            for(m=iagemin; m <= iagemax+3; m++)
             freq[i][jk][m]=0;              freq[i][s2][m]=0;
               
       for (i=1; i<=nlstate; i++)          for (i=1; i<=nlstate; i++)  {
         for(m=iagemin; m <= iagemax+3; m++)          for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;            prop[i][m]=0;
           posprop[i]=0;
           pospropt[i]=0;
         }
         for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
           idq[z1]=0.;
           meanq[z1]=0.;
           stdq[z1]=0.;
         }
         /* for (z1=1; z1<= nqtveff; z1++) { */
         /*   for(m=1;m<=lastpass;m++){ */
         /*          meanqt[m][z1]=0.; */
         /*        } */
         /* }       */
         /* dateintsum=0; */
         /* k2cpt=0; */
               
       dateintsum=0;        /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
       k2cpt=0;        for (iind=1; iind<=imx; iind++) { /* For each individual iind */
       for (i=1; i<=imx; i++) { /* For each individual i */  
         bool=1;          bool=1;
         if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */          if(j !=0){
           for (z1=1; z1<=cptcoveff; z1++)                   if(anyvaryingduminmodel==0){ /* If All fixed covariates */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){              if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                 /* Tests if the value of each of the covariates of i is equal to filter j1 */                for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
               bool=0;                  /* if(Tvaraff[z1] ==-20){ */
               /* 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",                   /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),                  /* }else  if(Tvaraff[z1] ==-10){ */
                 j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/                  /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/                  /* }else  */
             }                   if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
         } /* cptcovn > 0 */                    /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
                     bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
         if (bool==1){                    /* 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*/
                   } /* Onlyf fixed */
                 } /* end z1 */
               } /* cptcovn > 0 */
             } /* end any */
           }/* end j==0 */
           if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
           /* for(m=firstpass; m<=lastpass; m++){ */            /* for(m=firstpass; m<=lastpass; m++){ */
           for(mi=1; mi<wav[i];mi++){            for(mi=1; mi<wav[iind];mi++){ /* For each wave */
             m=mw[mi][i];              m=mw[mi][iind];
             /* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i]              if(j!=0){
                and mw[mi+1][i]. dh depends on stepm. */                if(anyvaryingduminmodel==1){ /* Some are varying covariates */
             agebegin=agev[m][i]; /* Age at beginning of wave before transition*/                  for (z1=1; z1<=cptcoveff; z1++) {
             ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /* Age at end of wave and transition */                    if( Fixed[Tmodelind[z1]]==1){
             if(m >=firstpass && m <=lastpass){                      iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
               k2=anint[m][i]+(mint[m][i]/12.);                      if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's 
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/                                                                                        value is -1, we don't select. It differs from the 
               if(agev[m][i]==0) agev[m][i]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */                                                                                        constant and age model which counts them. */
               if(agev[m][i]==1) agev[m][i]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */                        bool=0; /* not selected */
               if (s[m][i]>0 && s[m][i]<=nlstate)  /* If status at wave m is known and a live state */                    }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
                 prop[s[m][i]][(int)agev[m][i]] += weight[i];  /* At age of beginning of transition, where status is known */                      if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
               if (m<lastpass) {                        bool=0;
                 /* if(s[m][i]==4 && s[m+1][i]==4) */                      }
                 /*   printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */                    }
                 if(s[m][i]==-1)                  }
                   printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.));                }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */              } /* end j==0 */
                 /* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */              /* bool =0 we keep that guy which corresponds to the combination of dummy values */
                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */              if(bool==1){ /*Selected */
                 /* 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(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
                   if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
                   if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
                     prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
                   if (m<lastpass) {
                     /* 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)
                       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.));
                     freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                     for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
                       idq[z1]=idq[z1]+weight[iind];
                       meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */
                       stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
                     }
                     /* if((int)agev[m][iind] == 55) */
                     /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
                     /* 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 */
                   }
                 } /* end if between passes */  
                 if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
                   dateintsum=dateintsum+k2; /* on all covariates ?*/
                   k2cpt++;
                   /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
               }                }
             }                }else{
             if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {                bool=1;
               dateintsum=dateintsum+k2;              }/* end bool 2 */
               k2cpt++;  
               /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */  
             }  
             /*}*/  
           } /* end m */            } /* end m */
             /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
             /*   idq[z1]=idq[z1]+weight[iind]; */
             /*   meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /\* Computes mean of quantitative with selected filter *\/ */
             /*   stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/  /\* Computes mean of quantitative with selected filter *\/ */
             /* } */
         } /* end bool */          } /* end bool */
       } /* end i = 1 to imx */        } /* end iind = 1 to imx */
                /* prop[s][age] is feeded for any initial and valid live state as well as
            freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
         
         
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       pstamp(ficresp);        if(cptcoveff==0 && nj==1) /* no covariate and first pass */
       if  (cptcovn>0) {          pstamp(ficresp);
         if  (cptcoveff>0 && j!=0){
           pstamp(ficresp);
           printf( "\n#********** Variable "); 
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");           fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");           fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
           fprintf(ficlog, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++){          for (z1=1; z1<=cptcoveff; z1++){
           fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);            if(!FixedV[Tvaraff[z1]]){
           fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
           fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             }else{
               printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             }
         }          }
           fprintf(ficresp, "**********\n#");          printf( "**********\n#");
           fprintf(ficresp, "**********\n#");
         fprintf(ficresphtm, "**********</h3>\n");          fprintf(ficresphtm, "**********</h3>\n");
         fprintf(ficresphtmfr, "**********</h3>\n");          fprintf(ficresphtmfr, "**********</h3>\n");
         fprintf(ficlog, "\n#********** Variable ");   
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
         fprintf(ficlog, "**********\n");          fprintf(ficlog, "**********\n");
       }        }
         /*
           Printing means of quantitative variables if any
         */
         for (z1=1; z1<= nqfveff; z1++) {
           fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
           fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
           if(weightopt==1){
             printf(" Weighted mean and standard deviation of");
             fprintf(ficlog," Weighted mean and standard deviation of");
             fprintf(ficresphtmfr," Weighted mean and standard deviation of");
           }
           printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
           fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
           fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
         }
         /* for (z1=1; z1<= nqtveff; z1++) { */
         /*        for(m=1;m<=lastpass;m++){ */
         /*          fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
         /*   } */
         /* } */
   
       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");        fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
         if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
           fprintf(ficresp, " Age");
         if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
       for(i=1; i<=nlstate;i++) {        for(i=1; i<=nlstate;i++) {
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," 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(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
       }        }
       fprintf(ficresp, "\n");        if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
       fprintf(ficresphtm, "\n");        fprintf(ficresphtm, "\n");
               
       /* Header of frequency table by age */        /* Header of frequency table by age */
       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");        fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
       fprintf(ficresphtmfr,"<th>Age</th> ");        fprintf(ficresphtmfr,"<th>Age</th> ");
       for(jk=-1; jk <=nlstate+ndeath; jk++){        for(s2=-1; s2 <=nlstate+ndeath; s2++){
         for(m=-1; m <=nlstate+ndeath; m++){          for(m=-1; m <=nlstate+ndeath; m++){
           if(jk!=0 && m!=0)            if(s2!=0 && m!=0)
             fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);              fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
         }          }
       }        }
       fprintf(ficresphtmfr, "\n");        fprintf(ficresphtmfr, "\n");
             
       /* For each age */        /* For each age */
       for(i=iagemin; i <= iagemax+3; i++){        for(iage=iagemin; iage <= iagemax+3; iage++){
         fprintf(ficresphtm,"<tr>");          fprintf(ficresphtm,"<tr>");
         if(i==iagemax+1){          if(iage==iagemax+1){
           fprintf(ficlog,"1");            fprintf(ficlog,"1");
           fprintf(ficresphtmfr,"<tr><th>0</th> ");            fprintf(ficresphtmfr,"<tr><th>0</th> ");
         }else if(i==iagemax+2){          }else if(iage==iagemax+2){
           fprintf(ficlog,"0");            fprintf(ficlog,"0");
           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");            fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
         }else if(i==iagemax+3){          }else if(iage==iagemax+3){
           fprintf(ficlog,"Total");            fprintf(ficlog,"Total");
           fprintf(ficresphtmfr,"<tr><th>Total</th> ");            fprintf(ficresphtmfr,"<tr><th>Total</th> ");
         }else{          }else{
Line 3852  Title=%s <br>Datafile=%s Firstpass=%d La Line 4815  Title=%s <br>Datafile=%s Firstpass=%d La
             first=0;              first=0;
             printf("See log file for details...\n");              printf("See log file for details...\n");
           }            }
           fprintf(ficresphtmfr,"<tr><th>%d</th> ",i);            fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
           fprintf(ficlog,"Age %d", i);            fprintf(ficlog,"Age %d", iage);
         }          }
         for(jk=1; jk <=nlstate ; jk++){          for(s1=1; s1 <=nlstate ; s1++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
             pp[jk] += freq[jk][m][i];               pp[s1] += freq[s1][m][iage]; 
         }          }
         for(jk=1; jk <=nlstate ; jk++){          for(s1=1; s1 <=nlstate ; s1++){
           for(m=-1, pos=0; m <=0 ; m++)            for(m=-1, pos=0; m <=0 ; m++)
             pos += freq[jk][m][i];              pos += freq[s1][m][iage];
           if(pp[jk]>=1.e-10){            if(pp[s1]>=1.e-10){
             if(first==1){              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);                printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
             }              }
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
           }else{            }else{
             if(first==1)              if(first==1)
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
           }            }
         }          }
         
         for(jk=1; jk <=nlstate ; jk++){          for(s1=1; s1 <=nlstate ; s1++){ 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            /* posprop[s1]=0; */
             pp[jk] += freq[jk][m][i];            for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
         }                     pp[s1] += freq[s1][m][iage];
         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){          }       /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
           pos += pp[jk];        
           posprop += prop[jk][i];          for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
             pos += pp[s1]; /* pos is the total number of transitions until this age */
             posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
                                               from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
             pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
                                             from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
           }
           
           /* Writing ficresp */
           if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
             if( iage <= iagemax){
               fprintf(ficresp," %d",iage);
             }
           }else if( nj==2){
             if( iage <= iagemax){
               fprintf(ficresp," %d",iage);
               for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             }
         }          }
         for(jk=1; jk <=nlstate ; jk++){          for(s1=1; s1 <=nlstate ; s1++){
           if(pos>=1.e-5){            if(pos>=1.e-5){
             if(first==1)              if(first==1)
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);                printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
           }else{            }else{
             if(first==1)              if(first==1)
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);                printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
           }            }
           if( i <= iagemax){            if( iage <= iagemax){
             if(pos>=1.e-5){              if(pos>=1.e-5){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);                if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
               fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",i,prop[jk][i]/posprop, prop[jk][i],posprop);                  fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
               /*probs[i][jk][j1]= pp[jk]/pos;*/                }else if( nj==2){
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/                  fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
             }                }
             else{                fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);                /*probs[iage][s1][j1]= pp[s1]/pos;*/
               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",i, prop[jk][i],posprop);                /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
               } else{
                 if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
             }              }
           }            }
         }            pospropt[s1] +=posprop[s1];
                   } /* end loop s1 */
         for(jk=-1; jk <=nlstate+ndeath; jk++){          /* pospropt=0.; */
           for(s1=-1; s1 <=nlstate+ndeath; s1++){
           for(m=-1; m <=nlstate+ndeath; m++){            for(m=-1; m <=nlstate+ndeath; m++){
             if(freq[jk][m][i] !=0 ) { /* minimizing output */              if(freq[s1][m][iage] !=0 ) { /* minimizing output */
               if(first==1){                if(first==1){
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);                  printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
               }                }
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);                /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
                 fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
             }              }
             if(jk!=0 && m!=0)              if(s1!=0 && m!=0)
               fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][i]);                fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
           }            }
           } /* end loop s1 */
           posproptt=0.; 
           for(s1=1; s1 <=nlstate; s1++){
             posproptt += pospropt[s1];
         }          }
         fprintf(ficresphtmfr,"</tr>\n ");          fprintf(ficresphtmfr,"</tr>\n ");
         if(i <= iagemax){          fprintf(ficresphtm,"</tr>\n");
           fprintf(ficresp,"\n");          if((cptcoveff==0 && nj==1)|| nj==2 ) {
           fprintf(ficresphtm,"</tr>\n");            if(iage <= iagemax)
               fprintf(ficresp,"\n");
         }          }
         if(first==1)          if(first==1)
           printf("Others in log...\n");            printf("Others in log...\n");
         fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
       } /* end loop i */        } /* end loop age iage */
         
         fprintf(ficresphtm,"<tr><th>Tot</th>");
         for(s1=1; s1 <=nlstate ; s1++){
           if(posproptt < 1.e-5){
             fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt); 
           }else{
             fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);  
           }
         }
         fprintf(ficresphtm,"</tr>\n");
       fprintf(ficresphtm,"</table>\n");        fprintf(ficresphtm,"</table>\n");
       fprintf(ficresphtmfr,"</table>\n");        fprintf(ficresphtmfr,"</table>\n");
       /*}*/        if(posproptt < 1.e-5){
   } /* end j1 */          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(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
           printf("#  This combination (%d) is not valid and no result will be produced\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");
         fprintf(ficlog,"\n");
         if(j!=0){
           printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
           for(i=1,s1=1; i <=nlstate; i++){
             for(k=1; k <=(nlstate+ndeath); k++){
               if (k != i) {
                 for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
                   if(jj==1){  /* Constant case (in fact cste + age) */
                     if(j1==1){ /* All dummy covariates to zero */
                       freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
                       freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
                       printf("%d%d ",i,k);
                       fprintf(ficlog,"%d%d ",i,k);
                       printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
                       fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                       pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                     }
                   }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
                     for(iage=iagemin; iage <= iagemax+3; iage++){
                       x[iage]= (double)iage;
                       y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
                       /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
                     }
                     /* Some are not finite, but linreg will ignore these ages */
                     no=0;
                     linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
                     pstart[s1]=b;
                     pstart[s1-1]=a;
                   }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */ 
                     printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                     printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                     pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
                     printf("%d%d ",i,k);
                     fprintf(ficlog,"%d%d ",i,k);
                     printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
                   }else{ /* Other cases, like quantitative fixed or varying covariates */
                     ;
                   }
                   /* printf("%12.7f )", param[i][jj][k]); */
                   /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                   s1++; 
                 } /* end jj */
               } /* end k!= i */
             } /* end k */
           } /* end i, s1 */
         } /* end j !=0 */
       } /* end selected combination of covariate j1 */
       if(j==0){ /* We can estimate starting values from the occurences in each case */
         printf("#Freqsummary: Starting values for the constants:\n");
         fprintf(ficlog,"\n");
         for(i=1,s1=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(jj=1; jj <=ncovmodel; jj++){
                 pstart[s1]=p[s1]; /* Setting pstart to p values by default */
                 if(jj==1){ /* Age has to be done */
                   pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                   printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                   fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                 }
                 /* printf("%12.7f )", param[i][jj][k]); */
                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                 s1++; 
               }
               printf("\n");
               fprintf(ficlog,"\n");
             }
           }
         } /* end of state i */
         printf("#Freqsummary\n");
         fprintf(ficlog,"\n");
         for(s1=-1; s1 <=nlstate+ndeath; s1++){
           for(s2=-1; s2 <=nlstate+ndeath; s2++){
             /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
             printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
             fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
             /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
             /*   printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
             /*   fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
             /* } */
           }
         } /* end loop s1 */
         
         printf("\n");
         fprintf(ficlog,"\n");
       } /* end j=0 */
     } /* end j */
   
     if(mle == -2){  /* We want to use these values as starting values */
       for(i=1, jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j!=i){
             /*ca[0]= k+'a'-1;ca[1]='\0';*/
             printf("%1d%1d",i,j);
             fprintf(ficparo,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               /*    printf(" %lf",param[i][j][k]); */
               /*    fprintf(ficparo," %lf",param[i][j][k]); */
               p[jk]=pstart[jk];
               printf(" %f ",pstart[jk]);
               fprintf(ficparo," %f ",pstart[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficparo,"\n");
           }
         }
       }
     } /* end mle=-2 */
   dateintmean=dateintsum/k2cpt;     dateintmean=dateintsum/k2cpt; 
      date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
     
   fclose(ficresp);    fclose(ficresp);
   fclose(ficresphtm);    fclose(ficresphtm);
   fclose(ficresphtmfr);    fclose(ficresphtmfr);
   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);    free_vector(idq,1,nqfveff);
     free_vector(meanq,1,nqfveff);
     free_vector(stdq,1,nqfveff);
     free_matrix(meanqt,1,lastpass,1,nqtveff);
     free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_vector(pospropt,1,nlstate);
     free_vector(posprop,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);    /* End of freqsummary */
   /* End of Freq */  }
   
   /* Simple linear regression */
   int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
   
     /* y=a+bx regression */
     double   sumx = 0.0;                        /* sum of x                      */
     double   sumx2 = 0.0;                       /* sum of x**2                   */
     double   sumxy = 0.0;                       /* sum of x * y                  */
     double   sumy = 0.0;                        /* sum of y                      */
     double   sumy2 = 0.0;                       /* sum of y**2                   */
     double   sume2 = 0.0;                       /* sum of square or residuals */
     double yhat;
     
     double denom=0;
     int i;
     int ne=*no;
     
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       sumx  += x[i];       
       sumx2 += x[i]*x[i];  
       sumxy += x[i] * y[i];
       sumy  += y[i];      
       sumy2 += y[i]*y[i]; 
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     
     denom = (ne * sumx2 - sumx*sumx);
     if (denom == 0) {
       // vertical, slope m is infinity
       *b = INFINITY;
       *a = 0;
       if (r) *r = 0;
       return 1;
     }
     
     *b = (ne * sumxy  -  sumx * sumy) / denom;
     *a = (sumy * sumx2  -  sumx * sumxy) / denom;
     if (r!=NULL) {
       *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
         sqrt((sumx2 - sumx*sumx/ne) *
              (sumy2 - sumy*sumy/ne));
     }
     *no=ne;
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       yhat = y[i] - *a -*b* x[i];
       sume2  += yhat * yhat ;       
       
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
     *sa= *sb * sqrt(sumx2/ne);
     
     return 0; 
 }  }
   
 /************ Prevalence ********************/  /************ Prevalence ********************/
Line 3950  void prevalence(double ***probs, double Line 5145  void prevalence(double ***probs, double
      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, iv;
   int mi; /* Effective wave */    int mi; /* Effective wave */
   int iage;    int iage;
   double agebegin, ageend;    double agebegin, ageend;
Line 3964  void prevalence(double ***probs, double Line 5159  void prevalence(double ***probs, double
   iagemin= (int) agemin;    iagemin= (int) agemin;
   iagemax= (int) agemax;    iagemax= (int) agemax;
   /*pp=vector(1,nlstate);*/    /*pp=vector(1,nlstate);*/
   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   j1=0;    j1=0;
       
   /*j=cptcoveff;*/    /*j=cptcoveff;*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
   first=1;    first=0;
   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
     for (i=1; i<=nlstate; i++)        for (i=1; i<=nlstate; i++)  
       for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)        for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
                                 prop[i][iage]=0.0;          prop[i][iage]=0.0;
       printf("Prevalence combination of varying and fixed dummies %d\n",j1);
       /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
       fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
           
     for (i=1; i<=imx; i++) { /* Each individual */      for (i=1; i<=imx; i++) { /* Each individual */
       bool=1;        bool=1;
       if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */        /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
                                 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*/        for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
                                         if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])           m=mw[mi][i];
                                                 bool=0;          /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
       }           /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
       if (bool==1) { /* For this combination of covariates values, this individual fits */          for (z1=1; z1<=cptcoveff; z1++){
                                 /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */            if( Fixed[Tmodelind[z1]]==1){
                                 for(mi=1; mi<wav[i];mi++){              iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
                                         m=mw[mi][i];              if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
                                         agebegin=agev[m][i]; /* Age at beginning of wave before transition*/                bool=0;
                                         /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */            }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
                                         if(m >=firstpass && m <=lastpass){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                                                 y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */                bool=0;
                                                 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(bool==1){ /* Otherwise we skip that wave/person */
                                                         if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){            agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
                                                                 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);             /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
                                                                 exit(1);            if(m >=firstpass && m <=lastpass){
                                                         }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                                                         if (s[m][i]>0 && s[m][i]<=nlstate) {               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                                                                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                                                                 prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                                                                 prop[s[m][i]][iagemax+3] += weight[i];                 if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
                                                         } /* end valid statuses */                   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); 
                                                 } /* end selection of dates */                  exit(1);
                                         } /* end selection of waves */                }
                                 } /* end effective waves */                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       } /* end bool */                  /*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 bool */
         } /* end wave */
       } /* end individual */
     for(i=iagemin; i <= iagemax+3; i++){        for(i=iagemin; i <= iagemax+3; i++){  
       for(jk=1,posprop=0; jk <=nlstate ; jk++) {         for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                                 posprop += prop[jk][i];           posprop += prop[jk][i]; 
       }         } 
               
       for(jk=1; jk <=nlstate ; jk++){               for(jk=1; jk <=nlstate ; jk++){       
                                 if( i <=  iagemax){           if( i <=  iagemax){ 
                                         if(posprop>=1.e-5){             if(posprop>=1.e-5){ 
                                                 probs[i][jk][j1]= prop[jk][i]/posprop;              probs[i][jk][j1]= prop[jk][i]/posprop;
                                         } else{            } else{
                                                 if(first==1){              if(!first){
                                                         first=0;                first=1;
                                                         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]);                printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
                                                 }              }else{
                                         }                fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]);
                                 }               }
             }
           } 
       }/* end jk */         }/* end jk */ 
     }/* end i */       }/* end i */ 
     /*} *//* end i1 */       /*} *//* end i1 */
   } /* end j1 */    } /* end j1 */
       
   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /*free_vector(pp,1,nlstate);*/    /*free_vector(pp,1,nlstate);*/
   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);    free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
 }  /* End of prevalence */  }  /* End of prevalence */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
   
 void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 {  {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /* Concatenates waves: wav[i] is the number of effective (useful waves in the sense that a non interview is useless) of individual i.
      Death is a valid wave (if date is known).       Death is a valid wave (if date is known).
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]       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.       and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
      */    */
   
   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, firstwo, firsthree, firstfour;    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;
Line 4059  void  concatwav(int wav[], int **dh, int Line 5266  void  concatwav(int wav[], int **dh, int
   jmin=100000;    jmin=100000;
   jmax=-1;    jmax=-1;
   jmean=0.;    jmean=0.;
   
   /* Treating live states */
   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
     mi=0;      mi=0;  /* First valid wave */
       mli=0; /* Last valid wave */
     m=firstpass;      m=firstpass;
     while(s[m][i] <= nlstate){  /* a live state */      while(s[m][i] <= nlstate){  /* a live state */
       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 */        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 */
           mli=m-1;/* mw[++mi][i]=m-1; */
         }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 */
         mw[++mi][i]=m;          mw[++mi][i]=m;
           mli=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 */
       }        }
       if(m >=lastpass){        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(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
           if(firsthree == 0){            if(firsthree == 0){
             printf("Information! Unknown health 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.\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);              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 1-p_{%d%d} .\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, s[m][i], nlstate+ndeath);
             firsthree=1;              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.\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);            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 1-p_{%d%d} .\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, s[m][i], nlstate+ndeath);
           mw[++mi][i]=m;            mw[++mi][i]=m;
             mli=m;
         }          }
         if(s[m][i]==-2){ /* Vital status is really unknown */          if(s[m][i]==-2){ /* Vital status is really unknown */
           nbwarn++;            nbwarn++;
           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */            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);              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.\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;
         }          }
         break;          break;
       }  #endif
       else        }/* End m >= lastpass */
         m++;  
     }/* end while */      }/* end while */
       
       /* 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 */      /* After last pass */
   /* Treating death states */
     if (s[m][i] > nlstate){  /* In a death state */      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;
     }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */      } /* else not in a death state */
       /* m++; */  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
       /* mi++; */      else if ((int) andc[i] != 9999) {  /* Date of death is known */
       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */  
       /* mw[mi][i]=m; */  
       nberr++;  
       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
         if(firstwo==0){          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 */
           printf("Error! Death for individual %ld line=%d  occurred %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 );            nbwarn++;
           firstwo=1;            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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
         }          }
         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %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{ /* if date of interview is unknown */
       }else{ /* end date of interview is known */  
         /* death is known but not confirmed by death status at any wave */          /* death is known but not confirmed by death status at any wave */
         if(firstfour==0){          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 );            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 );
Line 4115  void  concatwav(int wav[], int **dh, int Line 5346  void  concatwav(int wav[], int **dh, int
         }          }
         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 );          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 */
     wav[i]=mi;  #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){
Line 4129  void  concatwav(int wav[], int **dh, int Line 5362  void  concatwav(int wav[], int **dh, int
     } /* end mi==0 */      } /* end mi==0 */
   } /* End individuals */    } /* End individuals */
   /* wav and mw are no more changed */    /* 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, but what if date is unknown? */
           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 */
Line 4165  void  concatwav(int wav[], int **dh, int Line 5398  void  concatwav(int wav[], int **dh, int
         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;
Line 4219  void  concatwav(int wav[], int **dh, int Line 5452  void  concatwav(int wav[], int **dh, int
   jmean=sum/k;    jmean=sum/k;
   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
  }  }
   
 /*********** Tricode ****************************/  /*********** 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;
   int modmaxcovj=0; /* Modality max of covariates j */     int modmaxcovj=0; /* Modality max of covariates j */
   int cptcode=0; /* Modality max of covariates j */     int cptcode=0; /* Modality max of covariates j */
   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++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
      for (k=1; k <= maxncov; k++)
   /* Loop on covariates without age and products */       for(j=1; j<=2; j++)
   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */         nbcode[k][j]=0; /* Valgrind */
     for (k=-1; k < maxncov; k++) Ndum[k]=0;  
     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the      /* Loop on covariates without age and products and no quantitative variable */
                                                                                                                                 modality of this covariate Vj*/      for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i       for (j=-1; (j < maxncov); j++) Ndum[j]=0;
                                                                                                                                                 * If product of Vn*Vm, still boolean *:       if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
                                                                                                                                                 * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables         switch(Fixed[k]) {
                                                                                                                                                 * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */         case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the           for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
                                       modality of the nth covariate of individual i. */             ij=(int)(covar[Tvar[k]][i]);
       if (ij > modmaxcovj)             /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
         modmaxcovj=ij;               * If product of Vn*Vm, still boolean *:
       else if (ij < modmincovj)               * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                 modmincovj=ij;               * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
       if ((ij < -1) && (ij > NCOVMAX)){             /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                 printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );                modality of the nth covariate of individual i. */
                                 exit(1);             if (ij > modmaxcovj)
       }else               modmaxcovj=ij; 
       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/             else if (ij < modmincovj) 
       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */               modmincovj=ij; 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/             if (ij <0 || ij >1 ){
       /* getting the maximum value of the modality of the covariate               printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and               fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
          female is 1, then modmaxcovj=1.*/             }
     } /* end for loop on individuals i */             if ((ij < -1) || (ij > NCOVMAX)){
     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);               printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);               exit(1);
     cptcode=modmaxcovj;             }else
     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */               Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
    /*for (i=0; i<=cptcode; i++) {*/             /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */             /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);             /* getting the maximum value of the modality of the covariate
       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);                (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */                female ies 1, then modmaxcovj=1.
                                 if( k != -1){             */
                                         ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th           } /* end for loop on individuals i */
                                                                                                                  covariate for which somebody answered excluding            printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
                                                                                                                  undefined. Usually 2: 0 and 1. */           fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
                                 }           cptcode=modmaxcovj;
                                 ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th           /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
                                                                                                                                 covariate for which somebody answered including            /*for (i=0; i<=cptcode; i++) {*/
                                                                                                                                 undefined. Usually 3: -1, 0 and 1. */           for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
       }             printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for             fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
                                  historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */             if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
     } /* Ndum[-1] number of undefined modalities */               if( j != -1){
                                  ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */                                    covariate for which somebody answered excluding 
     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.                                     undefined. Usually 2: 0 and 1. */
        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;               ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
        There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;                                       covariate for which somebody answered including 
        which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;                                       undefined. Usually 3: -1, 0 and 1. */
        defining two dummy variables: variables V1_1 and V1_2.             }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
        nbcode[Tvar[j]][ij]=k;                   * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
        nbcode[Tvar[j]][1]=0;           } /* Ndum[-1] number of undefined modalities */
        nbcode[Tvar[j]][2]=1;                          
        nbcode[Tvar[j]][3]=2;           /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
        To be continued (not working yet).           /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
     */           /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
     ij=0; /* ij is similar to i but can jump over null modalities */           /* modmincovj=3; modmaxcovj = 7; */
     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*/           /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
         if (Ndum[i] == 0) { /* If nobody responded to this modality k */           /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
                                 break;           /*              defining two dummy variables: variables V1_1 and V1_2.*/
                         }           /* nbcode[Tvar[j]][ij]=k; */
         ij++;           /* nbcode[Tvar[j]][1]=0; */
         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.*/           /* nbcode[Tvar[j]][2]=1; */
         cptcode = ij; /* New max modality for covar j */           /* nbcode[Tvar[j]][3]=2; */
     } /* end of loop on modality i=-1 to 1 or more */           /* To be continued (not working yet). */
                  ij=0; /* ij is similar to i but can jump over null modalities */
     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */  
     /*  /\*recode from 0 *\/ */           /* 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*/
     /*                               k is a modality. If we have model=V1+V1*sex  */           /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */           /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */            * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
     /*  } */           /*, could be restored in the future */
     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */           for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
     /*  if (ij > ncodemax[j]) { */             if (Ndum[i] == 0) { /* If nobody responded to this modality k */
     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */               break;
     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */             }
     /*    break; */             ij++;
     /*  } */             nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
     /*   }  /\* end of loop on modality k *\/ */             cptcode = ij; /* New max modality for covar j */
   } /* 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 modality i=-1 to 1 or more */
              break;
         for (k=-1; k< maxncov; k++) Ndum[k]=0;          case 1: /* Testing on varying covariate, could be simple and
                     * should look at waves or product of fixed *
   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */                   * varying. No time to test -1, assuming 0 and 1 only */
                 /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/            ij=0;
                 ij=Tvar[i]; /* Tvar might be -1 if status was unknown */            for(i=0; i<=1;i++){
                 Ndum[ij]++; /* Might be supersed V1 + V1*age */             nbcode[Tvar[k]][++ij]=i;
         }            }
                    break;
         ij=0;         default:
         for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */           break;
                 /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/         } /* end switch */
                 if((Ndum[i]!=0) && (i<=ncovcol)){       } /* end dummy test */
                         ij++;     } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/  
                         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/    
                         Tvaraff[ij]=i; /*For printing (unclear) */     for (k=-1; k< maxncov; k++) Ndum[k]=0; 
                 }else{     /* Look at fixed dummy (single or product) covariates to check empty modalities */
                         /* Tvaraff[ij]=0; */     for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
                 }       /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
         }       ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */ 
         /* ij--; */       Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
         cptcoveff=ij; /*Number of total covariates*/       /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
              } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 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 (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
        /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
        /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
        if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
          /* If product not in single variable we don't print results */
          /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
          ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
          Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
          Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
          TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
          if(Fixed[k]!=0)
            anyvaryingduminmodel=1;
          /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
          /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
          /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
          /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
          /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
          /*   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, but how to get k from ij?*/
      for(j=ij+1; j<= cptcovt; j++){
        Tvaraff[j]=0;
        Tmodelind[j]=0;
      }
      for(j=ntveff+1; j<= cptcovt; j++){
        TmodelInvind[j]=0;
      }
      /* To be sorted */
      ;
    }
   
   
 /*********** Health Expectancies ****************/  /*********** Health Expectancies ****************/
   
 void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )   void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres )
   
 {  {
   /* Health expectancies, no variances */    /* Health expectancies, no variances */
Line 4364  void evsij(double ***eij, double x[], in Line 5635  void evsij(double ***eij, double x[], in
   double ***p3mat;    double ***p3mat;
   double eip;    double eip;
   
   pstamp(ficreseij);    /* pstamp(ficreseij); */
   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   fprintf(ficreseij,"# Age");    fprintf(ficreseij,"# Age");
   for(i=1; i<=nlstate;i++){    for(i=1; i<=nlstate;i++){
Line 4395  void evsij(double ***eij, double x[], in Line 5666  void evsij(double ***eij, double x[], in
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.     /* 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        nhstepm is the number of hstepm from age to agelim 
      nstepm is the number of stepm from age to agelin.        nstepm is the number of stepm from age to agelin. 
      Look at hpijx to understand the reason of that which relies in memory size       Look at hpijx to understand the reason which relies in memory size consideration
      and note for a fixed period like estepm months */       and note for a fixed period like estepm months */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* 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       survival function given by stepm (the optimization length). Unfortunately it
Line 4427  void evsij(double ***eij, double x[], in Line 5698  void evsij(double ***eij, double x[], in
     /* 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 */
           
     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);  
           
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           
Line 4462  void evsij(double ***eij, double x[], in Line 5733  void evsij(double ***eij, double x[], in
       
 }  }
   
 void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[], int nres )
   
 {  {
   /* 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 4572  void cvevsij(double ***eij, double x[], Line 5843  void cvevsij(double ***eij, double x[],
        decrease memory allocation */         decrease memory allocation */
     for(theta=1; theta <=npar; theta++){      for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){         for(i=1; i<=npar; i++){ 
                                 xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                                 xm[i] = x[i] - (i==theta ?delti[theta]:0);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       }        }
       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);  
       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);  
                                                   
       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++){
                                                 gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                                                 gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
                                         }            }
                                 }          }
       }        }
                                                   
       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];
                                 }          }
     }/* End theta */      }/* End theta */
           
           
     for(h=0; h<=nhstepm-1; h++)      for(h=0; h<=nhstepm-1; h++)
       for(j=1; j<=nlstate*nlstate;j++)        for(j=1; j<=nlstate*nlstate;j++)
                                 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]);
                                 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] += 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,nres);  
     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]);*/
                                                                                   
                                 }          }
                   
       /* Standard deviation of expectancies ij */         
     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.;
       vip=0.;        vip=0.;
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
                                 eip += eij[i][j][(int)age];          eip += eij[i][j][(int)age];
                                 for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
                                         vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
                                 fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       }        }
       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     }      }
     fprintf(ficresstdeij,"\n");      fprintf(ficresstdeij,"\n");
                                   
       /* Variance of expectancies ij */           
     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++){
                                 cptj= (j-1)*nlstate+i;          cptj= (j-1)*nlstate+i;
                                 for(i2=1; i2<=nlstate;i2++)          for(i2=1; i2<=nlstate;i2++)
                                         for(j2=1; j2<=nlstate;j2++){            for(j2=1; j2<=nlstate;j2++){
                                                 cptj2= (j2-1)*nlstate+i2;              cptj2= (j2-1)*nlstate+i2;
                                                 if(cptj2 <= cptj)              if(cptj2 <= cptj)
                                                         fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
                                         }            }
       }        }
     fprintf(ficrescveij,"\n");      fprintf(ficrescveij,"\n");
                                   
Line 4672  void cvevsij(double ***eij, double x[], Line 5945  void cvevsij(double ***eij, double x[],
 }  }
     
 /************ Variance ******************/  /************ 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 *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])   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[], int nres)
  {   {
    /* Variance of health expectancies */     /** Variance of health expectancies 
    /*  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 **newm;*/      * double **newm;
    /* 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 movingaverage(); */     /* int movingaverage(); */
    double **dnewm,**doldm;     double **dnewm,**doldm;
    double **dnewmp,**doldmp;     double **dnewmp,**doldmp;
    int i, j, nhstepm, hstepm, h, nstepm ;     int i, j, nhstepm, hstepm, h, nstepm ;
      int first=0;
    int k;     int k;
    double *xp;     double *xp;
    double **gp, **gm;  /* for var eij */     double **gp, **gm;  /**< for var eij */
    double ***gradg, ***trgradg; /*for var eij */     double ***gradg, ***trgradg; /**< for var eij */
    double **gradgp, **trgradgp; /* for var p point j */     double **gradgp, **trgradgp; /**< for var p point j */
    double *gpp, *gmp; /* 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 **varppt; /**< for var p point j nlstate to nlstate+ndeath */
    double ***p3mat;     double ***p3mat;
    double age,agelim, hf;     double age,agelim, hf;
    /* double ***mobaverage; */     /* double ***mobaverage; */
Line 4729  void cvevsij(double ***eij, double x[], Line 6004  void cvevsij(double ***eij, double x[],
    fprintf(ficlog,"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);     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,"# 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,"# Selected quantitative variables and dummies");
      for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
        fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
      }
      for(j=1;j<=cptcoveff;j++) 
        fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
      fprintf(ficresprobmorprev,"\n");
   
    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
    for(j=nlstate+1; j<=(nlstate+ndeath);j++){     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
      fprintf(ficresprobmorprev," p.%-d SE",j);       fprintf(ficresprobmorprev," p.%-d SE",j);
Line 4742  void cvevsij(double ***eij, double x[], Line 6025  void cvevsij(double ***eij, double x[],
    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/     /* 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<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);     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
    /*   } */  
    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    pstamp(ficresvij);     pstamp(ficresvij);
    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
Line 4797  void cvevsij(double ***eij, double x[], Line 6080  void cvevsij(double ***eij, double x[],
        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
          xp[i] = x[i] + (i==theta ?delti[theta]:0);           xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }         }
                                  /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and 
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);          * returns into prlim .
                                   */
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
   
          /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
        if (popbased==1) {         if (popbased==1) {
          if(mobilav ==0){           if(mobilav ==0){
            for(i=1; i<=nlstate;i++)             for(i=1; i<=nlstate;i++)
Line 4809  void cvevsij(double ***eij, double x[], Line 6095  void cvevsij(double ***eij, double x[],
              prlim[i][i]=mobaverage[(int)age][i][ij];               prlim[i][i]=mobaverage[(int)age][i][ij];
          }           }
        }         }
                                  /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */          */                      
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
          /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
           * at horizon h in state j including mortality.
           */
        for(j=1; j<= nlstate; j++){         for(j=1; j<= nlstate; j++){
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
            for(i=1, gp[h][j]=0.;i<=nlstate;i++)             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
              gp[h][j] += prlim[i][i]*p3mat[i][j][h];               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
          }           }
        }         }
        /* Next for computing probability of death (h=1 means         /* Next for computing shifted+ probability of death (h=1 means
           computed over hstepm matrices product = hstepm*stepm months)             computed over hstepm matrices product = hstepm*stepm months) 
           as a weighted average of prlim.            as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
        */         */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){         for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gpp[j]=0.; i<= nlstate; i++)           for(i=1,gpp[j]=0.; i<= nlstate; i++)
            gpp[j] += prlim[i][i]*p3mat[i][j][1];             gpp[j] += prlim[i][i]*p3mat[i][j][1];
        }             }
        /* end probability of death */         
          /* Again with minus shift */
                                                   
        for(i=1; i<=npar; i++) /* Computes gradient x - delta */         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
          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,ncvyearp, ij);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
                                                   
        if (popbased==1) {         if (popbased==1) {
          if(mobilav ==0){           if(mobilav ==0){
Line 4842  void cvevsij(double ***eij, double x[], Line 6133  void cvevsij(double ***eij, double x[],
          }           }
        }         }
                                                   
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);           hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  
                                                   
        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
Line 4858  void cvevsij(double ***eij, double x[], Line 6149  void cvevsij(double ***eij, double x[],
          for(i=1,gmp[j]=0.; i<= nlstate; i++)           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];             gmp[j] += prlim[i][i]*p3mat[i][j][1];
        }             }    
        /* end probability of death */         /* end shifting computations */
                           
          /**< Computing gradient matrix at horizon h 
           */
        for(j=1; j<= nlstate; j++) /* vareij */         for(j=1; j<= nlstate; j++) /* vareij */
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
          }           }
                                  /**< Gradient of overall mortality p.3 (or p.j) 
        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          */
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
        }         }
                                                   
      } /* End theta */       } /* End theta */
                        
        /* We got the gradient matrix for each theta and state j */                
      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                                   
      for(h=0; h<=nhstepm; h++) /* veij */       for(h=0; h<=nhstepm; h++) /* veij */
Line 4881  void cvevsij(double ***eij, double x[], Line 6176  void cvevsij(double ***eij, double x[],
      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
        for(theta=1; theta <=npar; theta++)         for(theta=1; theta <=npar; theta++)
          trgradgp[j][theta]=gradgp[theta][j];           trgradgp[j][theta]=gradgp[theta][j];
                        /**< as well as its transposed matrix 
         */                
                                   
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(i=1;i<=nlstate;i++)       for(i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate;j++)         for(j=1;j<=nlstate;j++)
          vareij[i][j][(int)age] =0.;           vareij[i][j][(int)age] =0.;
                   
        /* Computing trgradg by matcov by gradg at age and summing over h
         * and k (nhstepm) formula 15 of article
         * Lievre-Brouard-Heathcote
         */
        
      for(h=0;h<=nhstepm;h++){       for(h=0;h<=nhstepm;h++){
        for(k=0;k<=nhstepm;k++){         for(k=0;k<=nhstepm;k++){
          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
Line 4898  void cvevsij(double ***eij, double x[], Line 6199  void cvevsij(double ***eij, double x[],
        }         }
      }       }
                                   
      /* pptj */       /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
         * p.j overall mortality formula 49 but computed directly because
         * we compute the grad (wix pijx) instead of grad (pijx),even if
         * wix is independent of theta.
         */
      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);       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);       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
      for(j=nlstate+1;j<=nlstate+ndeath;j++)       for(j=nlstate+1;j<=nlstate+ndeath;j++)
Line 4907  void cvevsij(double ***eij, double x[], Line 6212  void cvevsij(double ***eij, double x[],
      /* end ppptj */       /* end ppptj */
      /*  x centered again */       /*  x centered again */
                                   
      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
                                   
      if (popbased==1) {       if (popbased==1) {
        if(mobilav ==0){         if(mobilav ==0){
Line 4923  void cvevsij(double ***eij, double x[], Line 6228  void cvevsij(double ***eij, double x[],
         computed over hstepm (estepm) matrices product = hstepm*stepm months)           computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         as a weighted average of prlim.          as a weighted average of prlim.
      */       */
      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);         hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);  
      for(j=nlstate+1;j<=nlstate+ndeath;j++){       for(j=nlstate+1;j<=nlstate+ndeath;j++){
        for(i=1,gmp[j]=0.;i<= nlstate; i++)          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
          gmp[j] += prlim[i][i]*p3mat[i][j][1];            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
Line 4986  void cvevsij(double ***eij, double x[], Line 6291  void cvevsij(double ***eij, double x[],
  }  /* 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 *ncvyearp, int ij, char strstart[])   void varprevlim(char fileresvpl[], FILE *ficresvpl, 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[], int nres)
 {  {
   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/    /* 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 **dnewmpar,**doldm;
   int i, j, nhstepm, hstepm;    int i, j, nhstepm, hstepm;
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
Line 5001  void cvevsij(double ***eij, double x[], Line 6306  void cvevsij(double ***eij, double x[],
   int theta;    int theta;
       
   pstamp(ficresvpl);    pstamp(ficresvpl);
   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");    fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
   fprintf(ficresvpl,"# Age");    fprintf(ficresvpl,"# Age ");
     if(nresult >=1)
       fprintf(ficresvpl," Result# ");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
       fprintf(ficresvpl," %1d-%1d",i,i);        fprintf(ficresvpl," %1d-%1d",i,i);
   fprintf(ficresvpl,"\n");    fprintf(ficresvpl,"\n");
   
   xp=vector(1,npar);    xp=vector(1,npar);
   dnewm=matrix(1,nlstate,1,npar);    dnewmpar=matrix(1,nlstate,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    doldm=matrix(1,nlstate,1,nlstate);
       
   hstepm=1*YEARM; /* Every year of age */    hstepm=1*YEARM; /* Every year of age */
Line 5028  void cvevsij(double ***eij, double x[], Line 6335  void cvevsij(double ***eij, double x[],
       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);
       }        }
       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )        /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);        /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
       else        /* else */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
         gp[i] = prlim[i][i];          gp[i] = prlim[i][i];
         mgp[theta][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);
       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )        /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);        /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
       else        /* else */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
         gm[i] = prlim[i][i];          gm[i] = prlim[i][i];
         mgm[theta][i] = prlim[i][i];          mgm[theta][i] = prlim[i][i];
Line 5078  void cvevsij(double ***eij, double x[], Line 6385  void cvevsij(double ***eij, double x[],
     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){      if((int)age==79 ||(int)age== 80  ||(int)age== 81){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
     }else{      }else{
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      matprod2(doldm,dnewmpar,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 */
   
     fprintf(ficresvpl,"%.0f ",age );      fprintf(ficresvpl,"%.0f ",age );
     for(i=1; i<=nlstate;i++)      if(nresult >=1)
         fprintf(ficresvpl,"%d ",nres );
       for(i=1; i<=nlstate;i++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         /* for(j=1;j<=nlstate;j++) */
         /*        fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
       }
     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);
Line 5101  void cvevsij(double ***eij, double x[], Line 6413  void cvevsij(double ***eij, double x[],
   
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,npar);    free_matrix(doldm,1,nlstate,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);    free_matrix(dnewmpar,1,nlstate,1,nlstate);
   
 }  }
   
 /************ Variance of one-step probabilities  ******************/  
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])  /************ Variance of backprevalence limit ******************/
    void varbrevlim(char fileresvbl[], FILE  *ficresvbl, double **varbpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **bprlim, double ftolpl, int mobilavproj, int *ncvyearp, int ij, char strstart[], int nres)
 {  {
   int i, j=0,  k1, l1, tj;    /* Variance of backward prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
   int k2, l2, j1,  z1;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   int k=0, l;  
   int first=1, first1, first2;    double **dnewmpar,**doldm;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;    int i, j, nhstepm, hstepm;
   double **dnewm,**doldm;  
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
   double **mu;    double **mgm, **mgp;
   double age, cov[NCOVMAX+1];    double age,agelim;
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */  
   int theta;    int theta;
   char fileresprob[FILENAMELENGTH];    
   char fileresprobcov[FILENAMELENGTH];    pstamp(ficresvbl);
   char fileresprobcor[FILENAMELENGTH];    fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
   double ***varpij;    fprintf(ficresvbl,"# Age ");
     if(nresult >=1)
   strcpy(fileresprob,"PROB_");       fprintf(ficresvbl," Result# ");
   strcat(fileresprob,fileres);  
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);  
   }  
   strcpy(fileresprobcov,"PROBCOV_");   
   strcat(fileresprobcov,fileresu);  
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcov);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);  
   }  
   strcpy(fileresprobcor,"PROBCOR_");   
   strcat(fileresprobcor,fileresu);  
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcor);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);  
   }  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);  
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);  
   pstamp(ficresprob);  
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");  
   fprintf(ficresprob,"# Age");  
   pstamp(ficresprobcov);  
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");  
   fprintf(ficresprobcov,"# Age");  
   pstamp(ficresprobcor);  
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");  
   fprintf(ficresprobcor,"# Age");  
   
   
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
     for(j=1; j<=(nlstate+ndeath);j++){        fprintf(ficresvbl," %1d-%1d",i,i);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    fprintf(ficresvbl,"\n");
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  
     }    
  /* fprintf(ficresprob,"\n");  
   fprintf(ficresprobcov,"\n");  
   fprintf(ficresprobcor,"\n");  
  */  
   xp=vector(1,npar);    xp=vector(1,npar);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    dnewmpar=matrix(1,nlstate,1,npar);
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    doldm=matrix(1,nlstate,1,nlstate);
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    hstepm=1*YEARM; /* Every year of age */
   first=1;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   fprintf(ficgp,"\n# Routine varprob");    agelim = AGEINF;
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    for (age=fage; age>=bage; age --){ /* If stepm=6 months */
   fprintf(fichtm,"\n");      nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       mgp=matrix(1,npar,1,nlstate);
       mgm=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         if(mobilavproj > 0 )
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         else
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         for(i=1;i<=nlstate;i++){
           gp[i] = bprlim[i][i];
           mgp[theta][i] = bprlim[i][i];
         }
        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
          if(mobilavproj > 0 )
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
          else
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         for(i=1;i<=nlstate;i++){
           gm[i] = bprlim[i][i];
           mgm[theta][i] = bprlim[i][i];
         }
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
       /* 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++)
         varbpl[i][(int)age] =0.;
       if((int)age==79 ||(int)age== 80  ||(int)age== 81){
       matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
       }else{
       matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
       }
       for(i=1;i<=nlstate;i++)
         varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvbl,"%.0f ",age );
       if(nresult >=1)
         fprintf(ficresvbl,"%d ",nres );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
       fprintf(ficresvbl,"\n");
       free_vector(gp,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(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewmpar,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
    {
      int i, j=0,  k1, l1, tj;
      int k2, l2, j1,  z1;
      int k=0, l;
      int first=1, first1, first2;
      double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      double **dnewm,**doldm;
      double *xp;
      double *gp, *gm;
      double **gradg, **trgradg;
      double **mu;
      double age, cov[NCOVMAX+1];
      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
      int theta;
      char fileresprob[FILENAMELENGTH];
      char fileresprobcov[FILENAMELENGTH];
      char fileresprobcor[FILENAMELENGTH];
      double ***varpij;
   
      strcpy(fileresprob,"PROB_"); 
      strcat(fileresprob,fileres);
      if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
      }
      strcpy(fileresprobcov,"PROBCOV_"); 
      strcat(fileresprobcov,fileresu);
      if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcov);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
      strcpy(fileresprobcor,"PROBCOR_"); 
      strcat(fileresprobcor,fileresu);
      if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcor);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }
      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      pstamp(ficresprob);
      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
      pstamp(ficresprobcov);
      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      fprintf(ficresprobcov,"# Age");
      pstamp(ficresprobcor);
      fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
      fprintf(ficresprobcor,"# Age");
   
   
   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);     for(i=1; i<=nlstate;i++)
   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);       for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
          fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
      /* fprintf(ficresprob,"\n");
         fprintf(ficresprobcov,"\n");
         fprintf(ficresprobcor,"\n");
      */
      xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
      varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
      fprintf(ficgp,"\n# Routine varprob");
      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
      fprintf(fichtm,"\n");
   
      fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> 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. File %s</li>\n",optionfilehtmcov,optionfilehtmcov);
      fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
      fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
 and drawn. It helps understanding how is the covariance between two incidences.\  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 5194  standard deviations wide on each axis. < Line 6631  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]][codtabm(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]][codtabm(j1,z1)]);                          
         fprintf(ficresprobcov, "**********\n#\n");         fprintf(ficgp, "\n#********** Variable "); 
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficgp, "\n#********** Variable ");          fprintf(ficgp, "**********\n#\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                          
         fprintf(ficgp, "**********\n#\n");                          
                  fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** 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]][codtabm(j1,z1)]);                          
         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(ficresprobcor, "\n#********** Variable ");    
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprobcor, "\n#********** Variable ");             fprintf(ficresprobcor, "**********\n#");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(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));
         if(nagesqr==1)       for (age=bage; age<=fage; age ++){ 
           cov[3]= age*age;         cov[2]=age;
         for (k=1; k<=cptcovn;k++) {         if(nagesqr==1)
           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];           cov[3]= age*age;
           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4         for (k=1; k<=cptcovn;k++) {
                                                          * 1  1 1 1 1           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
                                                          * 2  2 1 1 1           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
                                                          * 3  1 2 1 1                                                                      * 1  1 1 1 1
                                                          */                                                                      * 2  2 1 1 1
           /* nbcode[1][1]=0 nbcode[1][2]=1;*/                                                                      * 3  1 2 1 1
         }                                                                      */
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];         }
         for (k=1; k<=cptcovprod;k++)         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
                  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)];
         for(theta=1; theta <=npar; theta++){                          
           for(i=1; i<=npar; i++)                          
             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);         for(theta=1; theta <=npar; theta++){
                      for(i=1; i<=npar; i++)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                                             
           k=0;           pmij(pmmij,cov,ncovmodel,xp,nlstate);
           for(i=1; i<= (nlstate); i++){                                  
             for(j=1; j<=(nlstate+ndeath);j++){           k=0;
               k=k+1;           for(i=1; i<= (nlstate); i++){
               gp[k]=pmmij[i][j];             for(j=1; j<=(nlstate+ndeath);j++){
             }               k=k+1;
           }               gp[k]=pmmij[i][j];
                        }
           for(i=1; i<=npar; i++)           }
             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);                                  
                for(i=1; i<=npar; i++)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
           k=0;                                  
           for(i=1; i<=(nlstate); i++){           pmij(pmmij,cov,ncovmodel,xp,nlstate);
             for(j=1; j<=(nlstate+ndeath);j++){           k=0;
               k=k+1;           for(i=1; i<=(nlstate); i++){
               gm[k]=pmmij[i][j];             for(j=1; j<=(nlstate+ndeath);j++){
             }               k=k+1;
           }               gm[k]=pmmij[i][j];
                   }
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)            }
             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];                                    
         }           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)         }
           for(theta=1; theta <=npar; theta++)  
             trgradg[j][theta]=gradg[theta][j];  
           
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);   
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  
   
         pmij(pmmij,cov,ncovmodel,x,nlstate);         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                    for(theta=1; theta <=npar; theta++)
         k=0;             trgradg[j][theta]=gradg[theta][j];
         for(i=1; i<=(nlstate); i++){                          
           for(j=1; j<=(nlstate+ndeath);j++){         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
             k=k+1;         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
             mu[k][(int) age]=pmmij[i][j];                          
           }         pmij(pmmij,cov,ncovmodel,x,nlstate);
         }                          
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)         k=0;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)         for(i=1; i<=(nlstate); i++){
             varpij[i][j][(int)age] = doldm[i][j];           for(j=1; j<=(nlstate+ndeath);j++){
              k=k+1;
         /*printf("\n%d ",(int)age);             mu[k][(int) age]=pmmij[i][j];
           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]));         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
           }*/           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
              varpij[i][j][(int)age] = doldm[i][j];
         fprintf(ficresprob,"\n%d ",(int)age);                          
         fprintf(ficresprobcov,"\n%d ",(int)age);         /*printf("\n%d ",(int)age);
         fprintf(ficresprobcor,"\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]));
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][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(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);         fprintf(ficresprobcov,"\n%d ",(int)age);
         }         fprintf(ficresprobcor,"\n%d ",(int)age);
         i=0;                          
         for (k=1; k<=(nlstate);k++){         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           for (l=1; l<=(nlstate+ndeath);l++){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
             i++;         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
             for (j=1; j<=i;j++){         }
               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */         i=0;
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);         for (k=1; k<=(nlstate);k++){
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));           for (l=1; l<=(nlstate+ndeath);l++){ 
             }             i++;
           }             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
         }/* end of loop for state */             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       } /* end of loop for age */             for (j=1; j<=i;j++){
       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);             }
                  }
       /* Confidence intervalle of pij  */         }/* end of loop for state */
       /*       } /* end of loop for age */
         fprintf(ficgp,"\nunset parametric;unset label");       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         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);       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);      
         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);       /* Confidence intervalle of pij  */
         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);       /*
       */         fprintf(ficgp,"\nunset parametric;unset label");
          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       first1=1;first2=2;         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);
       for (k2=1; k2<=(nlstate);k2++){         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         for (l2=1; l2<=(nlstate+ndeath);l2++){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           if(l2==k2) continue;         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           j=(k2-1)*(nlstate+ndeath)+l2;       */
           for (k1=1; k1<=(nlstate);k1++){                  
             for (l1=1; l1<=(nlstate+ndeath);l1++){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
               if(l1==k1) continue;       first1=1;first2=2;
               i=(k1-1)*(nlstate+ndeath)+l1;       for (k2=1; k2<=(nlstate);k2++){
               if(i<=j) continue;         for (l2=1; l2<=(nlstate+ndeath);l2++){ 
               for (age=bage; age<=fage; age ++){            if(l2==k2) continue;
                 if ((int)age %5==0){           j=(k2-1)*(nlstate+ndeath)+l2;
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;           for (k1=1; k1<=(nlstate);k1++){
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;             for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;               if(l1==k1) continue;
                   mu1=mu[i][(int) age]/stepm*YEARM ;               i=(k1-1)*(nlstate+ndeath)+l1;
                   mu2=mu[j][(int) age]/stepm*YEARM;               if(i<=j) continue;
                   c12=cv12/sqrt(v1*v2);               for (age=bage; age<=fage; age ++){ 
                   /* Computing eigen value of matrix of covariance */                 if ((int)age %5==0){
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   if ((lc2 <0) || (lc1 <0) ){                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     if(first2==1){                   mu1=mu[i][(int) age]/stepm*YEARM ;
                       first1=0;                   mu2=mu[j][(int) age]/stepm*YEARM;
                     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);                   c12=cv12/sqrt(v1*v2);
                     }                   /* Computing eigen value of matrix of covariance */
                     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=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* lc1=fabs(lc1); */ /* If we want to have them positive */                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* lc2=fabs(lc2); */                   if ((lc2 <0) || (lc1 <0) ){
                   }                     if(first2==1){
                        first1=0;
                   /* Eigen vectors */                       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);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));                     }
                   /*v21=sqrt(1.-v11*v11); *//* error */                     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);
                   v21=(lc1-v1)/cv12*v11;                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
                   v12=-v21;                     /* lc2=fabs(lc2); */
                   v22=v11;                   }
                   tnalp=v21/v11;                                                                  
                   if(first1==1){                   /* Eigen vectors */
                     first1=0;                   if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
                     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);                     printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                   }                     fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                   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);                     v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
                   /*printf(fignu*/                   }else
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */                   /*v21=sqrt(1.-v11*v11); *//* error */
                   if(first==1){                   v21=(lc1-v1)/cv12*v11;
                     first=0;                   v12=-v21;
                     fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");                   v22=v11;
                     fprintf(ficgp,"\nset parametric;unset label");                   tnalp=v21/v11;
                     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);                   if(first1==1){
                     fprintf(ficgp,"\nset ter svg size 640, 480");                     first1=0;
                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\                     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);
  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\                   }
 %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\                   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);
                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\                   /*printf(fignu*/
                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);                   if(first==1){
                     fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);                     first=0;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                     fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                     fprintf(ficgp,"\nset parametric;unset label");
                     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",\                     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);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\                     fprintf(ficgp,"\nset ter svg size 640, 480");
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                     fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
                   }else{   :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
                     first=0;  %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                     fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     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",\                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\                     fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   }/* if first */                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                 } /* age mod 5 */                     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",      \
               } /* end loop age */                             mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
               fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);                             mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
               first=1;                   }else{
             } /*l12 */                     first=0;
           } /* k12 */                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
         } /*l1 */                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       }/* k1 */                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       /* } */ /* loop covariates */                     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(fabs(lc2)),   \
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);                             mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);                   }/* if first */
   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));                 } /* age mod 5 */
   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);               } /* end loop age */
   free_vector(xp,1,npar);               fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
   fclose(ficresprob);               first=1;
   fclose(ficresprobcov);             } /*l12 */
   fclose(ficresprobcor);           } /* k12 */
   fflush(ficgp);         } /*l1 */
   fflush(fichtmcov);       }/* 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 fileresu[], 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 prevfcast, int backcast, int estepm , \                    int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
                   double jprev1, double mprev1,double anprev1, double dateprev1, \                    double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
                   double jprev2, double mprev2,double anprev2, double dateprev2){                    double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
   int jj1, k1, i1, cpt;    int jj1, k1, i1, cpt, k4, nres;
   
    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> model=1+age+%s\n \
   </ul>", model);
    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");
    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",     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,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
Line 5466  void printinghtml(char fileresu[], char Line 6911  void printinghtml(char fileresu[], char
  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",   - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));             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 (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));             subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - (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) 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): \
Line 5481  void printinghtml(char fileresu[], char Line 6926  void printinghtml(char fileresu[], char
    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
    }     }
   
 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;}
   
      fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
      jj1=0;
   
      fprintf(fichtm," \n<ul>");
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
        if(m != 1 && TKresult[nres]!= k1)
          continue;
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          fprintf(fichtm,"\">");
          
          /* if(nqfveff+nqtveff 0) */ /* Test to be done */
          fprintf(fichtm,"************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          if(invalidvarcomb[k1]){
            fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
            continue;
          }
          fprintf(fichtm,"</a></li>");
        } /* cptcovn >0 */
      }
        fprintf(fichtm," \n</ul>");
   
      jj1=0;
   
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
        if(m != 1 && TKresult[nres]!= k1)
          continue;
   
  jj1=0;       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
  for(k1=1; k1<=m;k1++){  
    /* for(i1=1; i1<=ncodemax[k1];i1++){ */  
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
          fprintf(fichtm,"\n<p><a name=\"rescov");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          fprintf(fichtm,"\"</a>");
    
        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]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);           printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
            /* 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); */
        }         }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
         }
          
          /* if(nqfveff+nqtveff 0) */ /* Test to be done */
        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 */       /* 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> \       fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
 <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);  <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
      /* Pij */       /* Pij */
      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> \       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-%d.svg\">%s_%d-2-%d.svg</a><br> \
 <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);       <img src=\"%s_%d-2-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);     
      /* Quasi-incidences */       /* Quasi-incidences */
      fprintf(fichtm,"<br>\n- I<sub>ij</sub> 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,\   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \   incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
 divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \  divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-%d.svg</a><br> \
 <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);   <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); 
      /* Survival functions (period) in state j */       /* Survival functions (period) in state j */
      for(cpt=1; cpt<=nlstate;cpt++){       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> \         fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%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);  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
      }       }
      /* State specific survival functions (period) */       /* State specific survival functions (period) */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\         fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
  Or probability to survive in various states (1 to %d) being in state %d at different ages.\   And probability to be observed in various states (up 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);   <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
      }       }
      /* Period (stable) prevalence in each health state */       /* Period (forward stable) prevalence in each health state */
      for(cpt=1; cpt<=nlstate;cpt++){       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> \         fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%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);  <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
      }       }
     if(backcast==1){       if(prevbcast==1){
      /* Period (stable) back prevalence in each health state */         /* Backward prevalence in each health state */
      for(cpt=1; cpt<=nlstate;cpt++){         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> \           fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%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);  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
          }
      }       }
     }       if(prevfcast==1){
     if(prevfcast==1){         /* Projection of prevalence up to period (forward stable) prevalence in each health state */
       /* 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>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</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-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
 <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);         }
       }       }
     }       if(prevbcast==1){
         /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
    from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
    account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
   with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
    <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
          }
        }
            
      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) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</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-%d.svg\">%s_%d-%d-%d.svg</a> <br> \
 <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);  <img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
      }       }
    /* } /\* 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> \   - 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> \   - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
Line 5561  variances but at the covariance matrix. Line 7079  variances but at the covariance matrix.
 covariance matrix of the one-step probabilities. \  covariance matrix of the one-step probabilities. \
 See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);  See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
   
  fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",     fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"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(fileresu,"PROBCOV_"),subdirf2(fileresu,"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(fileresu,"PROBCOR_"),subdirf2(fileresu,"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(fileresu,"CVE_"),subdirf2(fileresu,"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(fileresu,"STDE_"),subdirf2(fileresu,"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 forward (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(fileresu,"V_"),subdirf2(fileresu,"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(fileresu,"T_"),subdirf2(fileresu,"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 forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
          subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"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 5594  See page 'Matrix of variance-covariance Line 7112  See page 'Matrix of variance-covariance
 /*      <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);
      if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  m=pow(2,cptcoveff);     jj1=0;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
   
  jj1=0;     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
  for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
    /* for(i1=1; i1<=ncodemax[k1];i1++){ */       if(m != 1 && TKresult[nres]!= k1)
          continue;
        /* 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]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
            /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
   
        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,"\n<br>- Observed (cross-sectional) and period (incidence based) \         fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\  prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
 <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);    <img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);  
      }       }
      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:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\   observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
 <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);  <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
    /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
  }/* End k1 */     }/* End k1 */
  fprintf(fichtm,"</ul>");    }/* End nres */
  fflush(fichtm);     fprintf(fichtm,"</ul>");
      fflush(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;    char gplotcondition[132], gplotlabel[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
   int lv=0, vlv=0, kl=0;    int lv=0, vlv=0, kl=0;
   int ng=0;    int ng=0;
   int vpopbased;    int vpopbased;
         int ioffset; /* variable offset for columns */    int ioffset; /* variable offset for columns */
     int iyearc=1; /* variable column for year of projection  */
     int iagec=1; /* variable column for age of projection  */
     int nres=0; /* Index of resultline */
     int istart=1; /* For starting graphs in projections */
   
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
Line 5644  true period expectancies (those weighted Line 7182  true period expectancies (those weighted
   
   /*#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);
   
     /* diagram of the model */
     fprintf(ficgp,"\n#Diagram of the model \n");
     fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
     fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
     fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
   
     fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0)  ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
     fprintf(ficgp,"\n#show arrow\nunset label\n");
     fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
     fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0.  font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
     fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
     fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
     fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
   
   /* Contribution to likelihood */    /* Contribution to likelihood */
   /* Plot the probability implied in the 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# 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,"\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 svg size 640, 480"); */ /* Too big for svg */
     fprintf(ficgp,"\nset ter pngcairo size 640, 480");    fprintf(ficgp,"\nset ter pngcairo size 640, 480");
 /* nice for mle=4 plot by number of matrix products.  /* 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  "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)"  */  /* 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.svg\";",subdirf2(optionfilefiname,"ILK_")); */
     fprintf(ficgp,"\nset out \"%s-dest.png\";",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 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 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));    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 ++) {    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,"\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,"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);      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 ++) {      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,",\\\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");       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 */                  /* 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,"\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,"\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;unset log\n");
     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */    /* 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*/
   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */    for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
     for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */      for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */        for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");          /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */          if(m != 1 && TKresult[nres]!= k1)
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */            continue;
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* We are interested in selected combination by the resultline */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
                                 vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */          strcpy(gplotlabel,"(");
                         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */          for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
                                 fprintf(ficgp," V%d=%d ",k,vlv);            lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
       }            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
       fprintf(ficgp,"\n#\n");            /* 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]; /* vlv is the value of the covariate lv, 0 or 1 */
             /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
             /* printf(" V%d=%d ",Tvaraff[k],vlv); */
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }
           strcpy(gplotlabel+strlen(gplotlabel),")");
           /* printf("\n#\n"); */
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             /*k1=k1-1;*/ /* To be checked */
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
         
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
           fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
           /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
           fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
           /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
         /* k1-1 error should be nres-1*/
           for (i=1; i<= nlstate ; i ++) {
             if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
             else        fprintf(ficgp," %%*lf (%%*lf)");
           }
           fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
           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==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); 
           for (i=1; i<= nlstate ; i ++) {
             if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
             else fprintf(ficgp," %%*lf (%%*lf)");
           }  
           /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
           
           fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
           if(cptcoveff ==0){
             fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3",      2+3*(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)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                         2+cptcoveff*2+3*(cpt-1),  cpt );  /* 4 or 6 ?*/
               }else{
                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                 kl++;
               }
             } /* end covariate */
           } /* end if no covariate */
   
                         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);          if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
                         fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);            /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
                         fprintf(ficgp,"set xlabel \"Age\" \n\            fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
 set ylabel \"Probability\" \n   \            if(cptcoveff ==0){
 set ter svg size 640, 480\n     \              fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3",    2+(cpt-1),  cpt );
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);            }else{
                                       kl=0;
                         for (i=1; i<= nlstate ; i ++) {              for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
                                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");                lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                                 else        fprintf(ficgp," %%*lf (%%*lf)");                /* 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 */
                         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);                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                         for (i=1; i<= nlstate ; i ++) {                vlv= nbcode[Tvaraff[k]][lv];
                                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");                kl++;
                                 else fprintf(ficgp," %%*lf (%%*lf)");                /* 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 */ 
                         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);                 /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                         for (i=1; i<= nlstate ; i ++) {                /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");                if(k==cptcoveff){
                                 else fprintf(ficgp," %%*lf (%%*lf)");                  fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                         }                            2+cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
                         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));                }else{
                         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */                  fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                                 /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */                  kl++;
                                 fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */                }
                                 kl=0;              } /* end covariate */
                                 for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */            } /* end if no covariate */
                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */            if(prevbcast == 1){
                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */              fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */              /* k1-1 error should be nres-1*/
                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */              for (i=1; i<= nlstate ; i ++) {
                                         vlv= nbcode[Tvaraff[k]][lv];                if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                                         kl++;                else        fprintf(ficgp," %%*lf (%%*lf)");
                                         /* 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 */               fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
                                         /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */               for (i=1; i<= nlstate ; i ++) {
                                         /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/                if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                                         if(k==cptcoveff){                else fprintf(ficgp," %%*lf (%%*lf)");
                                                         fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, k,kl+1+1,nbcode[Tvaraff[k]][lv], \              } 
                                                                                 4+(cpt-1),  cpt );              fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); 
                                         }else{              for (i=1; i<= nlstate ; i ++) {
                                                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, k,kl+1+1,nbcode[Tvaraff[k]][lv]);                if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                                                 kl++;                else fprintf(ficgp," %%*lf (%%*lf)");
                                         }              } 
                                 } /* end covariate */              fprintf(ficgp,"\" t\"\" w l lt 4");
                         }            } /* end if backprojcast */
                         fprintf(ficgp,"\nset out \n");          } /* end if prevbcast */
           /* fprintf(ficgp,"\nset out ;unset label;\n"); */
           fprintf(ficgp,"\nset out ;unset title;\n");
         } /* nres */
     } /* k1 */      } /* k1 */
   } /* cpt */    } /* cpt */
   
     
   /*2 eme*/    /*2 eme*/
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++){  
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");        fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
         strcpy(gplotlabel,"(");
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        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 */          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(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* decodtabm(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 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                 vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
                                 fprintf(ficgp," V%d=%d ",k,vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }
         /* for(k=1; k <= ncovds; k++){ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       }        }
         strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;
         }
                                                   
                         fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
                         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
                                 if(vpopbased==0)          fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
                                         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);          if(vpopbased==0){
                                 else            fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
                                         fprintf(ficgp,"\nreplot ");          }else
                                 for (i=1; i<= nlstate+1 ; i ++) {            fprintf(ficgp,"\nreplot ");
                                         k=2*i;          for (i=1; i<= nlstate+1 ; 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);            k=2*i;
                                         for (j=1; j<= nlstate+1 ; j ++) {            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");            for (j=1; j<= nlstate+1 ; j ++) {
                                                 else fprintf(ficgp," %%*lf (%%*lf)");              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);            if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
                                         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);            else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
                                         for (j=1; j<= nlstate+1 ; j ++) {            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");            for (j=1; j<= nlstate+1 ; j ++) {
                                                 else fprintf(ficgp," %%*lf (%%*lf)");              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);            fprintf(ficgp,"\" t\"\" w l lt 0,");
                                         for (j=1; j<= nlstate+1 ; j ++) {            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");            for (j=1; j<= nlstate+1 ; j ++) {
                                                 else fprintf(ficgp," %%*lf (%%*lf)");              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");            if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
                                 } /* state */            else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
                         } /* vpopbased */          } /* state */
                         fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */        } /* vpopbased */
   } /* k1 */        fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
       } /* end nres */
     } /* k1 end 2 eme*/
                   
                   
   /*3eme*/    /*3eme*/
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++){
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);        if(m != 1 && TKresult[nres]!= k1)
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          continue;
                                 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 */        for (cpt=1; cpt<= nlstate ; cpt ++) {
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          strcpy(gplotlabel,"(");
                                 vlv= nbcode[Tvaraff[k]][lv];          for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                                 fprintf(ficgp," V%d=%d ",k,vlv);            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 */
       fprintf(ficgp,"\n#\n");            /* 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);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
           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.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
       fprintf(ficgp,"set ter svg size 640, 480\n\          fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
 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,"set ter svg size 640, 480\n\
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
                                 for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                                 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                                 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                                 for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                                 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                                                                   
       */          */
       for (i=1; i< nlstate ; i ++) {          for (i=1; i< nlstate ; i ++) {
                                 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(fileresu,"E_"),nres-1,nres-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(fileresu,"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_"),nres-1,nres-1,k+nlstate,cpt);
     }        }
   }        fprintf(ficgp,"\nunset label;\n");
       } /* end nres */
     } /* end kl 3eme */
       
     /* 4eme */
   /* Survival functions (period) from state i in state j by initial state i */    /* 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 covariate and each value */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);        if(m != 1 && TKresult[nres]!= k1)
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          continue;
         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          strcpy(gplotlabel,"(");
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
         vlv= nbcode[Tvaraff[k]][lv];            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
         fprintf(ficgp," V%d=%d ",k,vlv);            /* 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 */
       fprintf(ficgp,"\n#\n");            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
 set ter svg size 640, 480\n\  
 unset log y\n\  
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  
       k=3;  
       for (i=1; i<= nlstate ; i ++){  
         if(i==1){  
           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));  
         }else{  
           fprintf(ficgp,", '' ");  
         }          }
         l=(nlstate+ndeath)*(i-1)+1;          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         for (j=2; j<= nlstate+ndeath ; j ++)            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficgp,"+$%d",k+l+j-1);          }       
         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);          strcpy(gplotlabel+strlen(gplotlabel),")");
       } /* nlstate */          fprintf(ficgp,"\n#\n");
       fprintf(ficgp,"\nset out\n");          if(invalidvarcomb[k1]){
     } /* end cpt state*/             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
   } /* end covariate */              continue;
           }
         
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
           k=3;
           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/($%d",k1,k+l+(cpt-1),k+l);
             for (j=2; j<= nlstate+ndeath ; j ++)
               fprintf(ficgp,"+$%d",k+l+j-1);
             fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
           } /* nlstate */
           fprintf(ficgp,"\nset out; unset label;\n");
         } /* end cpt state*/ 
       } /* end nres */
     } /* end covariate k1 */  
   
   /* 5eme */
   /* Survival functions (period) from state i in state j by final state j */    /* 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 (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       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);        if(m != 1 && TKresult[nres]!= k1)
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          continue;
         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          strcpy(gplotlabel,"(");
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          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);
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
         vlv= nbcode[Tvaraff[k]][lv];            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
         fprintf(ficgp," V%d=%d ",k,vlv);            /* 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 */
       fprintf(ficgp,"\n#\n");            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
 set ter svg size 640, 480\n\          }
 unset log y\n\          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
 plot [%.f:%.f]  ", ageminpar, agemaxpar);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       k=3;            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */          }       
         if(j==1)          strcpy(gplotlabel+strlen(gplotlabel),")");
           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));          fprintf(ficgp,"\n#\n");
         else          if(invalidvarcomb[k1]){
           fprintf(ficgp,", '' ");            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
         l=(nlstate+ndeath)*(cpt-1) +j;            continue;
         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,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);          fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
       } /* nlstate */          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
       fprintf(ficgp,", '' ");  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);          k=3;
       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */          for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
         l=(nlstate+ndeath)*(cpt-1) +j;            if(j==1)
         if(j < nlstate)              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           fprintf(ficgp,"$%d +",k+l);            else
         else              fprintf(ficgp,", '' ");
           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);            l=(nlstate+ndeath)*(cpt-1) +j;
       }            fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
       fprintf(ficgp,"\nset out\n");            /* for (i=2; i<= nlstate+ndeath ; i ++) */
     } /* end cpt state*/             /*   fprintf(ficgp,"+$%d",k+l+i-1); */
   } /* end covariate */              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; unset label;\n");
         } /* end cpt state*/ 
       } /* end covariate */  
     } /* end nres */
     
   /* 6eme */
   /* CV preval stable (period) for each covariate */    /* 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 (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);      if(m != 1 && TKresult[nres]!= k1)
         continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
         strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        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 */          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(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* decodtabm(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 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
         fprintf(ficgp," V%d=%d ",k,vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
       }        }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         } 
         strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;
         }
         
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\n\  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
 unset log y\n\  
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  
       k=3; /* Offset */        k=3; /* Offset */
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){ /* State of origin */
         if(i==1)          if(i==1)
           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"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; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
         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/($%d",k1,k+l+(cpt-1),k+l);
         for (j=2; j<= nlstate ; j ++)          for (j=2; j<= nlstate ; j ++)
           fprintf(ficgp,"+$%d",k+l+j-1);            fprintf(ficgp,"+$%d",k+l+j-1);
         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out; unset label;\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
   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 */  /* 7eme */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */    if(prevbcast == 1){
         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);      /* CV backward prevalence  for each covariate */
       for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
           strcpy(gplotlabel,"(");      
           fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          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 */            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(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */            /* decodtabm(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 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",k,vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }          }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          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,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\n                                             \  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
 unset log y\n                                                           \  
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  
         k=3; /* Offset */          k=3; /* Offset */
         for (i=1; i<= nlstate ; i ++){          for (i=1; i<= nlstate ; i ++){ /* State of arrival */
           if(i==1)            if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
           else            else
             fprintf(ficgp,", '' ");              fprintf(ficgp,", '' ");
           /* l=(nlstate+ndeath)*(i-1)+1; */            /* l=(nlstate+ndeath)*(i-1)+1; */
           l=(nlstate+ndeath)*(cpt-1)+1;            l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
           /* 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); /\* 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/($%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 */            fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
           /* for (j=2; j<= nlstate ; j ++) */            /* for (j=2; j<= nlstate ; j ++) */
           /*    fprintf(ficgp,"+$%d",k+l+j-1); */            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
           /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */            /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);            fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
         } /* nlstate */          } /* nlstate */
         fprintf(ficgp,"\nset out\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end covariate */        } /* end covariate */  
   } /* End if backcast */    } /* End if prevbcast */
       
     /* 8eme */
   if(prevfcast==1){    if(prevfcast==1){
     /* Projection from cross-sectional to stable (period) for each covariate */      /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        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);          strcpy(gplotlabel,"(");      
                                 for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */          fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */          for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                         vlv= nbcode[Tvaraff[k]][lv];            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                         fprintf(ficgp," V%d=%d ",k,vlv);            vlv= nbcode[Tvaraff[k]][lv];
                                 }            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                                 fprintf(ficgp,"\n#\n");            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
                                           }
                                 fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                                 fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                                 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
 set ter svg size 640, 480\n     \          }       
 unset log y\n   \          strcpy(gplotlabel+strlen(gplotlabel),")");
 plot [%.f:%.f]  ", ageminpar, agemaxpar);          fprintf(ficgp,"\n#\n");
                                 for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */          if(invalidvarcomb[k1]){
                                         /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                         /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */               continue;
                                         /*# 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,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
                                                 fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
                                         }else{          fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
                                                 fprintf(ficgp,",\\\n '' ");          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
                                         }  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
                                         if(cptcoveff ==0){ /* No covariate */  
                                                 ioffset=2; /* Age is in 2 */          /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
                                                 /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/          istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
                                                 /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */          /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
                                                 /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/          for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
                                                 /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */            /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                                 fprintf(ficgp," u %d:(", ioffset);             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                                                 if(i==nlstate+1)            /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",                    \            /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );            if(i==istart){
                                                 else              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",                    \            }else{
                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );              fprintf(ficgp,",\\\n '' ");
                                         }else{ /* more than 2 covariates */            }
                                                 if(cptcoveff ==1){            if(cptcoveff ==0){ /* No covariate */
                                                         ioffset=4; /* Age is in 4 */              ioffset=2; /* Age is in 2 */
                                                 }else{              /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                                                         ioffset=6; /* Age is in 6 */              /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                                                 /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/              /*# 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 */              /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                                                 }                 fprintf(ficgp," u %d:(", ioffset); 
                                                 fprintf(ficgp," u %d:((",ioffset);               if(i==nlstate+1){
                                                 kl=0;                fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ",        \
                                                 for (k=1; k<=cptcoveff; k++){    /* For each covariate  */                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */                fprintf(ficgp,",\\\n '' ");
                                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                fprintf(ficgp," u %d:(",ioffset); 
                                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
                                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                       offyear,                           \
                                                         vlv= nbcode[Tvaraff[k]][lv];                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate );
                                                         kl++;              }else
                                                         /* 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 *\/ */                fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
                                                         /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                                                         /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */             }else{ /* more than 2 covariates */
                                                         /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/              ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
                                                         if(k==cptcoveff){              /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                                                 if(i==nlstate+1){              /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
                                                                         if(cptcoveff ==1){              iyearc=ioffset-1;
                                                                         fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \              iagec=ioffset;
                                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );              fprintf(ficgp," u %d:(",ioffset); 
                                                                         }else{              kl=0;
                                                                         fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \              strcpy(gplotcondition,"(");
                                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );              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 */
                                                                 }else{                /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                                                         if(cptcoveff ==1){                /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                                                                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                                                                                                 ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );                vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                                                                         }else{                kl++;
                                                                                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[k]][lv], \                sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                                                                                                                 ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );                kl++;
                                                                         }                if(k <cptcoveff && cptcoveff>1)
                                                                 }                  sprintf(gplotcondition+strlen(gplotcondition)," && ");
                                                         }else{ /* k < cptcoveff */              }
                                                                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[k]][lv]);              strcpy(gplotcondition+strlen(gplotcondition),")");
                                                                 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 */ 
                                                 } /* end covariate */              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                                         } /* end if covariate */              /* ''  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*/
                                 } /* nlstate */              if(i==nlstate+1){
                                 fprintf(ficgp,"\nset out\n");                fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
                         } /* end cpt state*/                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
                 } /* end covariate */                fprintf(ficgp,",\\\n '' ");
         } /* End if prevfcast */                fprintf(ficgp," u %d:(",iagec); 
                         fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
                                 iyearc, iagec, offyear,                           \
         /* proba elementaires */                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
         fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");  /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
               }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; unset label;\n");
         } /* end cpt state*/
       } /* end covariate */
     } /* End if prevfcast */
     
     if(prevbcast==1){
       /* Back projection from cross-sectional to stable (mixed) for each covariate */
       
       for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
           strcpy(gplotlabel,"(");      
           fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%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);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
           
           fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
   
           /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
           istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
           /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
           for (i=istart; 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==istart){
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
             }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)):1 t 'bw%d' with line lc variable ", \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",ioffset); 
                 fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
                        offbyear,                          \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
               }else
                 fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ",      \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
             }else{ /* more than 2 covariates */
               ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
               /*#  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 */
               iyearc=ioffset-1;
               iagec=ioffset;
               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 : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",iagec); 
                 /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
                 fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
                         iyearc,iagec,offbyear,                            \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
   /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
               }else{
                 /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
                 fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
               }
             } /* end if covariate */
           } /* nlstate */
           fprintf(ficgp,"\nset out; unset label;\n");
         } /* end cpt state*/
       } /* end covariate */
     } /* End if prevbcast */
     
     
     /* 9eme writing MLE parameters */
     fprintf(ficgp,"\n##############\n#9eme 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);      fprintf(ficgp,"# initial state %d\n",i);
     for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
Line 6092  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7947  plot [%.f:%.f]  ", ageminpar, agemaxpar)
         fprintf(ficgp,"\n");          fprintf(ficgp,"\n");
       }        }
     }      }
    }    }
   fprintf(ficgp,"##############\n#\n");    fprintf(ficgp,"##############\n#\n");
     
   /*goto avoid;*/    /*goto avoid;*/
   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");    /* 10eme Graphics of probabilities or incidences using written MLE parameters */
     fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");    fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");    fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
Line 6110  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7966  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");    fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");    fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
   fprintf(ficgp,"#\n");    fprintf(ficgp,"#\n");
    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
      fprintf(ficgp,"# ng=%d\n",ng);      fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);      fprintf(ficgp,"#model=%s \n",model);
      for(jk=1; jk <=m; jk++) {      fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
        fprintf(ficgp,"#    jk=%d\n",jk);      fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);      for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */
        fprintf(ficgp,"\nset ter svg size 640, 480 ");      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
        if (ng==1){        if(m != 1 && TKresult[nres]!= k1)
          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */          continue;
          fprintf(ficgp,"\nunset log y");        fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);
        }else if (ng==2){        strcpy(gplotlabel,"(");
          fprintf(ficgp,"\nset ylabel \"Probability\"\n");        /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
          fprintf(ficgp,"\nset log y");        for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
        }else if (ng==3){          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
          fprintf(ficgp,"\nset log y");          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
        }else          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
          fprintf(ficgp,"\nunset title ");          vlv= nbcode[Tvaraff[k]][lv];
        fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
        i=1;          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
        for(k2=1; k2<=nlstate; k2++) {        }
          k3=i;        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
          for(k=1; k<=(nlstate+ndeath); k++) {          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
            if (k != k2){          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
              switch( ng) {        } 
              case 1:        strcpy(gplotlabel+strlen(gplotlabel),")");
                if(nagesqr==0)        fprintf(ficgp,"\n#\n");
                  fprintf(ficgp," p%d+p%d*x",i,i+1);        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
                else /* nagesqr =1 */        fprintf(ficgp,"\nset key outside ");
                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);        /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
                break;        fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
              case 2: /* ng=2 */        fprintf(ficgp,"\nset ter svg size 640, 480 ");
                if(nagesqr==0)        if (ng==1){
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
                else /* nagesqr =1 */          fprintf(ficgp,"\nunset log y");
                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);        }else if (ng==2){
                break;          fprintf(ficgp,"\nset ylabel \"Probability\"\n");
              case 3:          fprintf(ficgp,"\nset log y");
                if(nagesqr==0)        }else if (ng==3){
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
                else /* nagesqr =1 */          fprintf(ficgp,"\nset log y");
                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);        }else
                break;          fprintf(ficgp,"\nunset title ");
              }        fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
              ij=1;/* To be checked else nbcode[0][0] wrong */        i=1;
              for(j=3; j <=ncovmodel-nagesqr; j++) {        for(k2=1; k2<=nlstate; k2++) {
                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */          k3=i;
                if(ij <=cptcovage) { /* Bug valgrind */          for(k=1; k<=(nlstate+ndeath); k++) {
                  if((j-2)==Tage[ij]) { /* Bug valgrind */            if (k != k2){
                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);              switch( ng) {
                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */              case 1:
                    ij++;                if(nagesqr==0)
                  }                  fprintf(ficgp," p%d+p%d*x",i,i+1);
                }                else /* nagesqr =1 */
                else                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                break;
              }              case 2: /* ng=2 */
            }else{                if(nagesqr==0)
              i=i-ncovmodel;                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */                else /* nagesqr =1 */
                fprintf(ficgp," (1.");                  fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
            }                break;
                          case 3:
            if(ng != 1){                if(nagesqr==0)
              fprintf(ficgp,")/(1");                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                              else /* nagesqr =1 */
              for(k1=1; k1 <=nlstate; k1++){                   fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                if(nagesqr==0)                break;
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              }
                else /* nagesqr =1 */              ij=1;/* To be checked else nbcode[0][0] wrong */
                  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);              ijp=1; /* product no age */
               /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
               for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
                 /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                 if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                   if(j==Tage[ij]) { /* Product by age  To be looked at!!*/
                     if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                       if(DummyV[j]==0){
                         fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
                       }else{ /* quantitative */
                         fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                         /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                       }
                       ij++;
                     }
                   } 
                 }else if(cptcovprod >0){
                   if(j==Tprod[ijp]) { /* */ 
                     /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                     if(ijp <=cptcovprod) { /* Product */
                       if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                         if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
                           /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                           fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                         }else{ /* Vn is dummy and Vm is quanti */
                           /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                           fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                         }
                       }else{ /* Vn*Vm Vn is quanti */
                         if(DummyV[Tvard[ijp][2]]==0){
                           fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
                         }else{ /* Both quanti */
                           fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                         }
                       }
                       ijp++;
                     }
                   } /* end Tprod */
                 } else{  /* simple covariate */
                   /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
                   if(Dummy[j]==0){
                     fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
                   }else{ /* quantitative */
                     fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                   }
                 } /* end simple */
               } /* end j */
             }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(cpt=1; cpt <=nlstate; cpt++){ 
                 if(nagesqr==0)
                   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
                                 
                ij=1;                ij=1;
                for(j=3; j <=ncovmodel-nagesqr; j++){                for(j=3; j <=ncovmodel-nagesqr; j++){
                  if(ij <=cptcovage) { /* Bug valgrind */                   if(cptcovage >0){ 
                    if((j-2)==Tage[ij]) { /* Bug valgrind */                     if((j-2)==Tage[ij]) { /* Bug valgrind */
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                       if(ij <=cptcovage) { /* Bug valgrind */
                      /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */                         fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
                      ij++;                         /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                          ij++;
                        }
                    }                     }
                  }                   }else
                  else                     fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                }
                }                fprintf(ficgp,")");
                fprintf(ficgp,")");              }
              }              fprintf(ficgp,")");
              fprintf(ficgp,")");              if(ng ==2)
              if(ng ==2)                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
                fprintf(ficgp," t \"p%d%d\" ", k2,k);              else /* ng= 3 */
              else /* ng= 3 */                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
                fprintf(ficgp," t \"i%d%d\" ", k2,k);            }else{ /* end ng <> 1 */
            }else{ /* end ng <> 1 */              if( k !=k2) /* logit p11 is hard to draw */
              if( k !=k2) /* logit p11 is hard to draw */                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);            }
            }            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)              fprintf(ficgp,",");
              fprintf(ficgp,",");            if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
            if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))              fprintf(ficgp,",");
              fprintf(ficgp,",");            i=i+ncovmodel;
            i=i+ncovmodel;          } /* end k */
          } /* end k */        } /* end k2 */
        } /* end k2 */        /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
        fprintf(ficgp,"\n set out\n");        fprintf(ficgp,"\n set out; unset title;set key default;\n");
      } /* end jk */      } /* end k1 */
    } /* end ng */    } /* end ng */
  /* avoid: */    /* avoid: */
    fflush(ficgp);     fflush(ficgp); 
 }  /* end gnuplot */  }  /* end gnuplot */
   
   
 /*************** Moving average **************/  /*************** Moving average **************/
 /* 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, double bageout, double fageout){ */
 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, cpt, cptcod;     int i, cpt, cptcod;
   int modcovmax =1;     int modcovmax =1;
   int mobilavrange, mob;     int mobilavrange, mob;
   int iage=0;     int iage=0;
      int firstA1=0, firstA2=0;
   
      double sum=0., sumr=0.;
      double age;
      double *sumnewp, *sumnewm, *sumnewmr;
      double *agemingood, *agemaxgood; 
      double *agemingoodr, *agemaxgoodr; 
     
     
      /* modcovmax=2*cptcoveff;  Max number of modalities. We suppose  */
      /*              a covariate has 2 modalities, should be equal to ncovcombmax   */
   
      sumnewp = vector(1,ncovcombmax);
      sumnewm = vector(1,ncovcombmax);
      sumnewmr = vector(1,ncovcombmax);
      agemingood = vector(1,ncovcombmax);  
      agemingoodr = vector(1,ncovcombmax); 
      agemaxgood = vector(1,ncovcombmax);
      agemaxgoodr = vector(1,ncovcombmax);
   
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
        sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
        sumnewp[cptcod]=0.;
        agemingood[cptcod]=0, agemingoodr[cptcod]=0;
        agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
      }
      if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
     
      if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
        if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
        else mobilavrange=mobilav;
        for (age=bage; age<=fage; age++)
          for (i=1; i<=nlstate;i++)
            for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        /* We keep the original values on the extreme ages bage, fage and for 
           fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           we use a 5 terms etc. until the borders are no more concerned. 
        */ 
        for (mob=3;mob <=mobilavrange;mob=mob+2){
          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
            for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
              sumnewm[cptcod]=0.;
              for (i=1; i<=nlstate;i++){
                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;
                sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
              } /* end i */
              if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
            } /* end cptcod */
          }/* end age */
        }/* end mob */
      }else{
        printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
        return -1;
      }
   
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
        /* 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;
        }
   
        for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
          sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
            agemingoodr[cptcod]=age;
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
              agemingood[cptcod]=age;
          }
        } /* age */
        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
          sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
            agemaxgoodr[cptcod]=age;
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
            agemaxgood[cptcod]=age;
          }
        } /* age */
        /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
        /* but they will change */
        firstA1=0;firstA2=0;
        for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
          sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
            if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
              agemaxgoodr[cptcod]=age;  /* age min */
              for (i=1; i<=nlstate;i++)
                mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }else{
            if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
              agemaxgood[cptcod]=age;
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }/* end else */
          sum=0.;sumr=0.;
          for (i=1; i<=nlstate;i++){
            sum+=mobaverage[(int)age][i][cptcod];
            sumr+=probs[(int)age][i][cptcod];
          }
          if(fabs(sum - 1.) > 1.e-3) { /* bad */
            if(!firstA1){
              firstA1=1;
              printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
            }
            fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
          } /* end bad */
          /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
          if(fabs(sumr - 1.) > 1.e-3) { /* bad */
            if(!firstA2){
              firstA2=1;
              printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
            }
            fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
          } /* end bad */
        }/* age */
   
        for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
          sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          } 
          if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
            if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
              agemingoodr[cptcod]=age;
              for (i=1; i<=nlstate;i++)
                mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }else{
            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 */
          }/* end else */
          sum=0.;sumr=0.;
          for (i=1; i<=nlstate;i++){
            sum+=mobaverage[(int)age][i][cptcod];
            sumr+=mobaverage[(int)age][i][cptcod];
          }
          if(fabs(sum - 1.) > 1.e-3) { /* bad */
            printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
          } /* end bad */
          /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
          if(fabs(sumr - 1.) > 1.e-3) { /* bad */
            printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage);
          } /* end bad */
        }/* age */
   
   double sum=0.;  
   double age;  
   double *sumnewp, *sumnewm;  
   double *agemingood, *agemaxgood; /* Currently identical for all covariates */  
     
     
   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose   
                            a covariate has 2 modalities, should be equal to ncovcombmax  */  
   
   sumnewp = vector(1,modcovmax);  
   sumnewm = vector(1,modcovmax);  
   agemingood = vector(1,modcovmax);       
   agemaxgood = vector(1,modcovmax);  
   
   for (cptcod=1;cptcod<=modcovmax;cptcod++){  
                 sumnewm[cptcod]=0.;  
                 sumnewp[cptcod]=0.;  
                 agemingood[cptcod]=0;  
                 agemaxgood[cptcod]=0;  
         }  
   if (cptcovn<1) modcovmax=1; /* At least 1 pass */  
     
   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){  
     if(mobilav==1) mobilavrange=5; /* default */  
     else mobilavrange=mobilav;  
     for (age=bage; age<=fage; age++)  
       for (i=1; i<=nlstate;i++)  
                                 for (cptcod=1;cptcod<=modcovmax;cptcod++)  
                                         mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];  
     /* We keep the original values on the extreme ages bage, fage and for   
        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2  
        we use a 5 terms etc. until the borders are no more concerned.   
     */   
     for (mob=3;mob <=mobilavrange;mob=mob+2){  
       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){  
                                 for (i=1; i<=nlstate;i++){  
                                         for (cptcod=1;cptcod<=modcovmax;cptcod++){  
                                                 mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];  
                                                 for (cpt=1;cpt<=(mob-1)/2;cpt++){  
                                                         mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];  
                                                         mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];  
                                                 }  
                                                 mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;  
                                         }  
                                 }  
       }/* end age */  
     }/* end mob */  
   }else  
     return -1;  
   for (cptcod=1;cptcod<=modcovmax;cptcod++){  
     /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */  
     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++){       for (age=bage; age<=fage; age++){
                         printf("%d %d ", cptcod, (int)age);         /* printf("%d %d ", cptcod, (int)age); */
                         sumnewp[cptcod]=0.;         sumnewp[cptcod]=0.;
                         sumnewm[cptcod]=0.;         sumnewm[cptcod]=0.;
                         for (i=1; i<=nlstate;i++){         for (i=1; i<=nlstate;i++){
                                 sumnewp[cptcod]+=probs[(int)age][i][cptcod];           sumnewp[cptcod]+=probs[(int)age][i][cptcod];
                                 sumnewm[cptcod]+=mobaverage[(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 ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
                         }         }
                         /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */         /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
                 }       }
                 /* printf("\n"); */       /* printf("\n"); */
     /* } */       /* } */
     /* brutal averaging */  
     for (i=1; i<=nlstate;i++){       /* brutal averaging */
       for (age=1; age<=bage; age++){       /* for (i=1; i<=nlstate;i++){ */
                                 mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];       /*   for (age=1; age<=bage; age++){ */
                                 /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */       /*          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];       /*   for (age=fage; age<=AGESUP; age++){ */
                                 /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */       /*          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++){       /* } /\* end i status *\/ */
       for (age=1; age<=AGESUP; age++){       /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
                                 /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/       /*   for (age=1; age<=AGESUP; age++){ */
                                 mobaverage[(int)age][i][cptcod]=0.;       /*          /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
       }       /*          mobaverage[(int)age][i][cptcod]=0.; */
     }       /*   } */
   }/* end cptcod */       /* } */
   free_vector(sumnewm,1, modcovmax);     }/* end cptcod */
   free_vector(sumnewp,1, modcovmax);     free_vector(agemaxgoodr,1, ncovcombmax);
   free_vector(agemaxgood,1, modcovmax);     free_vector(agemaxgood,1, ncovcombmax);
   free_vector(agemingood,1, modcovmax);     free_vector(agemingood,1, ncovcombmax);
   return 0;     free_vector(agemingoodr,1, ncovcombmax);
 }/* End movingaverage */     free_vector(sumnewmr,1, ncovcombmax);
      free_vector(sumnewm,1, ncovcombmax);
      free_vector(sumnewp,1, ncovcombmax);
      return 0;
    }/* End movingaverage */
     
   
    
 /************** Forecasting ******************/  /************** Forecasting ******************/
 void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){  /* void prevforecast(char fileres[], double dateintmean, double anprojd, double mprojd, double jprojd, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anprojf, double p[], int cptcoveff)*/
   /* proj1, year, month, day of starting projection   void prevforecast(char fileres[], double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
     /* dateintemean, mean date of interviews
        dateprojd, year, month, day of starting projection 
        dateprojf date of end of projection;year of end of projection (same day and month as proj1).
      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
      anproj2 year of en of projection (same day and month as proj1).  
   */    */
   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;    /* double anprojd, mprojd, jprojd; */
     /* double anprojf, mprojf, jprojf; */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, yp,yp1,yp2;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat;    double ***p3mat;
   /* double ***mobaverage; */    /* double ***mobaverage; */
Line 6399  void prevforecast(char fileres[], double Line 8412  void prevforecast(char fileres[], double
     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', please wait... \n", fileresf);    printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
   fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);    fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
Line 6410  void prevforecast(char fileres[], double Line 8423  void prevforecast(char fileres[], double
   if(estepm < stepm){    if(estepm < stepm){
     printf ("Problem %d lower than %d\n",estepm, stepm);      printf ("Problem %d lower than %d\n",estepm, stepm);
   }    }
   else  hstepm=estepm;       else{
       hstepm=estepm;   
     }
     if(estepm > stepm){ /* Yes every two year */
       stepsize=2;
     }
     hstepm=hstepm/stepm;
   
   hstepm=hstepm/stepm;     
   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and    /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
                                fractional in yp1 */    /*                              fractional in yp1 *\/ */
   anprojmean=yp;    /* aintmean=yp; */
   yp2=modf((yp1*12),&yp);    /* yp2=modf((yp1*12),&yp); */
   mprojmean=yp;    /* mintmean=yp; */
   yp1=modf((yp2*30.5),&yp);    /* yp1=modf((yp2*30.5),&yp); */
   jprojmean=yp;    /* jintmean=yp; */
   if(jprojmean==0) jprojmean=1;    /* if(jintmean==0) jintmean=1; */
   if(mprojmean==0) jprojmean=1;    /* if(mintmean==0) mintmean=1; */
   
   i1=cptcoveff;  
     /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
     /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
     /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
     i1=pow(2,cptcoveff);
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
       
   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2); 
       
   fprintf(ficresf,"#****** Routine prevforecast **\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
     
 /*            if (h==(int)(YEARM*yearp)){ */  /*            if (h==(int)(YEARM*yearp)){ */
   for(cptcov=1, k=0;cptcov<=i1;cptcov++){    for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    for(k=1; k<=i1;k++){
       k=k+1;      if(i1 != 1 && TKresult[nres]!= k)
       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");        continue;
       for(j=1;j<=cptcoveff;j++) {      if(invalidvarcomb[k]){
                                 fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        printf("\nCombination (%d) projection ignored because no cases \n",k); 
       }        continue;
       fprintf(ficresf," yearproj age");      }
       for(j=1; j<=nlstate+ndeath;j++){       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
                                 for(i=1; i<=nlstate;i++)                    for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," p%d%d",i,j);        fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                                 fprintf(ficresf," wp.%d",j);      }
       }      for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {        fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                                 fprintf(ficresf,"\n");      }
                                 fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);         fprintf(ficresf," yearproj age");
                                 for (agec=fage; agec>=(ageminpar-1); agec--){       for(j=1; j<=nlstate+ndeath;j++){ 
                                         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);         for(i=1; i<=nlstate;i++)        
                                         nhstepm = nhstepm/hstepm;           fprintf(ficresf," p%d%d",i,j);
                                         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresf," wp.%d",j);
                                         oldm=oldms;savm=savms;      }
                                         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);      for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
                                                 fprintf(ficresf,"\n");
                                         for (h=0; h<=nhstepm; h++){        fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);   
                                                 if (h*hstepm/YEARM*stepm ==yearp) {        /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
               fprintf(ficresf,"\n");        for (agec=fage; agec>=(bage); agec--){ 
               for(j=1;j<=cptcoveff;j++)           nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          nhstepm = nhstepm/hstepm; 
                                                         fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                                                 }           oldm=oldms;savm=savms;
                                                 for(j=1; j<=nlstate+ndeath;j++) {          /* We compute pii at age agec over nhstepm);*/
                                                         ppij=0.;          hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
                                                         for(i=1; i<=nlstate;i++) {          /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
                                                                 if (mobilav==1)           for (h=0; h<=nhstepm; h++){
                                                                         ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];            if (h*hstepm/YEARM*stepm ==yearp) {
                                                                 else {              break;
                                                                         ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];            }
                                                                 }          }
                                                                 if (h*hstepm/YEARM*stepm== yearp) {          fprintf(ficresf,"\n");
                                                                         fprintf(ficresf," %.3f", p3mat[i][j][h]);          for(j=1;j<=cptcoveff;j++) 
                                                                 }            fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                                                         } /* end i */          fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
                                                         if (h*hstepm/YEARM*stepm==yearp) {          
                                                                 fprintf(ficresf," %.3f", ppij);          for(j=1; j<=nlstate+ndeath;j++) {
                                                         }            ppij=0.;
                                                 }/* end j */            for(i=1; i<=nlstate;i++) {
                                         } /* end h */              if (mobilav>=1)
                                         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);               ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
                                 } /* end agec */              else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
       } /* end yearp */                  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
     } /* end cptcod */              }
   } /* end  cptcov */              fprintf(ficresf," %.3f", p3mat[i][j][h]);
             } /* end i */
             fprintf(ficresf," %.3f", ppij);
           }/* end j */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */
         /* diffyear=(int) anproj1+yearp-ageminpar-1; */
         /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
       } /* end yearp */
     } /* end  k */
                   
   fclose(ficresf);    fclose(ficresf);
   printf("End of Computing forecasting \n");    printf("End of Computing forecasting \n");
Line 6490  void prevforecast(char fileres[], double Line 8522  void prevforecast(char fileres[], double
   
 }  }
   
 /* /\************** Back Forecasting ******************\/ */  /************** 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){ */   /* void prevbackforecast(char fileres[], double ***prevacurrent, 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  */   void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
 /*      agemin, agemax range of age */    /* back1, year, month, day of starting backprojection
 /*      dateprev1 dateprev2 range of dates during which prevalence is computed */       agemin, agemax range of age
 /*      anback2 year of en of backection (same day and month as back1). */       dateprev1 dateprev2 range of dates during which prevalence is computed
 /*   *\/ */       anback2 year of end of backprojection (same day and month as back1).
 /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */       prevacurrent and prev are prevalences.
 /*   double agec; /\* generic age *\/ */    */
 /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
 /*   double *popeffectif,*popcount; */    double agec; /* generic age */
 /*   double ***p3mat; */    double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
 /*   /\* double ***mobaverage; *\/ */    double *popeffectif,*popcount;
 /*   char fileresfb[FILENAMELENGTH]; */    double ***p3mat;
             /* double ***mobaverage; */
 /*   agelim=AGESUP; */    char fileresfb[FILENAMELENGTH];
 /*   /\* 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). */    agelim=AGEINF;
 /*      We still use firstpass and lastpass as another selection. */    /* 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).
 /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */       We still use firstpass and lastpass as another selection.
 /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */    */
 /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */    /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
             /*          firstpass, lastpass,  stepm,  weightopt, model); */
 /*   strcpy(fileresfb,"FB_");  */  
 /*   strcat(fileresfb,fileresu); */    /*Do we need to compute prevalence again?*/
 /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */  
 /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */    /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
 /*     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);  */    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("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
     fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
       
 /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */    if (cptcoveff==0) ncodemax[cptcoveff]=1;
             
 /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */     
 /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */    stepsize=(int) (stepm+YEARM-1)/YEARM;
 /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */    if (stepm<=12) stepsize=1;
 /*       k=k+1; */    if(estepm < stepm){
 /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */      printf ("Problem %d lower than %d\n",estepm, stepm);
 /*       for(j=1;j<=cptcoveff;j++) { */    }
 /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */    else{
 /*       } */      hstepm=estepm;   
 /*       fprintf(ficresfb," yearbproj age"); */    }
 /*       for(j=1; j<=nlstate+ndeath;j++){  */    if(estepm >= stepm){ /* Yes every two year */
 /*                              for(i=1; i<=nlstate;i++)               */      stepsize=2;
 /*           fprintf(ficresfb," p%d%d",i,j); */    }
 /*                              fprintf(ficresfb," p.%d",j); */    
 /*       } */    hstepm=hstepm/stepm;
 /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */    /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
 /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */    /*                              fractional in yp1 *\/ */
 /*                              fprintf(ficresfb,"\n"); */    /* aintmean=yp; */
 /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */    /* yp2=modf((yp1*12),&yp); */
 /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */    /* mintmean=yp; */
 /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */    /* yp1=modf((yp2*30.5),&yp); */
 /*                                      nhstepm = nhstepm/hstepm;  */    /* jintmean=yp; */
 /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */    /* if(jintmean==0) jintmean=1; */
 /*                                      oldm=oldms;savm=savms; */    /* if(mintmean==0) jintmean=1; */
 /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */    
 /*                                      for (h=0; h<=nhstepm; h++){ */    i1=pow(2,cptcoveff);
 /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */    if (cptcovn < 1){i1=1;}
 /*               fprintf(ficresfb,"\n"); */    
 /*               for(j=1;j<=cptcoveff;j++)  */    fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
 /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */    printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
 /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */    
 /*                                              }  */    fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
 /*                                              for(j=1; j<=nlstate+ndeath;j++) { */    
 /*                                                      ppij=0.; */    for(nres=1; nres <= nresult; nres++) /* For each resultline */
 /*                                                      for(i=1; i<=nlstate;i++) { */    for(k=1; k<=i1;k++){
 /*                                                              if (mobilav==1)  */      if(i1 != 1 && TKresult[nres]!= k)
 /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */        continue;
 /*                                                              else { */      if(invalidvarcomb[k]){
 /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */        printf("\nCombination (%d) projection ignored because no cases \n",k); 
 /*                                                              } */        continue;
 /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */      }
 /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */      fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
 /*                                                              } */      for(j=1;j<=cptcoveff;j++) {
 /*                                                      } /\* end i *\/ */        fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */      }
 /*                                                              fprintf(ficresfb," %.3f", ppij); */      for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
 /*                                                      } */        fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
 /*                                              }/\* end j *\/ */      }
 /*                                      } /\* end h *\/ */      fprintf(ficresfb," yearbproj age");
 /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */      for(j=1; j<=nlstate+ndeath;j++){
 /*                              } /\* end agec *\/ */        for(i=1; i<=nlstate;i++)
 /*       } /\* end yearp *\/ */          fprintf(ficresfb," b%d%d",i,j);
 /*     } /\* end cptcod *\/ */        fprintf(ficresfb," b.%d",j);
 /*   } /\* end  cptcov *\/ */      }
               for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
 /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */        /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
                 fprintf(ficresfb,"\n");
 /*   fclose(ficresfb); */        fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
 /*   printf("End of Computing Back forecasting \n"); */        /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
 /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */        /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */
         for (agec=bage; agec<=fage; agec++){  /* testing */
           /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
           nhstepm=(int) (agec-agelim) *YEARM/stepm;/*     nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
           nhstepm = nhstepm/hstepm;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           /* computes hbxij at age agec over 1 to nhstepm */
           /* printf("####prevbackforecast debug  agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
           hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
           /* hpxij(p3mat,nhstepm,agec,hstepm,p,             nlstate,stepm,oldm,savm, k,nres); */
           /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
           /* printf(" agec=%.2f\n",agec);fflush(stdout); */
           for (h=0; h<=nhstepm; h++){
             if (h*hstepm/YEARM*stepm ==-yearp) {
               break;
             }
           }
           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 ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
           for(i=1; i<=nlstate+ndeath;i++) {
             ppij=0.;ppi=0.;
             for(j=1; j<=nlstate;j++) {
               /* if (mobilav==1) */
               ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
               ppi=ppi+prevacurrent[(int)agec][j][k];
               /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
               /* ppi=ppi+mobaverage[(int)agec][j][k]; */
                 /* else { */
                 /*        ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
                 /* } */
               fprintf(ficresfb," %.3f", p3mat[i][j][h]);
             } /* end j */
             if(ppi <0.99){
               printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
               fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
             }
             fprintf(ficresfb," %.3f", ppij);
           }/* end j */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */
       } /* end yearp */
     } /* end k */
     
     /* 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");
                   
 /* } */  }
   
   /* Variance of prevalence limit: varprlim */
    void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
       /*------- Variance of forward period (stable) prevalence------*/   
    
      char fileresvpl[FILENAMELENGTH];  
      FILE *ficresvpl;
      double **oldm, **savm;
      double **varpl; /* Variances of prevalence limits by age */   
      int i1, k, nres, j ;
      
       strcpy(fileresvpl,"VPL_");
       strcat(fileresvpl,fileresu);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of forward period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
       fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
       
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
       
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
         fprintf(ficresvpl,"\n#****** ");
         printf("\n#****** ");
         fprintf(ficlog,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
         fprintf(ficresvpl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       
       fclose(ficresvpl);
       printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
       fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
   
    }
   /* Variance of back prevalence: varbprlim */
    void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
         /*------- Variance of back (stable) prevalence------*/
   
      char fileresvbl[FILENAMELENGTH];  
      FILE  *ficresvbl;
   
      double **oldm, **savm;
      double **varbpl; /* Variances of back prevalence limits by age */   
      int i1, k, nres, j ;
   
      strcpy(fileresvbl,"VBL_");
      strcat(fileresvbl,fileresu);
      if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
        printf("Problem with variance of back (stable) prevalence  resultfile: %s\n", fileresvbl);
        exit(0);
      }
      printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
      fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
      
      
      i1=pow(2,cptcoveff);
      if (cptcovn < 1){i1=1;}
      
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
        for(k=1; k<=i1;k++){
          if(i1 != 1 && TKresult[nres]!= k)
            continue;
          fprintf(ficresvbl,"\n#****** ");
          printf("\n#****** ");
          fprintf(ficlog,"\n#****** ");
          for(j=1;j<=cptcoveff;j++) {
            fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
            fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
            printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          }
          for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
            printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
            fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
            fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
          }
          fprintf(ficresvbl,"******\n");
          printf("******\n");
          fprintf(ficlog,"******\n");
          
          varbpl=matrix(1,nlstate,(int) bage, (int) fage);
          oldm=oldms;savm=savms;
          
          varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
          free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
          /*}*/
        }
      
      fclose(ficresvbl);
      printf("done variance-covariance of back prevalence\n");fflush(stdout);
      fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
   
    } /* End of varbprlim */
   
 /************** Forecasting *****not tested NB*************/  /************** Forecasting *****not tested NB*************/
 void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, 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); */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   agelim=AGESUP;  /*   agelim=AGESUP; */
   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  /*   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
       
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);  /*   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,fileresu);  /*   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); */
   }  /*   } */
   printf("Computing forecasting: result on file '%s' \n", filerespop);  /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);  /*   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
   
   /* if (mobilav!=0) { */  /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
   /*   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 (mobilav!=0) { *\/ */
   if (stepm<=12) stepsize=1;  /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
   /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
   /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   /*   /\*   } *\/ */
   /*   /\* } *\/ */
   
   /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
   /*   if (stepm<=12) stepsize=1; */
       
   agelim=AGESUP;  /*   agelim=AGESUP; */
       
   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); */
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);  /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
     }   /*     }  */
     popage=ivector(0,AGESUP);  /*     popage=ivector(0,AGESUP); */
     popeffectif=vector(0,AGESUP);  /*     popeffectif=vector(0,AGESUP); */
     popcount=vector(0,AGESUP);  /*     popcount=vector(0,AGESUP); */
           
     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]][codtabm(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"); */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
       if (popforecast==1)  fprintf(ficrespop," [Population]");  /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
               
       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); */
             }   /*          }  */
             for(j=1; j<=nlstate+ndeath;j++) {  /*          for(j=1; j<=nlstate+ndeath;j++) { */
               kk1=0.;kk2=0;  /*            kk1=0.;kk2=0; */
               for(i=1; i<=nlstate;i++) {                /*            for(i=1; i<=nlstate;i++) {               */
                 if (mobilav==1)   /*              if (mobilav==1)  */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  /*                kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
                 else {  /*              else { */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  /*                kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
                 }  /*              } */
               }  /*            } */
               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))  /*          if (h==(int)(calagedatem+12*cpt)) */
               for(j=1; j<=nlstate;j++)   /*            for(j=1; j<=nlstate;j++)  */
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  /*              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--){  */
           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(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  /*            fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
             }   /*          }  */
             for(j=1; j<=nlstate+ndeath;j++) {  /*          for(j=1; j<=nlstate+ndeath;j++) { */
               kk1=0.;kk2=0;  /*            kk1=0.;kk2=0; */
               for(i=1; i<=nlstate;i++) {                /*            for(i=1; i<=nlstate;i++) {               */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      /*              kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
               }  /*            } */
               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);          /*            if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
             }  /*          } */
           }  /*        } */
           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); */
     free_vector(popcount,0,AGESUP);  /*     free_vector(popcount,0,AGESUP); */
   }  /*   } */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   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)
 {  {
Line 6918  void prwizard(int ncovmodel, int nlstate Line 9089  void prwizard(int ncovmodel, int nlstate
 /******************* Gompertz Likelihood ******************************/  /******************* Gompertz Likelihood ******************************/
 double gompertz(double x[])  double gompertz(double x[])
 {   { 
   double A,B,L=0.0,sump=0.,num=0.;    double A=0.0,B=0.,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;
   }    }
      L=0.0;
      /* agegomp=AGEGOMP; */
   /* for (i=0; i<=imx; i++)     /* for (i=0; i<=imx; i++) 
      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/       if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
   for (i=1;i<=imx ; i++)    for (i=1;i<=imx ; i++) {
     {      /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
       if (cens[i] == 1 && wav[i]>1)         mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));       * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month) 
              *   and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
       if (cens[i] == 0 && wav[i]>1)       * +
        * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
        */
        if (wav[i] > 1 || agedc[i] < AGESUP) {
          if (cens[i] == 1){
            A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
          } else if (cens[i] == 0){
         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))          A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);              +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
               } else
            printf("Gompertz cens[%d] neither 1 nor 0\n",i);
       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */        /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
       if (wav[i] > 1 ) { /* ??? */         L=L+A*weight[i];
         L=L+A*weight[i];  
         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/          /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
       }       }
     }    }
   
  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     
   return -2*L*num/sump;    return -2*L*num/sump;
 }  }
Line 6956  double gompertz(double x[]) Line 9133  double gompertz(double x[])
 /******************* Gompertz_f Likelihood ******************************/  /******************* Gompertz_f Likelihood ******************************/
 double gompertz_f(const gsl_vector *v, void *params)  double gompertz_f(const gsl_vector *v, void *params)
 {   { 
   double A,B,LL=0.0,sump=0.,num=0.;    double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
   double *x= (double *) v->data;    double *x= (double *) v->data;
   int i,n=0; /* n is the size of the sample */    int i,n=0; /* n is the size of the sample */
   
Line 7046  int readdata(char datafile[], int firsto Line 9223  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, v;
     int lstra;
   int linei, month, year,iout;    int linei, month, year,iout;
     int noffset=0; /* This is the offset if BOM data file */
   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;  
   
     DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
     FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
   
     for(v=1; v <=ncovcol;v++){
       DummyV[v]=0;
       FixedV[v]=0;
     }
     for(v=ncovcol+1; v <=ncovcol+nqv;v++){
       DummyV[v]=1;
       FixedV[v]=0;
     }
     for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
       DummyV[v]=0;
       FixedV[v]=1;
     }
     for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
       DummyV[v]=1;
       FixedV[v]=1;
     }
     for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
       printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
       fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
     }
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);      printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;      fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
   }    }
   
   i=1;      /* Is it a BOM UTF-8 Windows file? */
     /* First data line */
   linei=0;    linei=0;
     while(fgets(line, MAXLINE, fic)) {
       noffset=0;
       if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
       {
         noffset=noffset+3;
         printf("# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
         fprintf(ficlog,"# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
         fflush(ficlog); return 1;
       }
       /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
       else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
       {
         noffset=noffset+2;
         printf("# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
         fprintf(ficlog,"# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
         fflush(ficlog); return 1;
       }
       else if( line[0] == 0 && line[1] == 0)
       {
         if( line[2] == (char)0xFE && line[3] == (char)0xFF){
           noffset=noffset+4;
           printf("# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
           fprintf(ficlog,"# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
           fflush(ficlog); return 1;
         }
       } else{
         ;/*printf(" Not a BOM file\n");*/
       }
           /* If line starts with a # it is a comment */
       if (line[noffset] == '#') {
         linei=linei+1;
         break;
       }else{
         break;
       }
     }
     fclose(fic);
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
       fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
     }
     /* Not a Bom file */
     
     i=1;
   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {    while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
     linei=linei+1;      linei=linei+1;
     for(j=strlen(line); j>=0;j--){  /* Untabifies line */      for(j=strlen(line); j>=0;j--){  /* Untabifies line */
Line 7078  int readdata(char datafile[], int firsto Line 9324  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 */
             cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
             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; 
             cotvar[j][ntv+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){
Line 7109  int readdata(char datafile[], int firsto Line 9427  int readdata(char datafile[], int firsto
         return 1;          return 1;
       }        }
       anint[j][i]= (double) year;         anint[j][i]= (double) year; 
       mint[j][i]= (double)month;         mint[j][i]= (double)month;
         /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
         /*        printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
         /*        fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
         /* } */
       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){
     }      }
Line 7121  int readdata(char datafile[], int firsto Line 9444  int readdata(char datafile[], int firsto
       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){
     }      }
Line 7137  int readdata(char datafile[], int firsto Line 9461  int readdata(char datafile[], int firsto
     }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);
       for (j=1;j<=maxwav;j++){
         if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
           printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j,(int)moisnais[i],(int)annais[i]);
           fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j, (int)moisnais[i],(int)annais[i]);
         }
       }
   
     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 7161  int readdata(char datafile[], int firsto Line 9493  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 7178  int readdata(char datafile[], int firsto Line 9533  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 7199  int readdata(char datafile[], int firsto Line 9554  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 7211  int readdata(char datafile[], int firsto Line 9566  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 removefirstspace(char **stri){/*, char stro[]) {*/
     char *p1 = *stri, *p2 = *stri;
     while (*p2 == ' ')
       p2++; 
     /* while ((*p1++ = *p2++) !=0) */
     /*   ; */
     /* do */
     /*   while (*p2 == ' ') */
     /*     p2++; */
     /* while (*p1++ == *p2++); */
     *stri=p2; 
   }
   
   int decoderesult ( char resultline[], int nres)
   /**< This routine decode one result line and returns the combination # of dummy covariates only **/
   {
     int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
     char resultsav[MAXLINE];
     int resultmodel[MAXLINE];
     int modelresult[MAXLINE];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     removefirstspace(&resultline);
   
     if (strstr(resultline,"v") !=0){
       printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
       fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
       return 1;
     }
     trimbb(resultsav, resultline);
     if (strlen(resultsav) >1){
       j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
     }
     if(j == 0){ /* Resultline but no = */
       TKresult[nres]=0; /* Combination for the nresult and the model */
       return (0);
     }
     if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
       printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
       fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
     }
     for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
       if(nbocc(resultsav,'=') >1){
          cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' 
                                         resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
          cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
       }else
         cutl(strc,strd,resultsav,'=');
       Tvalsel[k]=atof(strc); /* 1 */
       
       cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
       Tvarsel[k]=atoi(strc);
       /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
       /* cptcovsel++;     */
       if (nbocc(stra,'=') >0)
         strcpy(resultsav,stra); /* and analyzes it */
     }
     /* Checking for missing or useless values in comparison of current model needs */
     for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       if(Typevar[k1]==0){ /* Single covariate in model */
         match=0;
         for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
           if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5   */
             modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
             match=1;
             break;
           }
         }
         if(match == 0){
           printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
         }
       }
     }
     /* Checking for missing or useless values in comparison of current model needs */
     for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
       match=0;
       for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         if(Typevar[k1]==0){ /* Single */
           if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
             resultmodel[k1]=k2;  /* resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
             ++match;
           }
         }
       }
       if(match == 0){
         printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
       }else if(match > 1){
         printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
       }
     }
         
     /* We need to deduce which combination number is chosen and save quantitative values */
     /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
     /* result line V4=1 V5=25.1 V3=0  V2=8 V1=1 */
     /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
     /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
     /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
     /*    1 0 0 0 */
     /*    2 1 0 0 */
     /*    3 0 1 0 */ 
     /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 */
     /*    5 0 0 1 */
     /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 */
     /*    7 0 1 1 */
     /*    8 1 1 1 */
     /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
     /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
     /* V5*age V5 known which value for nres?  */
     /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
     for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
       if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
         k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
         k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
         k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */
         Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */
         Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
         Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
         printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
         k4++;;
       }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
         k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
         k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
         Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
         Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
         Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
         printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
         k4q++;;
       }
     }
     
     TKresult[nres]=++k; /* Combination for the nresult and the model */
     return (0);
 }  }
 void removespace(char *str) {  
   char *p1 = str, *p2 = str;  int decodemodel( char model[], int lastobs)
   do   /**< This routine decodes the model and returns:
     while (*p2 == ' ')          * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
       p2++;          * - nagesqr = 1 if age*age in the model, otherwise 0.
   while (*p1++ == *p2++);          * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
 }          * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
           * - cptcovage number of covariates with age*products =2
 int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:          * - cptcovs number of simple covariates
    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+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
    * - nagesqr = 1 if age*age in the model, otherwise 0.          *     which is a new column after the 9 (ncovcol) variables. 
    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age          * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
    * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age          * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
    * - cptcovage number of covariates with age*products =2          *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
    * - cptcovs number of simple covariates          * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10          */
    *     which is a new column after the 9 (ncovcol) variables.   
    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual  
    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage  
    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.  
    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .  
  */  
 {  {
   int i, j, k, ks;    int i, j, k, ks, v;
   int  j1, k1, k2;    int  j1, k1, k2, k3, k4;
   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;    char *strpt;
Line 7270  int decodemodel ( char model[], int last Line 9750  int decodemodel ( char model[], int last
     if ((strpt=strstr(model,"age*age")) !=0){      if ((strpt=strstr(model,"age*age")) !=0){
       printf(" strpt=%s, model=%s\n",strpt, model);        printf(" strpt=%s, model=%s\n",strpt, model);
       if(strpt != model){        if(strpt != model){
       printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model);   corresponding column of parameters.\n",model);
       fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model); fflush(ficlog);   corresponding column of parameters.\n",model); fflush(ficlog);
       return 1;          return 1;
     }        }
   
       nagesqr=1;        nagesqr=1;
       if (strstr(model,"+age*age") !=0)        if (strstr(model,"+age*age") !=0)
         substrchaine(modelsav, model, "+age*age");          substrchaine(modelsav, model, "+age*age");
Line 7291  int decodemodel ( char model[], int last Line 9770  int decodemodel ( char model[], int last
     if (strlen(modelsav) >1){      if (strlen(modelsav) >1){
       j=nbocc(modelsav,'+'); /**< j=Number of '+' */        j=nbocc(modelsav,'+'); /**< j=Number of '+' */
       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */        j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */        cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
       cptcovt= j+1; /* Number of total covariates in the model, not including        cptcovt= j+1; /* Number of total covariates in the model, not including
                    * cst, age and age*age                        * cst, age and age*age 
                    * V1+V1*age+ V3 + V3*V4+age*age=> 4*/                       * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
                   /* including age products which are counted in cptcovage.        /* including age products which are counted in cptcovage.
                   * but the covariates which are products must be treated          * but the covariates which are products must be treated 
                   * separately: ncovn=4- 2=2 (V1+V3). */         * separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */        cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */        cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
         
             
       /*   Design        /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight         *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >         *  <          ncovcol=8                >
Line 7309  int decodemodel ( char model[], int last Line 9788  int decodemodel ( char model[], int last
        *   k=  1    2      3       4     5       6      7        8         *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8         *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:         *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)         *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8         *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and          *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k         *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1         *       if products, new covar are created after ncovcol with k1
Line 7335  int decodemodel ( char model[], int last Line 9814  int decodemodel ( char model[], int last
        *       {2,   1,     4,      8,    5,      6,     3,       7}         *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []         * Struct []
        */         */
         
       /* This loop fills the array Tvar from the string 'model'.*/        /* 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 */        /* 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  */        /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
Line 7350  int decodemodel ( char model[], int last Line 9829  int decodemodel ( char model[], int last
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */        /* for (k=1; k<=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 */         * 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 */        for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
         Tvar[k]=0;          Tvar[k]=0; Tprod[k]=0; Tposprod[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 '+' 
Line 7366  int decodemodel ( char model[], int last Line 9846  int decodemodel ( char model[], int last
             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; V1+V1*age Tvar[2]=1 */              Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
               Typevar[k]=1;  /* 1 for age product */
             cptcovage++; /* Sums the number of covariates which include age as a product */              cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */              Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
             /*printf("stre=%s ", stre);*/              /*printf("stre=%s ", stre);*/
Line 7373  int decodemodel ( char model[], int last Line 9854  int decodemodel ( char model[], int last
             cptcovprod--;              cptcovprod--;
             cutl(stre,strb,strc,'V');              cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);              Tvar[k]=atoi(stre);
               Typevar[k]=1;  /* 1 for age product */
             cptcovage++;              cptcovage++;
             Tage[cptcovage]=k;              Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/            } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
Line 7380  int decodemodel ( char model[], int last Line 9862  int decodemodel ( char model[], int last
             cptcovn++;              cptcovn++;
             cptcovprodnoage++;k1++;              cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/              cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but              Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
                                    because this model-covariate is a construction we invent a new column                                                  because this model-covariate is a construction we invent a new column
                                    ncovcol + k1                                                  which is after existing variables ncovcol+nqv+ntv+nqtv + k1
                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2                                                  If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */                                                  Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
               Typevar[k]=2;  /* 2 for double fixed dummy covariates */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */              cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */              Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
               Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/              Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/              Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;              k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */              /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */              /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
               /*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   */
             for (i=1; i<=lastobs;i++){              for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of                /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */                   covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
Line 7403  int decodemodel ( char model[], int last Line 9889  int decodemodel ( char model[], int last
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
           /*  scanf("%d",i);*/            /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');            cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */            ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
           cptcovn++;            cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
           Tvar[k]=atoi(strd);            Tvar[k]=atoi(strd);
             Typevar[k]=0;  /* 0 for simple covariates */
         }          }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */           strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                                  /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/                                    scanf("%d",i);*/
       } /* end of loop + on total covariates */        } /* end of loop + on total covariates */
     } /* end if strlen(modelsave == 0) age*age might exist */      } /* end if strlen(modelsave == 0) age*age might exist */
   } /* end if strlen(model == 0) */    } /* 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);*/  
   
   /* Until here, 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. But we know the # of each. */
   /* 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[k]      1    1   1     1       3       0    0 or 2   2        3
      Dummy[k]      1    0   0     0       3       1      1      2        3
             Tmodelind[combination of covar]=k;
   */  
   /* 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 */
     printf("Model=%s\n\
   Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
   Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
   Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
     fprintf(ficlog,"Model=%s\n\
   Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
   Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
   Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
     for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
     for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
       if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
         Fixed[k]= 0;
         Dummy[k]= 0;
         ncoveff++;
         ncovf++;
         nsd++;
         modell[k].maintype= FTYPE;
         TvarsD[nsd]=Tvar[k];
         TvarsDind[nsd]=k;
         TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
         TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
         Fixed[k]= 0;
         Dummy[k]= 0;
         ncoveff++;
         ncovf++;
         modell[k].maintype= FTYPE;
         TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
         TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
         Fixed[k]= 0;
         Dummy[k]= 1;
         nqfveff++;
         modell[k].maintype= FTYPE;
         modell[k].subtype= FQ;
         nsq++;
         TvarsQ[nsq]=Tvar[k];
         TvarsQind[nsq]=k;
         ncovf++;
         TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
         TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
         TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
       }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
         Fixed[k]= 1;
         Dummy[k]= 0;
         ntveff++; /* Only simple time varying dummy variable */
         modell[k].maintype= VTYPE;
         modell[k].subtype= VD;
         nsd++;
         TvarsD[nsd]=Tvar[k];
         TvarsDind[nsd]=k;
         ncovv++; /* Only simple time varying variables */
         TvarV[ncovv]=Tvar[k];
         TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
         TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4  TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
         TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
         printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
         printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
         Fixed[k]= 1;
         Dummy[k]= 1;
         nqtveff++;
         modell[k].maintype= VTYPE;
         modell[k].subtype= VQ;
         ncovv++; /* Only simple time varying variables */
         nsq++;
         TvarsQ[nsq]=Tvar[k];
         TvarsQind[nsq]=k;
         TvarV[ncovv]=Tvar[k];
         TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
         TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
         TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
         TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
         /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
         printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
         printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
       }else if (Typevar[k] == 1) {  /* product with age */
         ncova++;
         TvarA[ncova]=Tvar[k];
         TvarAind[ncova]=k;
         if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
           Fixed[k]= 2;
           Dummy[k]= 2;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APFD;
           /* ncoveff++; */
         }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
           Fixed[k]= 2;
           Dummy[k]= 3;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
           /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
         }else if( Tvar[k] <=ncovcol+nqv+ntv ){
           Fixed[k]= 3;
           Dummy[k]= 2;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APVD;                /*      Product age * varying dummy */
           /* ntveff++; /\* Only simple time varying dummy variable *\/ */
         }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
           Fixed[k]= 3;
           Dummy[k]= 3;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
           /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
         }
       }else if (Typevar[k] == 2) {  /* product without age */
         k1=Tposprod[k];
         if(Tvard[k1][1] <=ncovcol){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 0;
             modell[k].maintype= FTYPE;
             modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
             ncovf++; /* Fixed variables without age */
             TvarF[ncovf]=Tvar[k];
             TvarFind[ncovf]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 0;  /* or 2 ?*/
             Dummy[k]= 1;
             modell[k].maintype= FTYPE;
             modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
             ncovf++; /* Varying variables without age */
             TvarF[ncovf]=Tvar[k];
             TvarFind[ncovf]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 0;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }else if(Tvard[k1][1] <=ncovcol+nqv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 0;  /* or 2 ?*/
             Dummy[k]= 1;
             modell[k].maintype= FTYPE;
             modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
             ncovf++; /* Fixed variables without age */
             TvarF[ncovf]=Tvar[k];
             TvarFind[ncovf]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 0;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }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[k],Dummy[k]);
       printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
       fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
     }
     /* Searching for doublons in the model */
     for(k1=1; k1<= cptcovt;k1++){
       for(k2=1; k2 <k1;k2++){
         /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
         if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
           if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
             if(Tvar[k1]==Tvar[k2]){
               printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
               fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);
               return(1);
             }
           }else if (Typevar[k1] ==2){
             k3=Tposprod[k1];
             k4=Tposprod[k2];
             if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
               printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
               fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
               return(1);
             }
           }
         }
       }
     }
     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);
     printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
     fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
   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);
 }  }
   
 int 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 )
 {  {/* Check ages at death */
   int i, m;    int i, m;
   int firstone=0;    int firstone=0;
       
Line 7446  int calandcheckages(int imx, int maxwav, Line 10229  int calandcheckages(int imx, int maxwav,
         *nberr = *nberr + 1;          *nberr = *nberr + 1;
         if(firstone == 0){          if(firstone == 0){
           firstone=1;            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);          printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,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);          fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
         s[m][i]=-1;          s[m][i]=-1;  /* Droping the death status */
       }        }
       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 (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
         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 (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */          s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
       }        }
     }      }
   }    }
Line 7577  BOOL IsWow64() Line 10360  BOOL IsWow64()
 #endif  #endif
   
 void syscompilerinfo(int logged)  void syscompilerinfo(int logged)
  {  {
    /* #include "syscompilerinfo.h"*/  #include <stdint.h>
   
     /* #include "syscompilerinfo.h"*/
    /* command line Intel compiler 32bit windows, XP compatible:*/     /* command line Intel compiler 32bit windows, XP compatible:*/
    /* /GS /W3 /Gy     /* /GS /W3 /Gy
       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D        /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
Line 7613  void syscompilerinfo(int logged) Line 10398  void syscompilerinfo(int logged)
       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF        /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
       /NOLOGO /TLBID:1        /NOLOGO /TLBID:1
    */     */
   
   
 #if defined __INTEL_COMPILER  #if defined __INTEL_COMPILER
 #if defined(__GNUC__)  #if defined(__GNUC__)
         struct utsname sysInfo;  /* For Intel on Linux and OS/X */          struct utsname sysInfo;  /* For Intel on Linux and OS/X */
Line 7629  void syscompilerinfo(int logged) Line 10416  void syscompilerinfo(int logged)
    }     }
 #endif  #endif
   
 #include <stdint.h>  
   
    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");     printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
 #if defined(__clang__)  #if defined(__clang__)
    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */     printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
Line 7716  void syscompilerinfo(int logged) Line 10501  void syscompilerinfo(int logged)
 #endif  #endif
 #endif  #endif
   
    //   void main()     //   void main ()
    //   {     //   {
 #if defined(_MSC_VER)  #if defined(_MSC_VER)
    if (IsWow64()){     if (IsWow64()){
Line 7737  void syscompilerinfo(int logged) Line 10522  void syscompilerinfo(int logged)
 }  }
   
 int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/    /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/
   int i, j, k, i1 ;    int i, j, k, i1, k4=0, nres=0 ;
   /* double ftolpl = 1.e-10; */    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
   double tot;    double tot;
Line 7746  int prevalence_limit(double *p, double * Line 10531  int prevalence_limit(double *p, double *
   strcpy(filerespl,"PL_");    strcpy(filerespl,"PL_");
   strcat(filerespl,fileresu);    strcat(filerespl,fileresu);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    if((ficrespl=fopen(filerespl,"w"))==NULL) {
     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
   }    }
   printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);    printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
   fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);    fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
   pstamp(ficrespl);    pstamp(ficrespl);
   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);    fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
   fprintf(ficrespl,"#Age ");    fprintf(ficrespl,"#Age ");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
   fprintf(ficrespl,"\n");    fprintf(ficrespl,"\n");
Line 7762  int prevalence_limit(double *p, double * Line 10547  int prevalence_limit(double *p, double *
   agebase=ageminpar;    agebase=ageminpar;
   agelim=agemaxpar;    agelim=agemaxpar;
   
   i1=pow(2,cptcoveff);    /* i1=pow(2,ncoveff); */
     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
   
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){    for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        if(i1 != 1 && TKresult[nres]!= k)
     k=k+1;          continue;
     /* to clean */  
     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));        /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
     fprintf(ficrespl,"#******");        /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
     printf("#******");        //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
     fprintf(ficlog,"#******");        /* k=k+1; */
     for(j=1;j<=cptcoveff;j++) {        /* to clean */
       fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficrespl,"#******");
       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        printf("#******");
     }        fprintf(ficlog,"#******");
     fprintf(ficrespl,"******\n");        for(j=1;j<=cptcoveff ;j++) {/* all covariates */
     printf("******\n");          fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
     fprintf(ficlog,"******\n");          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)]);
         }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
         if(invalidvarcomb[k]){
           printf("\nCombination (%d) ignored because no case \n",k); 
           fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k); 
           fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k); 
           continue;
         }
   
     fprintf(ficrespl,"#Age ");        fprintf(ficrespl,"#Age ");
     for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
       fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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);        for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
     fprintf(ficrespl,"Total Years_to_converge\n");        fprintf(ficrespl,"Total Years_to_converge\n");
               
     for (age=agebase; age<=agelim; age++){        for (age=agebase; age<=agelim; age++){
       /* for (age=agebase; age<=agebase; age++){ */          /* for (age=agebase; age<=agebase; age++){ */
       prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);          prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
       fprintf(ficrespl,"%.0f ",age );          fprintf(ficrespl,"%.0f ",age );
       for(j=1;j<=cptcoveff;j++)          for(j=1;j<=cptcoveff;j++)
         fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);            fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       tot=0.;          tot=0.;
       for(i=1; i<=nlstate;i++){          for(i=1; i<=nlstate;i++){
         tot +=  prlim[i][i];            tot +=  prlim[i][i];
         fprintf(ficrespl," %.5f", prlim[i][i]);            fprintf(ficrespl," %.5f", prlim[i][i]);
       }          }
       fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);          fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
     } /* Age */        } /* Age */
     /* was end of cptcod */        /* was end of cptcod */
   } /* cptcov */      } /* cptcov */
     } /* nres */
   return 0;    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){  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) --------------*/          /*--------------- Back Prevalence limit  (backward stable prevalence) --------------*/
                   
         /* Computes the back prevalence limit  for any combination      of covariate values           /* Computes the back prevalence limit  for any combination      of covariate values 
    * at any age between ageminpar and agemaxpar     * at any age between ageminpar and agemaxpar
          */           */
   int i, j, k, i1 ;    int i, j, k, i1, nres=0 ;
   /* double ftolpl = 1.e-10; */    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
   double tot;    double tot;
Line 7824  int back_prevalence_limit(double *p, dou Line 10627  int back_prevalence_limit(double *p, dou
   strcpy(fileresplb,"PLB_");    strcpy(fileresplb,"PLB_");
   strcat(fileresplb,fileresu);    strcat(fileresplb,fileresu);
   if((ficresplb=fopen(fileresplb,"w"))==NULL) {    if((ficresplb=fopen(fileresplb,"w"))==NULL) {
     printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;      printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
     fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;      fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
   }    }
   printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);    printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
   fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);    fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
   pstamp(ficresplb);    pstamp(ficresplb);
   fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);    fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
   fprintf(ficresplb,"#Age ");    fprintf(ficresplb,"#Age ");
   for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
   fprintf(ficresplb,"\n");    fprintf(ficresplb,"\n");
Line 7845  int back_prevalence_limit(double *p, dou Line 10648  int back_prevalence_limit(double *p, dou
   i1=pow(2,cptcoveff);    i1=pow(2,cptcoveff);
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
       
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       if(i1 != 1 && TKresult[nres]!= k)
     k=k+1;          continue;
     /* to clean */        //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));        fprintf(ficresplb,"#******");
     fprintf(ficresplb,"#******");        printf("#******");
     printf("#******");        fprintf(ficlog,"#******");
     fprintf(ficlog,"#******");        for(j=1;j<=cptcoveff ;j++) {/* all covariates */
     for(j=1;j<=cptcoveff;j++) {          fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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)]);
       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(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        }
     }        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
     fprintf(ficresplb,"******\n");          printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
     printf("******\n");          fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
     fprintf(ficlog,"******\n");          fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][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 ");        fprintf(ficresplb,"#Age ");
     for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
       fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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);        for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
     fprintf(ficresplb,"Total Years_to_converge\n");        fprintf(ficresplb,"Total Years_to_converge\n");
           
           
     for (age=agebase; age<=agelim; age++){        for (age=agebase; age<=agelim; age++){
       /* for (age=agebase; age<=agebase; age++){ */          /* for (age=agebase; age<=agebase; age++){ */
       if(mobilavproj > 0){          if(mobilavproj > 0){
         /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */            /* 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, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
                                 bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);            bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
       }else if (mobilavproj == 0){          }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);            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);            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);            exit(1);
       }else{          }else{
                                 /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */            /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
                                 bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);            bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
       }            /* printf("TOTOT\n"); */
       fprintf(ficresplb,"%.0f ",age );            /* exit(1); */
       for(j=1;j<=cptcoveff;j++)          }
                                 fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresplb,"%.0f ",age );
       tot=0.;          for(j=1;j<=cptcoveff;j++)
       for(i=1; i<=nlstate;i++){            fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                                 tot +=  bprlim[i][i];          tot=0.;
                                 fprintf(ficresplb," %.5f", bprlim[i][i]);          for(i=1; i<=nlstate;i++){
       }            tot +=  bprlim[i][i];
       fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);            fprintf(ficresplb," %.5f", bprlim[i][i]);
     } /* Age */          }
     /* was end of cptcod */          fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
   } /* cptcov */        } /* Age */
           /* was end of cptcod */
         /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
       } /* end of any combination */
     } /* end of nres */  
   /* hBijx(p, bage, fage); */    /* hBijx(p, bage, fage); */
   /* fclose(ficrespijb); */    /* fclose(ficrespijb); */
       
Line 7911  int hPijx(double *p, int bage, int fage) Line 10727  int hPijx(double *p, int bage, int fage)
   int agelim;    int agelim;
   int hstepm;    int hstepm;
   int nhstepm;    int nhstepm;
   int h, i, i1, j, k;    int h, i, i1, j, k, k4, nres=0;
   
   double agedeb;    double agedeb;
   double ***p3mat;    double ***p3mat;
Line 7938  int hPijx(double *p, int bage, int fage) Line 10754  int hPijx(double *p, int bage, int fage)
                 /* 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++){*\/ */
                 /*      k=k+1;  */                  /*      k=k+1;  */
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
       fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
       fprintf(ficrespij,"******\n");        fprintf(ficrespij,"******\n");
               
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
Line 7952  int hPijx(double *p, int bage, int fage) Line 10775  int hPijx(double *p, int bage, int fage)
                   
         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, nres);  
         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");          fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
         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++)
Line 7982  int hPijx(double *p, int bage, int fage) Line 10805  int hPijx(double *p, int bage, int fage)
         int ageminl;          int ageminl;
   int hstepm;    int hstepm;
   int nhstepm;    int nhstepm;
   int h, i, i1, j, k;    int h, i, i1, j, k, nres;
                   
   double agedeb;    double agedeb;
   double ***p3mat;    double ***p3mat;
Line 7999  int hPijx(double *p, int bage, int fage) Line 10822  int hPijx(double *p, int bage, int fage)
   /*if (stepm<=24) stepsize=2;*/    /*if (stepm<=24) stepsize=2;*/
       
   /* agelim=AGESUP; */    /* agelim=AGESUP; */
   ageminl=30;    ageminl=AGEINF; /* was 30 */
   hstepm=stepsize*YEARM; /* Every year of age */    hstepm=stepsize*YEARM; /* Every year of age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
       
   /* hstepm=1;   aff par mois*/    /* hstepm=1;   aff par mois*/
   pstamp(ficrespijb);    pstamp(ficrespijb);
   fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");    fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
   i1= pow(2,cptcoveff);    i1= pow(2,cptcoveff);
   /* 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++){*\/ */
   /*    k=k+1;  */    /*    k=k+1;  */
   for (k=1; k <= (int) pow(2,cptcoveff); k++){    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     fprintf(ficrespijb,"\n#****** ");      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
     for(j=1;j<=cptcoveff;j++)        if(i1 != 1 && TKresult[nres]!= k)
       fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          continue;
     fprintf(ficrespijb,"******\n");        fprintf(ficrespijb,"\n#****** ");
             for(j=1;j<=cptcoveff;j++)
     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */          fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
       /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */          fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
       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 */        fprintf(ficrespijb,"******\n");
               if(invalidvarcomb[k]){  /* Is it necessary here? */
       /*          nhstepm=nhstepm*YEARM; aff par mois*/          fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
                 continue;
       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);   */        /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
       hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);        for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */          /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
       fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");          nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
       for(i=1; i<=nlstate;i++)          nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
         for(j=1; j<=nlstate+ndeath;j++)          
           fprintf(ficrespijb," %1d-%1d",i,j);          /*        nhstepm=nhstepm*YEARM; aff par mois*/
       fprintf(ficrespijb,"\n");          
       for (h=0; h<=nhstepm; h++){          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/          /* and memory limitations if stepm is small */
         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 ); */          /* 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, nres);
           /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
           fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
         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(ficrespijb," %.5f", p3mat[i][j][h]);              fprintf(ficrespijb," %1d-%1d",i,j);
         fprintf(ficrespijb,"\n");          fprintf(ficrespijb,"\n");
       }          for (h=0; h<=nhstepm; h++){
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
       fprintf(ficrespijb,"\n");            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");
         } /* end age deb */
       } /* end combination */
     } /* end nres */
   return 0;    return 0;
  } /*  hBijx */   } /*  hBijx */
   
Line 8066  int main(int argc, char *argv[]) Line 10901  int main(int argc, char *argv[])
   double ssval;    double ssval;
 #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, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
     /* 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 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 */
Line 8074  int main(int argc, char *argv[]) Line 10910  int main(int argc, char *argv[])
   int itimes;    int itimes;
   int NDIM=2;    int NDIM=2;
   int vpopbased=0;    int vpopbased=0;
     int nres=0;
     int endishere=0;
     int noffset=0;
     int ncurrv=0; /* Temporary variable */
     
   char ca[32], cb[32];    char ca[32], cb[32];
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */    /* FILE *ficgp;*/ /*Gnuplot File */
Line 8092  int main(int argc, char *argv[]) Line 10932  int main(int argc, char *argv[])
   char line[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
   char model[MAXLINE], modeltemp[MAXLINE];    char  modeltemp[MAXLINE];
     char resultline[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; /* nobs = lastobs-firstobs declared globally ;*/
   int c,  h , cpt, c2;    int c,  h , cpt, c2;
   int jl=0;    int jl=0;
   int i1, j1, jk, stepsize=0;    int i1, j1, jk, stepsize=0;
Line 8103  int main(int argc, char *argv[]) Line 10945  int main(int argc, char *argv[])
   
   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;    /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
     /* double anprojf, mprojf, jprojf; */
     /* double jintmean,mintmean,aintmean;   */
     int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
     int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
     double yrfproj= 10.0; /* Number of years of forward projections */
     double yrbproj= 10.0; /* Number of years of backward projections */
     int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm=0, nhstepm=0;    int hstepm=0, nhstepm=0;
   int agemortsup;    int agemortsup;
Line 8116  int main(int argc, char *argv[]) Line 10965  int main(int argc, char *argv[])
   double **prlim;    double **prlim;
   double **bprlim;    double **bprlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters */
   double  *p;    double ***paramstart; /* Matrix of starting parameter values */
     double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
   double **matcov; /* Matrix of covariance */    double **matcov; /* Matrix of covariance */
   double **hess; /* Hessian matrix */    double **hess; /* Hessian matrix */
   double ***delti3; /* Scale */    double ***delti3; /* Scale */
   double *delti; /* Scale */    double *delti; /* Scale */
   double ***eij, ***vareij;    double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */    double **varpl; /* Variances of prevalence limits by age */
   
   double *epj, vepp;    double *epj, vepp;
   
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;    double dateprev1, dateprev2;
   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;    double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
     double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
   
   
   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";
Line 8204  int main(int argc, char *argv[]) Line 11057  int main(int argc, char *argv[])
       if(pathr[0] == '\0') break; /* Dirty */        if(pathr[0] == '\0') break; /* Dirty */
     }      }
   }    }
     else if (argc<=2){
       strcpy(pathtot,argv[1]);
     }
   else{    else{
     strcpy(pathtot,argv[1]);      strcpy(pathtot,argv[1]);
       strcpy(z,argv[2]);
       printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
   }    }
   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/    /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
   /*cygwin_split_path(pathtot,path,optionfile);    /*cygwin_split_path(pathtot,path,optionfile);
Line 8283  int main(int argc, char *argv[]) Line 11141  int main(int argc, char *argv[])
     exit(70);       exit(70); 
   }    }
   
   
   
   strcpy(filereso,"o");    strcpy(filereso,"o");
   strcat(filereso,fileresu);    strcat(filereso,fileresu);
   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
Line 8293  int main(int argc, char *argv[]) Line 11149  int main(int argc, char *argv[])
     fflush(ficlog);      fflush(ficlog);
     goto end;      goto end;
   }    }
         /*-------- Rewriting parameter file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name */
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", rfileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
       fflush(ficlog);
       goto end;
     }
     fprintf(ficres,"#IMaCh %s\n",version);
   
                                         
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
   numlinepar=0;    numlinepar=0;
     /* Is it a BOM UTF-8 Windows file? */
     /* First parameter line */    /* First parameter line */
   while(fgets(line, MAXLINE, ficpar)) {    while(fgets(line, MAXLINE, ficpar)) {
       noffset=0;
       if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
       {
         noffset=noffset+3;
         printf("# File is an UTF8 Bom.\n"); // 0xBF
       }
   /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
       else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
       {
         noffset=noffset+2;
         printf("# File is an UTF16BE BOM file\n");
       }
       else if( line[0] == 0 && line[1] == 0)
       {
         if( line[2] == (char)0xFE && line[3] == (char)0xFF){
           noffset=noffset+4;
           printf("# File is an UTF16BE BOM file\n");
         }
       } else{
         ;/*printf(" Not a BOM file\n");*/
       }
     
     /* If line starts with a # it is a comment */      /* If line starts with a # it is a comment */
     if (line[0] == '#') {      if (line[noffset] == '#') {
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
         fputs(line,ficres);
       fputs(line,ficlog);        fputs(line,ficlog);
       continue;        continue;
     }else      }else
Line 8313  int main(int argc, char *argv[]) Line 11205  int main(int argc, char *argv[])
                         title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){                          title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
     if (num_filled != 5) {      if (num_filled != 5) {
       printf("Should be 5 parameters\n");        printf("Should be 5 parameters\n");
         fprintf(ficlog,"Should be 5 parameters\n");
     }      }
     numlinepar++;      numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);      printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
       fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
       fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
   }    }
   /* Second parameter line */    /* Second parameter line */
   while(fgets(line, MAXLINE, ficpar)) {    while(fgets(line, MAXLINE, ficpar)) {
     /* If line starts with a # it is a comment */      /* while(fscanf(ficpar,"%[^\n]", line)) { */
       /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
     if (line[0] == '#') {      if (line[0] == '#') {
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        printf("%s",line);
       fputs(line,ficparo);        fprintf(ficres,"%s",line);
       fputs(line,ficlog);        fprintf(ficparo,"%s",line);
         fprintf(ficlog,"%s",line);
       continue;        continue;
     }else      }else
       break;        break;
   }    }
   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \    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, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){                          &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
     if (num_filled != 8) {      if (num_filled != 11) {
       printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");        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("but line=%s\n",line);
         fprintf(ficlog,"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");
         fprintf(ficlog,"but line=%s\n",line);
     }      }
     printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);      if( lastpass > maxwav){
         printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
         fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
         fflush(ficlog);
         goto end;
       }
         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);
       fprintf(ficparo,"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);
       fprintf(ficres,"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, 0, weightopt);
       fprintf(ficlog,"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*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 */    /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
Line 8344  int main(int argc, char *argv[]) Line 11253  int main(int argc, char *argv[])
     /* If line starts with a # it is a comment */      /* If line starts with a # it is a comment */
     if (line[0] == '#') {      if (line[0] == '#') {
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        printf("%s",line);
       fputs(line,ficparo);        fprintf(ficres,"%s",line);
       fputs(line,ficlog);        fprintf(ficparo,"%s",line);
         fprintf(ficlog,"%s",line);
       continue;        continue;
     }else      }else
       break;        break;
   }    }
   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){    if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
     if (num_filled == 0)      if (num_filled != 1){
             model[0]='\0';        printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
     else if (num_filled != 1){        fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
       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';        model[0]='\0';
       goto end;        goto end;
     }      }
Line 8369  int main(int argc, char *argv[]) Line 11277  int main(int argc, char *argv[])
     }      }
     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */      /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
     printf("model=1+age+%s\n",model);fflush(stdout);      printf("model=1+age+%s\n",model);fflush(stdout);
       fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
       fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
       fprintf(ficlog,"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); */    /* 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 *\/ */    /* 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); */    /* 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 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 nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);    /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d 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]=='#'|| model[0]== '\0'){ */
   if(model[0]=='#'){    if(model[0]=='#'){
     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \      printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
  'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \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");          \   'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n");            \
     if(mle != -1){      if(mle != -1){
       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");        printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
       exit(1);        exit(1);
     }      }
   }    }
Line 8402  int main(int argc, char *argv[]) Line 11313  int main(int argc, char *argv[])
   ungetc(c,ficpar);    ungetc(c,ficpar);
   
         
   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */    covar=matrix(0,NCOVMAX,firstobs,lastobs);  /**< used in readdata */
     if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs);  /**< Fixed quantitative covariate */
     if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs);  /**< Time varying quantitative covariate */
     if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs);  /**< Time varying covariate (dummy and quantitative)*/
   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
Line 8424  int main(int argc, char *argv[]) Line 11338  int main(int argc, char *argv[])
   delti=delti3[1][1];    delti=delti3[1][1];
   /*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 */
   /* We could also provide initial parameters values giving by simple logistic regression 
    * only one way, that is without matrix product. We will have nlstate maximizations */
         /* for(i=1;i<nlstate;i++){ */
         /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
         /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
         /* } */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You chose 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 chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
Line 8432  int main(int argc, char *argv[]) Line 11352  int main(int argc, char *argv[])
     fclose (ficlog);      fclose (ficlog);
     goto end;      goto end;
     exit(0);      exit(0);
   }    }  else if(mle==-5) { /* Main Wizard */
   else if(mle==-3) { /* Main Wizard */  
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You chose 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 chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      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);      hess=matrix(1,npar,1,npar);
   }    }  else{ /* Begin of mle != -1 or -5 */
   else{  
     /* 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 8455  int main(int argc, char *argv[]) Line 11373  int main(int argc, char *argv[])
     ungetc(c,ficpar);      ungetc(c,ficpar);
           
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       paramstart= 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++;
           while((c=getc(ficpar))=='#' && c!= EOF){
             ungetc(c,ficpar);
             fgets(line, MAXLINE, ficpar);
             numlinepar++;
             fputs(line,stdout);
             fputs(line,ficparo);
             fputs(line,ficlog);
           }
           ungetc(c,ficpar);
         fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) || (j1 != jj)){          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 \
Line 8490  run imach with mle=-1 to get a correct t Line 11418  run imach with mle=-1 to get a correct t
       }        }
     }        }  
     fflush(ficlog);      fflush(ficlog);
       
     /* Reads scales values */      /* Reads parameters values */
     p=param[1][1];      p=param[1][1];
       pstart=paramstart[1][1];
           
     /* Reads comments: lines beginning with '#' */      /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
Line 8529  run imach with mle=-1 to get a correct t Line 11458  run imach with mle=-1 to get a correct t
       }        }
     }      }
     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 8546  run imach with mle=-1 to get a correct t Line 11475  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);      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 */      /* Scans npar lines */
     for(i=1; i <=npar; i++){      for(i=1; i <=npar; i++){
       count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);        count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
       if(count != 3){        if(count != 3){
         printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\          printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
 This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\  This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
Line 8563  Please run with mle=-1 to get a correct Line 11492  Please run with mle=-1 to get a correct
 This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\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);  Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
         exit(1);          exit(1);
       }else        }else{
         if(mle==1)          if(mle==1)
           printf("%1d%1d%1d",i1,j1,jk);            printf("%1d%1d%d",i1,j1,jk);
       fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);        }
       fprintf(ficparo,"%1d%1d%1d",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 8579  Please run with mle=-1 to get a correct Line 11509  Please run with mle=-1 to get a correct
       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");
     }      }
Line 8594  Please run with mle=-1 to get a correct Line 11524  Please run with mle=-1 to get a correct
           
     fflush(ficlog);      fflush(ficlog);
           
     /*-------- Rewriting parameter file ----------*/  
     strcpy(rfileres,"r");    /* "Rparameterfile */  
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
     strcat(rfileres,".");    /* */  
     strcat(rfileres,optionfilext);    /* Other files have txt extension */  
     if((ficres =fopen(rfileres,"w"))==NULL) {  
       printf("Problem writing new parameter file: %s\n", rfileres);goto end;  
       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;  
     }  
     fprintf(ficres,"#%s\n",version);  
   }    /* End of mle != -3 */    }    /* End of mle != -3 */
       
   /*  Main data    /*  Main data
    */     */
   n= lastobs;    nobs=lastobs-firstobs+1; /* was = 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); */
   agedc=vector(1,n);    /* weight=vector(1,n); */
   cod=ivector(1,n);    /* agedc=vector(1,n); */
   weight=vector(1,n);    /* cod=ivector(1,n); */
   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    /* for(i=1;i<=n;i++){ */
   mint=matrix(1,maxwav,1,n);    num=lvector(firstobs,lastobs);
   anint=matrix(1,maxwav,1,n);    moisnais=vector(firstobs,lastobs);
   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */     annais=vector(firstobs,lastobs);
     moisdc=vector(firstobs,lastobs);
     andc=vector(firstobs,lastobs);
     weight=vector(firstobs,lastobs);
     agedc=vector(firstobs,lastobs);
     cod=ivector(firstobs,lastobs);
     for(i=firstobs;i<=lastobs;i++){
       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,firstobs,lastobs);
     anint=matrix(1,maxwav,firstobs,lastobs);
     s=imatrix(1,maxwav+1,firstobs,lastobs); /* 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 */    ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
Line 8630  Please run with mle=-1 to get a correct Line 11568  Please run with mle=-1 to get a correct
     goto end;      goto end;
   
   /* Calculation of the number of parameters from char model */    /* Calculation of the number of parameters from char model */
     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4          k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
         k=3 V4 Tvar[k=3]= 4 (from V4)          k=3 V4 Tvar[k=3]= 4 (from V4)
         k=2 V1 Tvar[k=2]= 1 (from V1)          k=2 V1 Tvar[k=2]= 1 (from V1)
         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. */
     TvarsDind=ivector(1,NCOVMAX); /*  */
     TvarsD=ivector(1,NCOVMAX); /*  */
     TvarsQind=ivector(1,NCOVMAX); /*  */
     TvarsQ=ivector(1,NCOVMAX); /*  */
     TvarF=ivector(1,NCOVMAX); /*  */
     TvarFind=ivector(1,NCOVMAX); /*  */
     TvarV=ivector(1,NCOVMAX); /*  */
     TvarVind=ivector(1,NCOVMAX); /*  */
     TvarA=ivector(1,NCOVMAX); /*  */
     TvarAind=ivector(1,NCOVMAX); /*  */
     TvarFD=ivector(1,NCOVMAX); /*  */
     TvarFDind=ivector(1,NCOVMAX); /*  */
     TvarFQ=ivector(1,NCOVMAX); /*  */
     TvarFQind=ivector(1,NCOVMAX); /*  */
     TvarVD=ivector(1,NCOVMAX); /*  */
     TvarVDind=ivector(1,NCOVMAX); /*  */
     TvarVQ=ivector(1,NCOVMAX); /*  */
     TvarVQind=ivector(1,NCOVMAX); /*  */
   
     Tvalsel=vector(1,NCOVMAX); /*  */
     Tvarsel=ivector(1,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 8646  Please run with mle=-1 to get a correct Line 11609  Please run with mle=-1 to get a correct
     ncovcol + k1      ncovcol + k1
     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
     Tvar[3=V1*V4]=4+1 etc */      Tvar[3=V1*V4]=4+1 etc */
   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */    Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
     Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3    /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)       if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
        Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2 
   */    */
   Tvaraff=ivector(1,NCOVMAX); /* Unclear */    Tvaraff=ivector(1,NCOVMAX); /* Unclear */
   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm    Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
Line 8658  Please run with mle=-1 to get a correct Line 11623  Please run with mle=-1 to get a correct
                          4 covariates (3 plus signs)                           4 covariates (3 plus signs)
                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                       */                          */  
     Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
                                   * individual dummy, fixed or varying:
                                   * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
                                   * 3, 1, 0, 0, 0, 0, 0, 0},
                                   * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 , 
                                   * V1 df, V2 qf, V3 & V4 dv, V5 qv
                                   * Tmodelind[1]@9={9,0,3,2,}*/
     TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
     TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
                                   * individual quantitative, fixed or varying:
                                   * Tmodelqind[1]=1,Tvaraff[1]@9={4,
                                   * 3, 1, 0, 0, 0, 0, 0, 0},
                                   * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
 /* Main decodemodel */  /* Main decodemodel */
   
   
   if(decodemodel(model, lastobs) == 1)    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 8683  Please run with mle=-1 to get a correct Line 11660  Please run with mle=-1 to get a correct
   
   
   agegomp=(int)agemin;    agegomp=(int)agemin;
   free_vector(moisnais,1,n);    free_vector(moisnais,firstobs,lastobs);
   free_vector(annais,1,n);    free_vector(annais,firstobs,lastobs);
   /* 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); */
Line 8708  Please run with mle=-1 to get a correct Line 11685  Please run with mle=-1 to get a correct
   */    */
   
   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);
   /* */    /* Concatenates waves */
     
   free_vector(moisdc,1,n);    free_vector(moisdc,firstobs,lastobs);
   free_vector(andc,1,n);    free_vector(andc,firstobs,lastobs);
   
   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */    /* 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-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */    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    /* 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).*/       V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
   /* 1 to ncodemax[j] which is the maximum value of this jth covariate */    /* 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) */    /*  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));*/    /*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).*/    /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
Line 8735  Please run with mle=-1 to get a correct Line 11719  Please run with mle=-1 to get a correct
    */     */
   
   h=0;    h=0;
   
   
   /*if (cptcovn > 0) */    /*if (cptcovn > 0) */
         
    
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
     
           /**< 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
Line 8806  Please run with mle=-1 to get a correct Line 11786  Please run with mle=-1 to get a correct
      *                  2211       *                  2211
      *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1       *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
      *                  V3=2       *                  V3=2
                    * codtabm and decodtabm are identical
      */       */
   
   /* /\* for(h=1; h <=100 ;h++){  *\/ */  
   /*   /\* printf("h=%2d ", h); *\/ */  
   /*    /\* for(k=1; k <=10; k++){ *\/ */  
   /*      /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */  
   /*    /\*   codtab[h][k]=codtabm(h,k); *\/ */  
   /*    /\* } *\/ */  
   /*    /\* printf("\n"); *\/ */  
   /* } */  
   /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */  
   /*   for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/  */  
   /*     for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */  
   /*    for(cpt=1; cpt <=pow(2,k-1); cpt++){  /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/  */  
   /*      h++; */  
   /*      if (h>m)  */  
   /*        h=1; */  
   /*      codtab[h][k]=j; */  
   /*      /\* codtab[12][3]=1; *\/ */  
   /*      /\*codtab[h][Tvar[k]]=j;*\/ */  
   /*      /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */  
   /*    }  */  
   /*     } */  
   /*   } */  
   /* }  */  
   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);   
      codtab[1][2]=1;codtab[2][2]=2; */  
   /* for(i=1; i <=m ;i++){  */  
   /*    for(k=1; k <=cptcovn; k++){ */  
   /*      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */  
   /*    } */  
   /*    printf("\n"); */  
   /* } */  
   /*   scanf("%d",i);*/  
   
  free_ivector(Ndum,-1,NCOVMAX);   free_ivector(Ndum,-1,NCOVMAX);
   
Line 8914  Title=%s <br>Datafile=%s Firstpass=%d La Line 11863  Title=%s <br>Datafile=%s Firstpass=%d La
 #endif  #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, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
               firstpass, lastpass,  stepm,  weightopt, model);                firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\
             ftol, stepm);
     fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
     ncurrv=1;
     for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv); 
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li>Number of time varying  quantitative covariates: nqtv=%d ", nqtv);
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
              nlstate, ndeath, maxwav, mle, weightopt);
   
     fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
   <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
   
     
     fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
 Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\  Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\  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] */
Line 8938  Interval (in months) between two waves: Line 11909  Interval (in months) between two waves:
   /* For mortality only */    /* For mortality only */
   if (mle==-3){    if (mle==-3){
     ximort=matrix(1,NDIM,1,NDIM);       ximort=matrix(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); */      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);      cens=ivector(firstobs,lastobs);
     ageexmed=vector(1,n);      ageexmed=vector(firstobs,lastobs);
     agecens=vector(1,n);      agecens=vector(firstobs,lastobs);
     dcwave=ivector(1,n);      dcwave=ivector(firstobs,lastobs);
                    
     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++)
                                 if (s[m][i]>nlstate) {          if (s[m][i]>nlstate) {
                                         dcwave[i]=m;            dcwave[i]=m;
                                         /*      printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/            /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
                                         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;
                                 }else if (ageexmed[i]< 1)           }else if (ageexmed[i]< 1) 
                                         cens[i]= -1;            cens[i]= -1;
                                 if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)          if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
                                         cens[i]=0 ;            cens[i]=0 ;
       }        }
       else cens[i]=-1;        else cens[i]=-1;
     }      }
           
     for (i=1;i<=NDIM;i++) {      for (i=1;i<=NDIM;i++) {
       for (j=1;j<=NDIM;j++)        for (j=1;j<=NDIM;j++)
                                 ximort[i][j]=(i == j ? 1.0 : 0.0);          ximort[i][j]=(i == j ? 1.0 : 0.0);
     }      }
           
     /*p[1]=0.0268; p[NDIM]=0.083;*/      p[1]=0.0268; p[NDIM]=0.083;
     /*printf("%lf %lf", p[1], p[2]);*/      /* printf("%lf %lf", p[1], p[2]); */
           
           
 #ifdef GSL  #ifdef GSL
Line 9086  Interval (in months) between two waves: Line 12060  Interval (in months) between two waves:
   
     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 ");      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]);                                  fprintf(ficlog,"%f ",matcov[i][j]);
       }        }
       printf("\n ");  fprintf(ficlog,"\n ");        printf("\n ");  fprintf(ficlog,"\n ");
     }      }
Line 9103  Interval (in months) between two waves: Line 12077  Interval (in months) between two waves:
       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]));        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(agegomp,AGESUP);
     lpop=vector(1,AGESUP);      lpop=vector(agegomp,AGESUP);
     tpop=vector(1,AGESUP);      tpop=vector(agegomp,AGESUP);
     lsurv[agegomp]=100000;      lsurv[agegomp]=100000;
           
     for (k=agegomp;k<=AGESUP;k++) {      for (k=agegomp;k<=AGESUP;k++) {
Line 9134  Interval (in months) between two waves: Line 12108  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 / */
                   ageminpar=50;
                   agemaxpar=100;
     if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){      if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\          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\  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
Line 9141  Please run with mle=-1 to get a correct Line 12117  Please run with mle=-1 to get a correct
         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\          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\  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);  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
     }else      }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);        printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
                   }
     printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \      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,agegomp,AGESUP);
     free_vector(lpop,1,AGESUP);      free_vector(lpop,agegomp,AGESUP);
     free_vector(tpop,1,AGESUP);      free_vector(tpop,agegomp,AGESUP);
 #ifdef GSL  
     free_ivector(cens,1,n);  
     free_vector(agecens,1,n);  
     free_ivector(dcwave,1,n);  
     free_matrix(ximort,1,NDIM,1,NDIM);      free_matrix(ximort,1,NDIM,1,NDIM);
       free_ivector(dcwave,firstobs,lastobs);
       free_vector(agecens,firstobs,lastobs);
       free_vector(ageexmed,firstobs,lastobs);
       free_ivector(cens,firstobs,lastobs);
   #ifdef GSL
 #endif  #endif
   } /* Endof if mle==-3 mortality only */    } /* Endof if mle==-3 mortality only */
   /* Standard  */    /* Standard  */
Line 9168  Please run with mle=-1 to get a correct Line 12148  Please run with mle=-1 to get a correct
     printf("\n");      printf("\n");
     if(mle>=1){ /* Could be 1 or 2, Real Maximization */      if(mle>=1){ /* Could be 1 or 2, Real Maximization */
       /* mlikeli uses func not funcone */        /* mlikeli uses func not funcone */
         /* for(i=1;i<nlstate;i++){ */
         /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
         /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
         /* } */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }      }
     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */      if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
Line 9183  Please run with mle=-1 to get a correct Line 12167  Please run with mle=-1 to get a correct
     printf("\n");      printf("\n");
           
     /*--------- 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=1+age+%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 9229  Please run with mle=-1 to get a correct Line 12213  Please run with mle=-1 to get a correct
         }          }
       }        }
     } /* end of hesscov and Wald tests */      } /* 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");
Line 9338  Please run with mle=-1 to get a correct Line 12322  Please run with mle=-1 to get a correct
           
     fflush(ficlog);      fflush(ficlog);
     fflush(ficres);      fflush(ficres);
       while(fgets(line, MAXLINE, ficpar)) {      while(fgets(line, MAXLINE, ficpar)) {
     /* If line starts with a # it is a comment */        /* If line starts with a # it is a comment */
     if (line[0] == '#') {        if (line[0] == '#') {
       numlinepar++;          numlinepar++;
       fputs(line,stdout);          fputs(line,stdout);
       fputs(line,ficparo);          fputs(line,ficparo);
       fputs(line,ficlog);          fputs(line,ficlog);
       continue;          fputs(line,ficres);
     }else          continue;
       break;        }else
   }          break;
       }
       
     /* 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 9360  Please run with mle=-1 to get a correct Line 12345  Please run with mle=-1 to get a correct
           
     estepm=0;      estepm=0;
     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=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) {        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);          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);          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;          goto end;
         }
         printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
     }      }
     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 */
   /* 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); */      /* 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) {
Line 9381  Please run with mle=-1 to get a correct Line 12366  Please run with mle=-1 to get a correct
     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 ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);      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, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);      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 */          /* Other stuffs, more or less useful */    
     while((c=getc(ficpar))=='#' && c!= EOF){      while(fgets(line, MAXLINE, ficpar)) {
       ungetc(c,ficpar);        /* If line starts with a # it is a comment */
       fgets(line, MAXLINE, ficpar);        if (line[0] == '#') {
       fputs(line,stdout);          numlinepar++;
       fputs(line,ficparo);          fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           fputs(line,ficres);
           continue;
         }else
           break;
     }      }
     ungetc(c,ficpar);  
           if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);        
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        if (num_filled != 7) {
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          goto end;
             }
     while((c=getc(ficpar))=='#' && c!= EOF){        printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       ungetc(c,ficpar);        fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fgets(line, MAXLINE, ficpar);        fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fputs(line,stdout);        fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fputs(line,ficparo);      }
   
       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);
           fputs(line,ficres);
           continue;
         }else
           break;
     }      }
     ungetc(c,ficpar);  
           
           
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;      dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
           
     fscanf(ficpar,"pop_based=%d\n",&popbased);      if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
     fprintf(ficlog,"pop_based=%d\n",popbased);        if (num_filled != 1) {
     fprintf(ficparo,"pop_based=%d\n",popbased);             printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
     fprintf(ficres,"pop_based=%d\n",popbased);             fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               goto end;
     while((c=getc(ficpar))=='#' && c!= EOF){        }
       ungetc(c,ficpar);        printf("pop_based=%d\n",popbased);
       fgets(line, MAXLINE, ficpar);        fprintf(ficlog,"pop_based=%d\n",popbased);
       fputs(line,stdout);        fprintf(ficparo,"pop_based=%d\n",popbased);   
       fputs(line,ficparo);        fprintf(ficres,"pop_based=%d\n",popbased);   
     }  
     ungetc(c,ficpar);  
       
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);  
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
     /* day and month of proj2 are not used but only year anproj2.*/  
       
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);  
       fputs(line,stdout);  
       fputs(line,ficparo);  
     }      }
     ungetc(c,ficpar);       
           /* Results */
     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);      endishere=0;
     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);      nresult=0;
     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);      parameterline=0;
     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);      do{
     /* day and month of proj2 are not used but only year anproj2.*/        if(!fgets(line, MAXLINE, ficpar)){
               endishere=1;
           parameterline=15;
         }else if (line[0] == '#') {
           /* If line starts with a # it is a comment */
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           fputs(line,ficres);
           continue;
         }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
           parameterline=11;
         else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
           parameterline=12;
         else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
           parameterline=13;
         }
         else{
           parameterline=14;
         }
         switch (parameterline){ /* =0 only if only comments */
         case 11:
           if((num_filled=sscanf(line,"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)) !=EOF && (num_filled == 8)){
                     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             /* day and month of proj2 are not used but only year anproj2.*/
             dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
             dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
             prvforecast = 1;
           } 
           else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
             printf("prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
             fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
             fprintf(ficres,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
             prvforecast = 2;
           }
           else {
             printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             goto end;
           }
           break;
         case 12:
           if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){
             fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             /* day and month of back2 are not used but only year anback2.*/
             dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
             dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
             prvbackcast = 1;
           } 
           else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
             printf("prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
             fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
             fprintf(ficres,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
             prvbackcast = 2;
           }
           else {
             printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             goto end;
           }
           break;
         case 13:
           num_filled=sscanf(line,"result:%[^\n]\n",resultline);
           nresult++; /* Sum of resultlines */
           printf("Result %d: result:%s\n",nresult, resultline);
           if(nresult > MAXRESULTLINES){
             printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINES,nresult,rfileres);
             fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINES,nresult,rfileres);
             goto end;
           }
           decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
           fprintf(ficparo,"result: %s\n",resultline);
           fprintf(ficres,"result: %s\n",resultline);
           fprintf(ficlog,"result: %s\n",resultline);
           break;
         case 14:
           printf("Error: Unknown command '%s'\n",line);
           fprintf(ficlog,"Error: Unknown command '%s'\n",line);
           if(ncovmodel >=2 && nresult==0 ){
             printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
             fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
           }
           /* goto end; */
           break;
         case 15:
           printf("End of resultlines.\n");
           fprintf(ficlog,"End of resultlines.\n");
           break;
         default: /* parameterline =0 */
           nresult=1;
           decoderesult(".",nresult ); /* No covariate */
         } /* End switch parameterline */
       }while(endishere==0); /* End do */
           
      /* 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 / */
     if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){      if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\        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\  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);  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\        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\  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);  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
     }else      }else{
       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);        /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
             /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\        /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \        if(prvforecast==1){
                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);          dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
                 jprojd=jproj1;
    /*------------ free_vector  -------------*/          mprojd=mproj1;
    /*  chdir(path); */          anprojd=anproj1;
            dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
           jprojf=jproj2;
           mprojf=mproj2;
           anprojf=anproj2;
         } else if(prvforecast == 2){
           dateprojd=dateintmean;
           date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
           dateprojf=dateintmean+yrfproj;
           date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
         }
         if(prvbackcast==1){
           datebackd=(jback1+12*mback1+365*anback1)/365;
           jbackd=jback1;
           mbackd=mback1;
           anbackd=anback1;
           datebackf=(jback2+12*mback2+365*anback2)/365;
           jbackf=jback2;
           mbackf=mback2;
           anbackf=anback2;
         } else if(prvbackcast == 2){
           datebackd=dateintmean;
           date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
           datebackf=dateintmean-yrbproj;
           date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
         }
         
         printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
       }
       printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
                    jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
                   
       /*------------ free_vector  -------------*/
       /*  chdir(path); */
                   
     /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */      /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
     /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */      /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
     /* free_imatrix(bh,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_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
     free_lvector(num,1,n);      free_lvector(num,firstobs,lastobs);
     free_vector(agedc,1,n);      free_vector(agedc,firstobs,lastobs);
     /*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)*/      /* 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);      prlim=matrix(1,nlstate,1,nlstate);
Line 9490  Please run with mle=-1 to get a correct Line 12609  Please run with mle=-1 to get a correct
     /*#include "hpijx.h"*/      /*#include "hpijx.h"*/
     hPijx(p, bage, fage);      hPijx(p, bage, fage);
     fclose(ficrespij);      fclose(ficrespij);
       
     ncovcombmax=  pow(2,cptcoveff);      /* ncovcombmax=  pow(2,cptcoveff); */
     /*-------------- Variance of one-step probabilities---*/      /*-------------- 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] */      /* Prevalence for each covariate combination in probs[age][status][cov] */
     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);      probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
     for(i=1;i<=AGESUP;i++)      for(i=AGEINF;i<=AGESUP;i++)
       for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */        for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
                                 for(k=1;k<=ncovcombmax;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);      prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, 
                  ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     if (mobilav!=0 ||mobilavproj !=0 ) {      if (mobilav!=0 ||mobilavproj !=0 ) {
       mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);        mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
                         for(i=1;i<=AGESUP;i++)        for(i=AGEINF;i<=AGESUP;i++)
                                 for(j=1;j<=nlstate;j++)          for(j=1;j<=nlstate+ndeath;j++)
                                         for(k=1;k<=ncovcombmax;k++)            for(k=1;k<=ncovcombmax;k++)
                                                 mobaverages[i][j][k]=0.;              mobaverages[i][j][k]=0.;
       mobaverage=mobaverages;        mobaverage=mobaverages;
       if (mobilav!=0) {        if (mobilav!=0) {
                                 if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){          printf("Movingaveraging observed prevalence\n");
                                         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);          fprintf(ficlog,"Movingaveraging observed prevalence\n");
                                         printf(" Error in movingaverage mobilav=%d\n",mobilav);          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) {
       else if (mobilavproj !=0) {          printf("Movingaveraging projected observed prevalence\n");
                                 if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){          fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
                                         fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
                                         printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);            fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
                                 }            printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
           }
         }else{
           printf("Internal error moving average\n");
           fflush(stdout);
           exit(1);
       }        }
     }/* end if moving average */      }/* end if moving average */
                       
     /*---------- Forecasting ------------------*/      /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/      if(prevfcast==1){ 
     if(prevfcast==1){        /*   /\*    if(stepm ==1){*\/ */
       /*    if(stepm ==1){*/        /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        /*This done previously after freqsummary.*/
         /*   dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
         /*   dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
         
         /* } else if (prvforecast==2){ */
         /*   /\*    if(stepm ==1){*\/ */
         /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
         /* } */
         /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
         prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
     }      }
     if(backcast==1){  
       /* Prevbcasting */
       if(prevbcast==1){
       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);                ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
       ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);                ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
       ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
Line 9540  Please run with mle=-1 to get a correct Line 12676  Please run with mle=-1 to get a correct
       /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/        /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
   
       bprlim=matrix(1,nlstate,1,nlstate);        bprlim=matrix(1,nlstate,1,nlstate);
   
       back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);        back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
       fclose(ficresplb);        fclose(ficresplb);
   
       hBijx(p, bage, fage, mobaverage);        hBijx(p, bage, fage, mobaverage);
       fclose(ficrespijb);        fclose(ficrespijb);
       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */  
   
       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,        /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */        /* /\*                   mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
         /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
         /*                       mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
         prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
                          mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
   
         
         varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
         
         free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
     }      }    /* end  Prevbcasting */
        
     
     /* ------ Other prevalence ratios------------ */      /* ------ Other prevalence ratios------------ */
   
Line 9573  Please run with mle=-1 to get a correct Line 12719  Please run with mle=-1 to get a correct
     }      }
     printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
   
       pstamp(ficreseij);
                                   
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
       if (cptcovn < 1){i1=1;}
       
       for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
         printf("\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
       }        }
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
         printf("******\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;
       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);          evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);  
               
       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     }      }
     fclose(ficreseij);      fclose(ficreseij);
     printf("done evsij\n");fflush(stdout);      printf("done evsij\n");fflush(stdout);
     fprintf(ficlog,"done evsij\n");fflush(ficlog);      fprintf(ficlog,"done evsij\n");fflush(ficlog);
   
                                   
     /*---------- Health expectancies and variances ------------*/      /*---------- State-specific expectancies and variances ------------*/
                   
                                   
     strcpy(filerest,"T_");      strcpy(filerest,"T_");
     strcat(filerest,fileresu);      strcat(filerest,fileresu);
Line 9602  Please run with mle=-1 to get a correct Line 12763  Please run with mle=-1 to get a correct
     }      }
     printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);      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); fflush(ficlog);      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,fileresu);
     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 State specific 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 State specific 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 State-specific 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 State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
     strcpy(filerescve,"CVE_");      strcpy(filerescve,"CVE_");
     strcat(filerescve,fileresu);      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. State-specific 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. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
     }      }
     printf("    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      printf("    Computing Covar. of State-specific 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 State-specific Expectancies: result on file '%s' \n", filerescve);
   
     strcpy(fileresv,"V_");      strcpy(fileresv,"V_");
     strcat(fileresv,fileresu);      strcat(fileresv,fileresu);
Line 9628  Please run with mle=-1 to get a correct Line 12787  Please run with mle=-1 to get a correct
       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' ... ", fileresv);fflush(stdout);      printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
     fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);      fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
   
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/      if (cptcovn < 1){i1=1;}
                 
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for(nres=1; nres <= nresult; nres++) /* For each resultline */
       fprintf(ficrest,"\n#****** ");      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
       for(j=1;j<=cptcoveff;j++)         if(i1 != 1 && TKresult[nres]!= k)
                                 fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          continue;
         printf("\n#****** Result for:");
         fprintf(ficrest,"\n#****** Result for:");
         fprintf(ficlog,"\n#****** Result for:");
         for(j=1;j<=cptcoveff;j++){ 
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
       fprintf(ficrest,"******\n");        fprintf(ficrest,"******\n");
         fprintf(ficlog,"******\n");
         printf("******\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]][codtabm(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]][codtabm(k,j)]);          fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
       fprintf(ficresstdeij,"******\n");        fprintf(ficresstdeij,"******\n");
       fprintf(ficrescveij,"******\n");        fprintf(ficrescveij,"******\n");
               
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
         /* pstamp(ficresvij); */
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
                                 fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][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;
       printf(" cvevsij %d, ",k);        printf(" cvevsij ");
       fprintf(ficlog, " cvevsij %d, ",k);        fprintf(ficlog, " cvevsij ");
       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);        cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
       printf(" end cvevsij \n ");        printf(" end cvevsij \n ");
       fprintf(ficlog, " end cvevsij \n ");        fprintf(ficlog, " end cvevsij \n ");
               
Line 9669  Please run with mle=-1 to get a correct Line 12851  Please run with mle=-1 to get a correct
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       pstamp(ficrest);        pstamp(ficrest);
               
               epj=vector(1,nlstate+1);
       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
         oldm=oldms;savm=savms; /* ZZ Segmentation fault */          oldm=oldms;savm=savms; /* ZZ Segmentation fault */
         cptcod= 0; /* To be deleted */          cptcod= 0; /* To be deleted */
         printf("varevsij %d \n",vpopbased);          printf("varevsij vpopbased=%d \n",vpopbased);
         fprintf(ficlog, "varevsij %d \n",vpopbased);          fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
         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 */          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* 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 ");          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)          if(vpopbased==1)
           fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);            fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
         else          else
           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");            fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");          fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");          fprintf(ficrest,"\n");
         /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */          /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
         epj=vector(1,nlstate+1);          printf("Computing age specific forward period (stable) prevalences in each health state \n");
         printf("Computing age specific period (stable) prevalences in each health state \n");          fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");  
         for(age=bage; age <=fage ;age++){          for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */            prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
           if (vpopbased==1) {            if (vpopbased==1) {
             if(mobilav ==0){              if(mobilav ==0){
               for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++)
Line 9723  Please run with mle=-1 to get a correct Line 12904  Please run with mle=-1 to get a correct
           fprintf(ficrest,"\n");            fprintf(ficrest,"\n");
         }          }
       } /* End vpopbased */        } /* End vpopbased */
         free_vector(epj,1,nlstate+1);
       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
       free_ma3x(vareij,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 selection\n");fflush(stdout);
       printf("done \n");fflush(stdout);        fprintf(ficlog,"done selection\n");fflush(ficlog);
       fprintf(ficlog,"done\n");fflush(ficlog);  
               
       /*}*/      } /* End k selection */
     } /* End k */  
     free_vector(weight,1,n);      printf("done State-specific expectancies\n");fflush(stdout);
       fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
   
       /* variance-covariance of forward period prevalence*/
       varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
       
       free_vector(weight,firstobs,lastobs);
     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,firstobs,lastobs);
     free_matrix(anint,1,maxwav,1,n);       free_matrix(anint,1,maxwav,firstobs,lastobs); 
     free_matrix(mint,1,maxwav,1,n);      free_matrix(mint,1,maxwav,firstobs,lastobs);
     free_ivector(cod,1,n);      free_ivector(cod,firstobs,lastobs);
     free_ivector(tab,1,NCOVMAX);      free_ivector(tab,1,NCOVMAX);
     fclose(ficresstdeij);      fclose(ficresstdeij);
     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------*/         
   
     strcpy(fileresvpl,"VPL_");  
     strcat(fileresvpl,fileresu);  
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);  
       exit(0);  
     }  
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", 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(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/  
             
     for (k=1; k <= (int) pow(2,cptcoveff); k++){  
         fprintf(ficresvpl,"\n#****** ");  
                         for(j=1;j<=cptcoveff;j++)   
                                 fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
                         fprintf(ficresvpl,"******\n");  
         
                         varpl=matrix(1,nlstate,(int) bage, (int) fage);  
                         oldm=oldms;savm=savms;  
                         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);  
                         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
       /*}*/  
     }  
                   
     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 ||mobilavproj !=0)      if (mobilav!=0 ||mobilavproj !=0)
       free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */        free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
     free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);      free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
   }  /* mle==-3 arrives here for freeing */  
  /* 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);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    }  /* mle==-3 arrives here for freeing */
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    /* endfree:*/
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(covar,0,NCOVMAX,1,n);    free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(matcov,1,npar,1,npar);    free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(hess,1,npar,1,npar);    if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
     /*free_vector(delti,1,npar);*/    if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);     if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
     free_matrix(agev,1,maxwav,1,imx);    free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_matrix(matcov,1,npar,1,npar);
     free_matrix(hess,1,npar,1,npar);
     free_ivector(ncodemax,1,NCOVMAX);    /*free_vector(delti,1,npar);*/
     free_ivector(ncodemaxwundef,1,NCOVMAX);    free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_ivector(Tvar,1,NCOVMAX);    free_matrix(agev,1,maxwav,1,imx);
     free_ivector(Tprod,1,NCOVMAX);    free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     free_ivector(Tvaraff,1,NCOVMAX);    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     free_ivector(Tage,1,NCOVMAX);    
     free_ivector(ncodemax,1,NCOVMAX);
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);    free_ivector(ncodemaxwundef,1,NCOVMAX);
     /* free_imatrix(codtab,1,100,1,10); */    free_ivector(Dummy,-1,NCOVMAX);
     free_ivector(Fixed,-1,NCOVMAX);
     free_ivector(DummyV,1,NCOVMAX);
     free_ivector(FixedV,1,NCOVMAX);
     free_ivector(Typevar,-1,NCOVMAX);
     free_ivector(Tvar,1,NCOVMAX);
     free_ivector(TvarsQ,1,NCOVMAX);
     free_ivector(TvarsQind,1,NCOVMAX);
     free_ivector(TvarsD,1,NCOVMAX);
     free_ivector(TvarsDind,1,NCOVMAX);
     free_ivector(TvarFD,1,NCOVMAX);
     free_ivector(TvarFDind,1,NCOVMAX);
     free_ivector(TvarF,1,NCOVMAX);
     free_ivector(TvarFind,1,NCOVMAX);
     free_ivector(TvarV,1,NCOVMAX);
     free_ivector(TvarVind,1,NCOVMAX);
     free_ivector(TvarA,1,NCOVMAX);
     free_ivector(TvarAind,1,NCOVMAX);
     free_ivector(TvarFQ,1,NCOVMAX);
     free_ivector(TvarFQind,1,NCOVMAX);
     free_ivector(TvarVD,1,NCOVMAX);
     free_ivector(TvarVDind,1,NCOVMAX);
     free_ivector(TvarVQ,1,NCOVMAX);
     free_ivector(TvarVQind,1,NCOVMAX);
     free_ivector(Tvarsel,1,NCOVMAX);
     free_vector(Tvalsel,1,NCOVMAX);
     free_ivector(Tposprod,1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);
     free_ivector(invalidvarcomb,1,ncovcombmax);
     free_ivector(Tage,1,NCOVMAX);
     free_ivector(Tmodelind,1,NCOVMAX);
     free_ivector(TmodelInvind,1,NCOVMAX);
     free_ivector(TmodelInvQind,1,NCOVMAX);
     
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     /* 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. Please look at the log file for details.\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. Please look at the log file for details.\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);
Line 9826  Please run with mle=-1 to get a correct Line 13016  Please run with mle=-1 to get a correct
   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));    printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     
   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));    printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));    fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));    fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
Line 9839  Please run with mle=-1 to get a correct Line 13029  Please run with mle=-1 to get a correct
   fclose(ficgp);    fclose(ficgp);
   fclose(ficlog);    fclose(ficlog);
   /*------ End -----------*/    /*------ End -----------*/
     
   
   /* Executes gnuplot */
    printf("Before Current directory %s!\n",pathcd);    
     printf("Before Current directory %s!\n",pathcd);
 #ifdef WIN32  #ifdef WIN32
    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)
 #else  #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   #endif 
     printf("Current directory %s!\n",pathcd);      printf("Current directory %s!\n",pathcd);
   /*strcat(plotcmd,CHARSEPARATOR);*/    /*strcat(plotcmd,CHARSEPARATOR);*/
Line 9875  Please run with mle=-1 to get a correct Line 13067  Please run with mle=-1 to get a correct
       
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
     strcpy(pplotcmd,plotcmd);
     
   if((outcmd=system(plotcmd)) != 0){    if((outcmd=system(plotcmd)) != 0){
     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);      printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");      printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);      sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
     if((outcmd=system(plotcmd)) != 0)      if((outcmd=system(plotcmd)) != 0){
       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);        printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
         strcpy(plotcmd,pplotcmd);
       }
   }    }
   printf(" Successful, please wait...");    printf(" Successful, please wait...");
   while (z[0] != 'q') {    while (z[0] != 'q') {
Line 9903  Please run with mle=-1 to get a correct Line 13098  Please run with mle=-1 to get a correct
     else if (z[0] == 'g') system(plotcmd);      else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);      else if (z[0] == 'q') exit(0);
   }    }
   end:  end:
   while (z[0] != 'q') {    while (z[0] != 'q') {
     printf("\nType  q for exiting: "); fflush(stdout);      printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);      scanf("%s",z);
   }    }
     printf("End\n");
     exit(0);
 }  }

Removed from v.1.219  
changed lines
  Added in v.1.308


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