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Diff for /imach/src/imach.c between versions 1.271 and 1.359

-version 1.271, 2017/06/27 10:17:50
+version 1.359, 2024/04/24 21:21:17
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.359  2024/04/24 21:21:17  brouard
+   Summary: First IMaCh version using Brent Praxis software based on Buckhardt and Gegenfürtner C codes
+   Revision 1.6  2024/04/24 21:10:29  brouard
+   Summary: First IMaCh version using Brent Praxis software based on Buckhardt and Gegenfürtner C codes
+   Revision 1.5  2023/10/09 09:10:01  brouard
+   Summary: trying to reconsider
+   Revision 1.4  2023/06/22 12:50:51  brouard
+   Summary: stil on going
+   Revision 1.3  2023/06/22 11:28:07  brouard
+   *** empty log message ***
+   Revision 1.2  2023/06/22 11:22:40  brouard
+   Summary: with svd but not working yet
+   Revision 1.353  2023/05/08 18:48:22  brouard
+   *** empty log message ***
+   Revision 1.352  2023/04/29 10:46:21  brouard
+   *** empty log message ***
+   Revision 1.351  2023/04/29 10:43:47  brouard
+   Summary: 099r45
+   Revision 1.350  2023/04/24 11:38:06  brouard
+   *** empty log message ***
+   Revision 1.349  2023/01/31 09:19:37  brouard
+   Summary: Improvements in models with age*Vn*Vm
+   Revision 1.347  2022/09/18 14:36:44  brouard
+   Summary: version 0.99r42
+   Revision 1.346  2022/09/16 13:52:36  brouard
+   * src/imach.c (Module): 0.99r41 Was an error when product of timevarying and fixed. Using FixedV[of name] now. Thank you  Feinuo
+   Revision 1.345  2022/09/16 13:40:11  brouard
+   Summary: Version 0.99r41
+   * imach.c (Module): 0.99r41 Was an error when product of timevarying and fixed. Using FixedV[of name] now. Thank you  Feinuo
+   Revision 1.344  2022/09/14 19:33:30  brouard
+   Summary: version 0.99r40
+   * imach.c (Module): Fixing names of variables in T_ (thanks to Feinuo)
+   Revision 1.343  2022/09/14 14:22:16  brouard
+   Summary: version 0.99r39
+   * imach.c (Module): Version 0.99r39 with colored dummy covariates
+   (fixed or time varying), using new last columns of
+   ILK_parameter.txt file.
+   Revision 1.342  2022/09/11 19:54:09  brouard
+   Summary: 0.99r38
+   * imach.c (Module): Adding timevarying products of any kinds,
+   should work before shifting cotvar from ncovcol+nqv columns in
+   order to have a correspondance between the column of cotvar and
+   the id of column.
+   (Module): Some cleaning and adding covariates in ILK.txt
+   Revision 1.341  2022/09/11 07:58:42  brouard
+   Summary: Version 0.99r38
+   After adding change in cotvar.
+   Revision 1.340  2022/09/11 07:53:11  brouard
+   Summary: Version imach 0.99r37
+   * imach.c (Module): Adding timevarying products of any kinds,
+   should work before shifting cotvar from ncovcol+nqv columns in
+   order to have a correspondance between the column of cotvar and
+   the id of column.
+   Revision 1.339  2022/09/09 17:55:22  brouard
+   Summary: version 0.99r37
+   * imach.c (Module): Many improvements for fixing products of fixed
+   timevarying as well as fixed * fixed, and test with quantitative
+   covariate.
+   Revision 1.338  2022/09/04 17:40:33  brouard
+   Summary: 0.99r36
+   * imach.c (Module): Now the easy runs i.e. without result or
+   model=1+age only did not work. The defautl combination should be 1
+   and not 0 because everything hasn't been tranformed yet.
+   Revision 1.337  2022/09/02 14:26:02  brouard
+   Summary: version 0.99r35
+   * src/imach.c: Version 0.99r35 because it outputs same results with
++age+V1+V1*age for females and 1+age for females only
+   (education=1 noweight)
+   Revision 1.336  2022/08/31 09:52:36  brouard
+   *** empty log message ***
+   Revision 1.335  2022/08/31 08:23:16  brouard
+   Summary: improvements...
+   Revision 1.334  2022/08/25 09:08:41  brouard
+   Summary: In progress for quantitative
+   Revision 1.333  2022/08/21 09:10:30  brouard
+   * src/imach.c (Module): Version 0.99r33 A lot of changes in
+   reassigning covariates: my first idea was that people will always
+   use the first covariate V1 into the model but in fact they are
+   producing data with many covariates and can use an equation model
+   with some of the covariate; it means that in a model V2+V3 instead
+   of codtabm(k,Tvaraff[j]) which calculates for combination k, for
+   three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
+   the equation model is restricted to two variables only (V2, V3)
+   and the combination for V2 should be codtabm(k,1) instead of
+   (codtabm(k,2), and the code should be
+   codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
+   made. All of these should be simplified once a day like we did in
+   hpxij() for example by using precov[nres] which is computed in
+   decoderesult for each nres of each resultline. Loop should be done
+   on the equation model globally by distinguishing only product with
+   age (which are changing with age) and no more on type of
+   covariates, single dummies, single covariates.
+   Revision 1.332  2022/08/21 09:06:25  brouard
+   Summary: Version 0.99r33
+   * src/imach.c (Module): Version 0.99r33 A lot of changes in
+   reassigning covariates: my first idea was that people will always
+   use the first covariate V1 into the model but in fact they are
+   producing data with many covariates and can use an equation model
+   with some of the covariate; it means that in a model V2+V3 instead
+   of codtabm(k,Tvaraff[j]) which calculates for combination k, for
+   three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
+   the equation model is restricted to two variables only (V2, V3)
+   and the combination for V2 should be codtabm(k,1) instead of
+   (codtabm(k,2), and the code should be
+   codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
+   made. All of these should be simplified once a day like we did in
+   hpxij() for example by using precov[nres] which is computed in
+   decoderesult for each nres of each resultline. Loop should be done
+   on the equation model globally by distinguishing only product with
+   age (which are changing with age) and no more on type of
+   covariates, single dummies, single covariates.
+   Revision 1.331  2022/08/07 05:40:09  brouard
+   *** empty log message ***
+   Revision 1.330  2022/08/06 07:18:25  brouard
+   Summary: last 0.99r31
+   *  imach.c (Module): Version of imach using partly decoderesult to rebuild xpxij function
+   Revision 1.329  2022/08/03 17:29:54  brouard
+   *  imach.c (Module): Many errors in graphs fixed with Vn*age covariates.
+   Revision 1.328  2022/07/27 17:40:48  brouard
+   Summary: valgrind bug fixed by initializing to zero DummyV as well as Tage
+   Revision 1.327  2022/07/27 14:47:35  brouard
+   Summary: Still a problem for one-step probabilities in case of quantitative variables
+   Revision 1.326  2022/07/26 17:33:55  brouard
+   Summary: some test with nres=1
+   Revision 1.325  2022/07/25 14:27:23  brouard
+   Summary: r30
+   * imach.c (Module): Error cptcovn instead of nsd in bmij (was
+   coredumped, revealed by Feiuno, thank you.
+   Revision 1.324  2022/07/23 17:44:26  brouard
+   *** empty log message ***
+   Revision 1.323  2022/07/22 12:30:08  brouard
+   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
+   Revision 1.322  2022/07/22 12:27:48  brouard
+   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
+   Revision 1.321  2022/07/22 12:04:24  brouard
+   Summary: r28
+   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
+   Revision 1.320  2022/06/02 05:10:11  brouard
+   *** empty log message ***
+   Revision 1.319  2022/06/02 04:45:11  brouard
+   * imach.c (Module): Adding the Wald tests from the log to the main
+   htm for better display of the maximum likelihood estimators.
+   Revision 1.318  2022/05/24 08:10:59  brouard
+   * imach.c (Module): Some attempts to find a bug of wrong estimates
+   of confidencce intervals with product in the equation modelC
+   Revision 1.317  2022/05/15 15:06:23  brouard
+   * imach.c (Module):  Some minor improvements
+   Revision 1.316  2022/05/11 15:11:31  brouard
+   Summary: r27
+   Revision 1.315  2022/05/11 15:06:32  brouard
+   *** empty log message ***
+   Revision 1.314  2022/04/13 17:43:09  brouard
+   * imach.c (Module): Adding link to text data files
+   Revision 1.313  2022/04/11 15:57:42  brouard
+   * imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed
+   Revision 1.312  2022/04/05 21:24:39  brouard
+   *** empty log message ***
+   Revision 1.311  2022/04/05 21:03:51  brouard
+   Summary: Fixed quantitative covariates
+           Fixed covariates (dummy or quantitative)
+         with missing values have never been allowed but are ERRORS and
+         program quits. Standard deviations of fixed covariates were
+         wrongly computed. Mean and standard deviations of time varying
+         covariates are still not computed.
+   Revision 1.310  2022/03/17 08:45:53  brouard
+   Summary: 99r25
+   Improving detection of errors: result lines should be compatible with
+   the model.
+   Revision 1.309  2021/05/20 12:39:14  brouard
+   Summary: Version 0.99r24
+   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
- Line 678
+ Line 1046
    The same imach parameter file can be used but the option for mle should be -3.
-   Agnès, who wrote this part of the code, tried to keep most of the
+   Agnès, who wrote this part of the code, tried to keep most of the
    former routines in order to include the new code within the former code.
    The output is very simple: only an estimate of the intercept and of
- Line 857  Important routines
+ Line 1225  Important routines
  - 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
+   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
    from the European Union.
    It is copyrighted identically to a GNU software product, ie programme and
- Line 927  Important routines
+ Line 1295  Important routines
  #define POWELLNOF3INFF1TEST /* Skip test */
  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
+ /* #define FLATSUP  *//* Suppresses directions where likelihood is flat */
+ /* #define POWELLORIGINCONJUGATE  /\* Don't use conjugate but biggest decrease if valuable *\/ */
+ /* #define NOTMINFIT */
  #include <math.h>
  #include <stdio.h>
- Line 978  typedef struct {
+ Line 1349  typedef struct {
  /* #include <libintl.h> */
  /* #define _(String) gettext (String) */
- #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
+ #define MAXLINE 16384 /* Was 256 and 1024 and 2048. Overflow with 312 with 2 states and 4 covariates. Should be ok */
  #define GNUPLOTPROGRAM "gnuplot"
+ #define GNUPLOTVERSION 5.1
+ double gnuplotversion=GNUPLOTVERSION;
  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- #define FILENAMELENGTH 132
+ #define FILENAMELENGTH 256
  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
+ #define MAXPARM 216 /**< Maximum number of parameters for the optimization was 128 */
  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
  #define NINTERVMAX 8
  #define NLSTATEMAX 8 /**< Maximum number of live 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 30  /**< Maximum number of covariates used in the model, including generated covariates V1*V2 or V1*age */
  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
  /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
  #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
- #define MAXN 20000
+ /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
  #define YEARM 12. /**< Number of months per year */
  /* #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 AGEBASE 40
- Line 1020  typedef struct {
+ Line 1394  typedef struct {
  /* $State$ */
  #include "version.h"
  char version[]=__IMACH_VERSION__;
- char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
+ char copyright[]="April 2023,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 2021-202, INED 2000-2022";
  char fullversion[]="$Revision$ $Date$";
  char strstart[80];
  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ int debugILK=0; /* debugILK is set by a #d in a comment line */
  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
- /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
+ /* Number of covariates model (1)=V2+V1+ V3*age+V2*V4 */
- int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
+ /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
- int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
+ int cptcovn=0; /**< cptcovn decodemodel: number of covariates k of the models excluding age*products =6 and age*age but including products */
- int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
+ int cptcovt=0; /**< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
- int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
+ int cptcovs=0; /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
+ 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 cptcovprodage=0; /**< Number of fixed covariates with age: V3*age or V2*V3*age 1 */
+ int cptcovprodvage=0; /**< Number of varying covariates with age: V7*age or V7*V6*age */
+ int cptcovdageprod=0; /**< Number of doubleproducts with age, since 0.99r44 only: age*Vn*Vm for gnuplot printing*/
  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 single dummy covariates (fixed or time varying) to vary for printing results (2**cptcoveff combinations of dummies)(computed in tricode as cptcov) */
  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 ncovvt=0; /* Total number of effective (wave) varying covariates (dummy or quantitative or products [without age]) in the model */
+ int ncovvta=0; /*  +age*V6 + age*V7+ age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 Total number of expandend products [with age]) in the model */
+ int ncovta=0; /*age*V3*V2 +age*V2+agev3+ageV4  +age*V6 + age*V7+ age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 Total number of expandend products [with age]) in the model */
+ int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (single or product, dummy or quantitative) in the model */
+ int ncovva=0; /* +age*V6 + age*V7+ge*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 Total number of effective (wave and stepm) varying with age covariates (single or product, dummy or 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 */
- Line 1044  int nqfveff=0; /**< nqfveff Number of Qu
+ Line 1427  int nqfveff=0; /**< nqfveff Number of Qu
  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 firstobs=1, lastobs=10; /* nobs = lastobs-firstobs+1 declared globally ;*/
+ int nobs=10;  /* Number of observations in the data lastobs-firstobs */
  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 ndeath=1; /* Number of dead states */
  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 nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable*/
+ int ncovcolt=0; /* ncovcolt=ncovcol+nqv+ntv+nqtv; total of covariates in the data, not in the model equation*/
  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
  int maxwav=0; /* Maxim number of waves */
  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- int gipmx=0, gsw=0; /* Global variables on the number of contributions
+ int gipmx = 0;
+ double gsw = 0; /* Global variables on the number of contributions
                     to the likelihood and the sum of weights (done by funcone)*/
  int mle=1, weightopt=0;
  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- Line 1120  extern time_t time();
+ Line 1507  extern time_t time();
  struct tm start_time, end_time, curr_time, last_time, forecast_time;
  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
+ time_t   rlast_btime; /* raw time */
  struct tm tm;
  char strcurr[80], strfor[80];
- Line 1182  int *ncodemaxwundef;  /* ncodemax[j]= Nu
+ Line 1570  int *ncodemaxwundef;  /* ncodemax[j]= Nu
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  double **pmmij, ***probs; /* Global pointer */
  double ***mobaverage, ***mobaverages; /* New global variable */
+ double **precov; /* New global variable to store for each resultline, values of model covariates given by the resultlines (in order to speed up)  */
  double *ageexmed,*agecens;
  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;
  int **s; /* Status */
  double *agedc;
- Line 1192  double  **covar; /**< covar[j,i], value
+ Line 1586  double  **covar; /**< covar[j,i], value
                    * covar=matrix(0,NCOVMAX,1,n);
                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
  double **coqvar; /* Fixed quantitative covariate nqv */
- double ***cotvar; /* Time varying covariate ntv */
+ double ***cotvar; /* Time varying covariate start at ncovcol + nqv + (1 to ntv) */
  double ***cotqvar; /* Time varying quantitative covariate itqv */
  double  idx;
  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
- /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ /* Some documentation */
- /*k          1  2   3   4     5    6    7     8    9 */
+       /*   Design original data
- /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */
+        *  V1   V2   V3   V4  V5  V6  V7  V8  Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12
- /* Tndvar[k]    1   2   3               4          5 */
+        *  <          ncovcol=6   >   nqv=2 (V7 V8)                   dv dv  dv  qtv    dv dv  dvv qtv
- /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */
+        *                                                             ntv=3     nqtv=1
- /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */
+        *  cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11
- /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */
+        * For time varying covariate, quanti or dummies
- /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */
+        *       cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
- /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */
+        *       cotvar[wav][ncovcol+nqv+ iv(1 to nqtv)][i]= [(1 to nqtv)][i]=(V12) quanti
- /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */
+        *       cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
- /* Tprod[i]=k           4               7            */
+        *       cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
- /* Tage[i]=k                  5               8      */
+        *       covar[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:
- /* */
+        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
+        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + V9 + V9*age + V10
+        *   k=  1    2      3       4     5       6      7        8   9     10       11
+        */
+ /* According to the model, more columns can be added to covar by the product of covariates */
+ /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
+   # States 1=Coresidence, 2 Living alone, 3 Institution
+   # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
+ */
+ /*           V5+V4+ V3+V4*V3 +V5*age+V2 +V1*V2+V1*age+V1+V4*V3*age */
+ /*    kmodel  1  2   3    4     5     6    7     8     9    10 */
+ /*Typevar[k]=  0  0   0   2     1    0    2     1     0    3 *//*0 for simple covariate (dummy, quantitative,*/
+                                                                /* fixed or varying), 1 for age product, 2 for*/
+                                                                /* product without age, 3 for age and double product   */
+ /*Dummy[k]=    1  0   0   1     3    1    1     2     0     3  *//*Dummy[k] 0=dummy (0 1), 1 quantitative */
+                                                                 /*(single or product without age), 2 dummy*/
+                                                                /* with age product, 3 quant with age product*/
+ /*Tvar[k]=     5  4   3   6     5    2    7     1     1     6 */
+ /*    nsd         1   2                               3 */ /* Counting single dummies covar fixed or tv */
+ /*TnsdVar[Tvar]   1   2                               3 */
+ /*Tvaraff[nsd]    4   3                               1 */ /* ID of single dummy cova fixed or timevary*/
+ /*TvarsD[nsd]     4   3                               1 */ /* ID of single dummy cova fixed or timevary*/
+ /*TvarsDind[nsd]  2   3                               9 */ /* position K of single dummy cova */
+ /*    nsq      1                     2                  */ /* Counting single quantit tv */
+ /* TvarsQ[k]   5                     2                  */ /* Number of single quantitative cova */
+ /* TvarsQind   1                     6                  */ /* position K of single quantitative cova */
+ /* Tprod[i]=k             1               2             */ /* Position in model of the ith prod without age */
+ /* cptcovage                    1               2         3 */ /* Counting cov*age in the model equation */
+ /* Tage[cptcovage]=k            5               8         10 */ /* Position in the model of ith cov*age */
+ /* model="V2+V3+V4+V6+V7+V6*V2+V7*V2+V6*V3+V7*V3+V6*V4+V7*V4+age*V2+age*V3+age*V4+age*V6+age*V7+age*V6*V2+age*V6*V3+age*V7*V3+age*V6*V4+age*V7*V4\r"*/
+ /*  p Tvard[1][1]@21 = {6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0}*/
+ /*  p Tvard[2][1]@21 = {7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0 <repeats 11 times>} */
+ /* p Tvardk[1][1]@24 = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0}*/
+ /* p Tvardk[1][1]@22 = {0, 0, 0, 0, 0, 0, 0, 0, 6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0} */
+ /* Tvard[1][1]@4={4,3,1,2}    V4*V3 V1*V2               */ /* Position in model of the ith prod without age */
+ /* Tvardk[4][1]=4;Tvardk[4][2]=3;Tvardk[7][1]=1;Tvardk[7][2]=2 */ /* Variables of a prod at position in the model equation*/
+ /* TvarF TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
+ /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
  /* Type                    */
  /* V         1  2  3  4  5 */
  /*           F  F  V  V  V */
  /*           D  Q  D  D  Q */
  /*                         */
  int *TvarsD;
+ int *TnsdVar;
  int *TvarsDind;
  int *TvarsQ;
  int *TvarsQind;
- #define MAXRESULTLINES 10
+ #define MAXRESULTLINESPONE 10+1
  int nresult=0;
  int parameterline=0; /* # of the parameter (type) line */
- int TKresult[MAXRESULTLINES];
+ int TKresult[MAXRESULTLINESPONE]; /* TKresult[nres]=k for each resultline nres give the corresponding combination of dummies */
- int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
+ int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model corresponds to the k3 position in the resultline */
- int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
+ int modelresult[MAXRESULTLINESPONE][NCOVMAX];/* modelresult[k3]=k1: k1th position in the model corresponds to the k3 position in the resultline */
- int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
+ int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline */
- double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
+ int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line  */
- double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
+ double TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */
- int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
+ int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvresult[nres][result_position]= name of the dummy variable at the result_position in the nres resultline */
+ double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
+ double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
+ int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline */
+ /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
+   # States 1=Coresidence, 2 Living alone, 3 Institution
+   # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
+ */
  /* 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 */
- Line 1245  int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3
+ Line 1684  int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3
  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 *TvarVV; /* We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
+ int *TvarVVind; /* We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
+ int *TvarVVA; /* We count ncovvt time varying covariates (single or products with age) and put their name into TvarVVA */
+ int *TvarVVAind; /* We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
+ int *TvarAVVA; /* We count ALL ncovta time varying covariates (single or products with age) and put their name into TvarVVA */
+ int *TvarAVVAind; /* We count ALL ncovta time varying covariates (single or products without age) and put their name into TvarVV */
+       /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
+       /* model V1+V3+age*V1+age*V3+V1*V3 + V1*V3*age */
+       /*  Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
+       /* TvarVV={3,1,3,1,3}, for V3 and then the product V1*V3 is decomposed into V1 and V3 */
+       /* TvarVVind={2,5,5,6,6}, for V3 and then the product V1*V3 is decomposed into V1 and V3 and V1*V3*age into 6,6 */
  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 *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product, 3 age*Vn*Vm */
  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 */
- Line 1261  int *TmodelInvQind; /** Tmodelqind[1]=1
+ Line 1710  int *TmodelInvQind; /** Tmodelqind[1]=1
  int *Ndum; /** Freq of modality (tricode */
  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
  int **Tvard;
+ int **Tvardk;
  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 */
- Line 1384  char *trimbb(char *out, char *in)
+ Line 1834  char *trimbb(char *out, char *in)
    return s;
  }
+ char *trimbtab(char *out, char *in)
+ { /* Trim  blanks or tabs in line but keeps first blanks if line starts with blanks */
+   char *s;
+   s=out;
+   while (*in != '\0'){
+     while( (*in == ' ' || *in == '\t')){ /* && *(in+1) != '\0'){*/
+       in++;
+     }
+     *out++ = *in++;
+   }
+   *out='\0';
+   return s;
+ }
  /* char *substrchaine(char *out, char *in, char *chain) */
  /* { */
  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
- Line 1410  char *trimbb(char *out, char *in)
+ Line 1874  char *trimbb(char *out, char *in)
  char *substrchaine(char *out, char *in, char *chain)
  {
    /* Substract chain 'chain' from 'in', return and output 'out' */
-   /* in="V1+V1*age+age*age+V2", chain="age*age" */
+   /* in="V1+V1*age+age*age+V2", chain="+age*age" out="V1+V1*age+V2" */
    char *strloc;
-   strcpy (out, in);
+   strcpy (out, in);                   /* out="V1+V1*age+age*age+V2" */
-   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
+   strloc = strstr(out, chain); /* strloc points to out at "+age*age+V2"  */
-   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
+   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out); /* strloc=+age*age+V2 chain="+age*age", out="V1+V1*age+age*age+V2" */
    if(strloc != NULL){
-     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
+     /* will affect out */ /* strloc+strlen(chain)=|+V2 = "V1+V1*age+age*age|+V2" */ /* Will also work in Unicodek */
-     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
+     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1); /* move number of bytes corresponding to the length of "+V2" which is 3, plus one is 4 (including the null)*/
-     /* strcpy (strloc, strloc +strlen(chain));*/
+     /* equivalent to strcpy (strloc, strloc +strlen(chain)) if no overlap; Copies from "+V2" to V1+V1*age+ */
    }
-   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
+   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);  /* strloc=+V2 chain="+age*age", in="V1+V1*age+age*age+V2", out="V1+V1*age+V2" */
    return out;
  }
- Line 1430  char *substrchaine(char *out, char *in,
+ Line 1894  char *substrchaine(char *out, char *in,
  char *cutl(char *blocc, char *alocc, char *in, char occ)
  {
    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
-      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+      and alocc starts after first occurence of char 'occ' : ex cutl(blocc,alocc,"abcdef2ghi2j",'2')
-      gives blocc="abcdef" and alocc="ghi2j".
+      gives alocc="abcdef" and blocc="ghi2j".
       If occ is not found blocc is null and alocc is equal to in. Returns blocc
    */
    char *s, *t;
- Line 1496  int nbocc(char *s, char occ)
+ Line 1960  int nbocc(char *s, char occ)
    return j;
  }
+ int nboccstr(char *textin, char *chain)
+ {
+   /* Counts the number of occurence of "chain"  in string textin */
+   /*  in="+V7*V4+age*V2+age*V3+age*V4"  chain="age" */
+   char *strloc;
+   int i,j=0;
+   i=0;
+   strloc=textin; /* strloc points to "^+V7*V4+age+..." in textin */
+   for(;;) {
+     strloc= strstr(strloc,chain); /* strloc points to first character of chain in textin if found. Example strloc points^ to "+V7*V4+^age" in textin  */
+     if(strloc != NULL){
+       strloc = strloc+strlen(chain); /* strloc points to "+V7*V4+age^" in textin */
+       j++;
+     }else
+       break;
+   }
+   return j;
+ }
  /* void cutv(char *u,char *v, char*t, char occ) */
  /* { */
  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
- Line 1713  char *subdirf(char fileres[])
+ Line 2199  char *subdirf(char fileres[])
  /*************** function subdirf2 ***********/
  char *subdirf2(char fileres[], char *preop)
  {
+   /* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte"
+  Errors in subdirf, 2, 3 while printing tmpout is
+  rewritten within the same printf. Workaround: many printfs */
    /* Caution optionfilefiname is hidden */
    strcpy(tmpout,optionfilefiname);
    strcat(tmpout,"/");
- Line 2084  void linmin(double p[], double xi[], int
+ Line 2572  void linmin(double p[], double xi[], int
  #endif
  #ifdef LINMINORIGINAL
  #else
-         if(fb == fx){ /* Flat function in the direction */
+   if(fb == fx){ /* Flat function in the direction */
-                 xmin=xx;
+     xmin=xx;
      *flat=1;
-         }else{
+   }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) */
- Line 2142  void linmin(double p[], double xi[], int
+ Line 2630  void linmin(double p[], double xi[], int
    free_vector(pcom,1,n);
  }
+ /**** praxis gegen ****/
+ /* This has been tested by Visual C from Microsoft and works */
+ /* meaning tha valgrind could be wrong */
+ /*********************************************************************/
+ /*      f u n c t i o n     p r a x i s                              */
+ /*                                                                   */
+ /* praxis is a general purpose routine for the minimization of a     */
+ /* function in several variables. the algorithm used is a modifi-    */
+ /* cation of conjugate gradient search method by powell. the changes */
+ /* are due to r.p. brent, who gives an algol-w program, which served */
+ /* as a basis for this function.                                     */
+ /*                                                                   */
+ /* references:                                                       */
+ /*     - powell, m.j.d., 1964. an efficient method for finding       */
+ /*       the minimum of a function in several variables without      */
+ /*       calculating derivatives, computer journal, 7, 155-162       */
+ /*     - brent, r.p., 1973. algorithms for minimization without      */
+ /*       derivatives, prentice hall, englewood cliffs.               */
+ /*                                                                   */
+ /*     problems, suggestions or improvements are always wellcome     */
+ /*                       karl gegenfurtner   07/08/87                */
+ /*                                           c - version             */
+ /*********************************************************************/
+ /*                                                                   */
+ /* usage: min = praxis(tol, macheps, h, n, prin, x, func)      */
+ /* macheps has been suppressed because it is replaced by DBL_EPSILON */
+ /* and if it was an argument of praxis (as it is in original brent)  */
+ /* it should be declared external */
+ /* usage: min = praxis(tol, h, n, prin, x, func)      */
+ /* was    min = praxis(fun, x, n);                                   */
+ /*                                                                   */
+ /*  fun        the function to be minimized. fun is called from      */
+ /*             praxis with x and n as arguments                      */
+ /*  x          a double array containing the initial guesses for     */
+ /*             the minimum, which will contain the solution on       */
+ /*             return                                                */
+ /*  n          an integer specifying the number of unknown           */
+ /*             parameters                                            */
+ /*  min        praxis returns the least calculated value of fun      */
+ /*                                                                   */
+ /* some additional global variables control some more aspects of     */
+ /* the inner workings of praxis. setting them is optional, they      */
+ /* are all set to some reasonable default values given below.        */
+ /*                                                                   */
+ /*   prin      controls the printed output from the routine.         */
+ /*             0 -> no output                                        */
+ /*             1 -> print only starting and final values             */
+ /*             2 -> detailed map of the minimization process         */
+ /*             3 -> print also eigenvalues and vectors of the        */
+ /*                  search directions                                */
+ /*             the default value is 1                                */
+ /*  tol        is the tolerance allowed for the precision of the     */
+ /*             solution. praxis returns if the criterion             */
+ /*             2 * ||x[k]-x[k-1]|| <= sqrt(macheps) * ||x[k]|| + tol */
+ /*             is fulfilled more than ktm times.                     */
+ /*             the default value depends on the machine precision    */
+ /*  ktm        see just above. default is 1, and a value of 4 leads  */
+ /*             to a very(!) cautious stopping criterion.             */
+ /*  h0 or step       is a steplength parameter and should be set equal     */
+ /*             to the expected distance from the solution.           */
+ /*             exceptionally small or large values of step lead to   */
+ /*             slower convergence on the first few iterations        */
+ /*             the default value for step is 1.0                     */
+ /*  scbd       is a scaling parameter. 1.0 is the default and        */
+ /*             indicates no scaling. if the scales for the different */
+ /*             parameters are very different, scbd should be set to  */
+ /*             a value of about 10.0.                                */
+ /*  illc       should be set to true (1) if the problem is known to  */
+ /*             be ill-conditioned. the default is false (0). this    */
+ /*             variable is automatically set, when praxis finds      */
+ /*             the problem to be ill-conditioned during iterations.  */
+ /*  maxfun     is the maximum number of calls to fun allowed. praxis */
+ /*             will return after maxfun calls to fun even when the   */
+ /*             minimum is not yet found. the default value of 0      */
+ /*             indicates no limit on the number of calls.            */
+ /*             this return condition is only checked every n         */
+ /*             iterations.                                           */
+ /*                                                                   */
+ /*********************************************************************/
+ #include <math.h>
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <float.h> /* for DBL_EPSILON */
+ /* #include "machine.h" */
+ /* extern void minfit(int n, double eps, double tol, double **ab, double q[]); */
+ /* extern void minfit(int n, double eps, double tol, double ab[N][N], double q[]); */
+ /* control parameters */
+ /* control parameters */
+ #define SQREPSILON 1.0e-19
+ /* #define EPSILON 1.0e-8 */ /* in main */
+ double tol = SQREPSILON,
+        scbd = 1.0,
+        step = 1.0;
+ int    ktm = 1,
+        /* prin = 2, */
+        maxfun = 0,
+        illc = 0;
+ /* some global variables */
+ static int i, j, k, k2, nl, nf, kl, kt;
+ /* static double s; */
+ double sl, dn, dmin,
+        fx, f1, lds, ldt, sf, df,
+        qf1, qd0, qd1, qa, qb, qc,
+        m2, m4, small_windows, vsmall, large,
+        vlarge, ldfac, t2;
+ /* static double d[N], y[N], z[N], */
+ /*        q0[N], q1[N], v[N][N]; */
+ static double *d, *y, *z;
+ static double  *q0, *q1, **v;
+ double *tflin; /* used in flin: return (*fun)(tflin, n); */
+ double *e; /* used in minfit, don't konw how to free memory and thus made global */
+ /* static double s, sl, dn, dmin, */
+ /*        fx, f1, lds, ldt, sf, df, */
+ /*        qf1, qd0, qd1, qa, qb, qc, */
+ /*        m2, m4, small, vsmall, large,  */
+ /*        vlarge, ldfac, t2; */
+ /* static double d[N], y[N], z[N], */
+ /*        q0[N], q1[N], v[N][N]; */
+ /* these will be set by praxis to point to it's arguments */
+ static int prin; /* added */
+ static int n;
+ static double *x;
+ static double (*fun)();
+ /* static double (*fun)(double *x, int n); */
+ /* these will be set by praxis to the global control parameters */
+ /* static double h, macheps, t; */
+ extern double macheps;
+ static double h;
+ static double t;
+ static double
+ drandom()       /* return random no between 0 and 1 */
+ {
+    return (double)(rand()%(8192*2))/(double)(8192*2);
+ }
+ static void sort()              /* d and v in descending order */
+ {
+    int k, i, j;
+    double s;
+    for (i=1; i<=n-1; i++) {
+        k = i; s = d[i];
+        for (j=i+1; j<=n; j++) {
+            if (d[j] > s) {
+               k = j;
+               s = d[j];
+            }
+        }
+        if (k > i) {
+           d[k] = d[i];
+           d[i] = s;
+           for (j=1; j<=n; j++) {
+               s = v[j][i];
+               v[j][i] = v[j][k];
+               v[j][k] = s;
+           }
+        }
+    }
+ }
+ double randbrent ( int *naught )
+ {
+   double ran1, ran3[127], half;
+   int ran2, q, r, i, j;
+   int init=0; /* false */
+   double rr;
+   /* REAL*8 RAN1,RAN3(127),HALF */
+   /*     INTEGER RAN2,Q,R */
+   /*     LOGICAL INIT */
+   /*     DATA INIT/.FALSE./ */
+   /*     IF (INIT) GO TO 3 */
+   if(!init){
+ /*       R = MOD(NAUGHT,8190) + 1 *//* 1804289383 rand () */
+     r = *naught % 8190 + 1;/* printf(" naught r %d %d",*naught,r); */
+     ran2=127;
+     for(i=ran2; i>0; i--){
+ /*       RAN2 = 128 */
+ /*       DO 2 I=1,127 */
+       ran2 = ran2-1;
+ /*          RAN2 = RAN2 - 1 */
+       ran1 = -pow(2.0,55);
+ /*          RAN1 = -2.D0**55 */
+ /*          DO 1 J=1,7 */
+       for(j=1; j<=7;j++){
+ /*             R = MOD(1756*R,8191) */
+         r = (1756*r) % 8191;/* printf(" i=%d (1756*r)%8191=%d",j,r); */
+         q=r/32;
+ /*             Q = R/32 */
+ /* 1           RAN1 = (RAN1 + Q)*(1.0D0/256) */
+         ran1 =(ran1+q)*(1.0/256);
+       }
+ /* 2        RAN3(RAN2) = RAN1 */
+       ran3[ran2] = ran1; /* printf(" ran2=%d ran1=%.7g \n",ran2,ran1); */
+     }
+ /*       INIT = .TRUE. */
+     init=1;
+ /* 3     IF (RAN2.EQ.1) RAN2 = 128 */
+   }
+   if(ran2 == 0) ran2 = 126;
+   else ran2 = ran2 -1;
+   /* RAN2 = RAN2 - 1 */
+   /* RAN1 = RAN1 + RAN3(RAN2) */
+   ran1 = ran1 + ran3[ran2];/* printf("BIS ran2=%d ran1=%.7g \n",ran2,ran1);  */
+   half= 0.5;
+   /* HALF = .5D0 */
+   /* IF (RAN1.GE.0.D0) HALF = -HALF */
+   if(ran1 >= 0.) half =-half;
+   ran1 = ran1 +half;
+   ran3[ran2] = ran1;
+   rr= ran1+0.5;
+   /* RAN1 = RAN1 + HALF */
+   /*   RAN3(RAN2) = RAN1 */
+   /*   RANDOM = RAN1 + .5D0 */
+ /*   r = ( ( double ) ( *seed ) ) * 4.656612875E-10; */
+   return rr;
+ }
+ static void matprint(char *s, double **v, int m, int n)
+ /* char *s; */
+ /* double v[N][N]; */
+ {
+ #define INCX 8
+   int i;
+   int i2hi;
+   int ihi;
+   int ilo;
+   int i2lo;
+   int jlo=1;
+   int j;
+   int j2hi;
+   int jhi;
+   int j2lo;
+   ilo=1;
+   ihi=n;
+   jlo=1;
+   jhi=n;
+   printf ("\n" );
+   printf ("%s\n", s );
+   for ( j2lo = jlo; j2lo <= jhi; j2lo = j2lo + INCX )
+   {
+     j2hi = j2lo + INCX - 1;
+     if ( n < j2hi )
+     {
+       j2hi = n;
+     }
+     if ( jhi < j2hi )
+     {
+       j2hi = jhi;
+     }
+     /* fprintf ( ficlog, "\n" ); */
+     printf ("\n" );
+ /*
+   For each column J in the current range...
+   Write the header.
+ */
+     /* fprintf ( ficlog, "  Col:  "); */
+     printf ("Col:");
+     for ( j = j2lo; j <= j2hi; j++ )
+     {
+       /* fprintf ( ficlog, "  %7d     ", j - 1 ); */
+       /* printf (" %9d      ", j - 1 ); */
+       printf (" %9d      ", j );
+     }
+     /* fprintf ( ficlog, "\n" ); */
+     /* fprintf ( ficlog, "  Row\n" ); */
+     /* fprintf ( ficlog, "\n" ); */
+     printf ("\n" );
+     printf ("  Row\n" );
+     printf ("\n" );
+ /*
+   Determine the range of the rows in this strip.
+ */
+     if ( 1 < ilo ){
+       i2lo = ilo;
+     }else{
+       i2lo = 1;
+     }
+     if ( m < ihi ){
+       i2hi = m;
+     }else{
+       i2hi = ihi;
+     }
+     for ( i = i2lo; i <= i2hi; i++ ){
+ /*
+   Print out (up to) 5 entries in row I, that lie in the current strip.
+ */
+       /* fprintf ( ficlog, "%5d:", i - 1 ); */
+       /* printf ("%5d:", i - 1 ); */
+       printf ("%5d:", i );
+       for ( j = j2lo; j <= j2hi; j++ )
+       {
+         /* fprintf ( ficlog, "  %14g", a[i-1+(j-1)*m] ); */
+         /* printf ("%14.7g  ", a[i-1+(j-1)*m] ); */
+            /* printf("%14.7f  ", v[i-1][j-1]); */
+            printf("%14.7f  ", v[i][j]);
+         /* fprintf ( stdout, "  %14g", a[i-1+(j-1)*m] ); */
+       }
+       /* fprintf ( ficlog, "\n" ); */
+       printf ("\n" );
+     }
+   }
+    /* printf("%s\n", s); */
+    /* for (k=0; k<n; k++) { */
+    /*     for (i=0; i<n; i++) { */
+    /*         /\* printf("%20.10e ", v[k][i]); *\/ */
+    /*     } */
+    /*     printf("\n"); */
+    /* } */
+ #undef INCX
+ }
+ void vecprint(char *s, double *x, int n)
+ /* char *s; */
+ /* double x[N]; */
+ {
+    int i=0;
+    printf(" %s", s);
+    /* for (i=0; i<n; i++) */
+    for (i=1; i<=n; i++)
+      printf ("  %14.7g",  x[i] );
+      /* printf("  %8d: %14g\n", i, x[i]); */
+    printf ("\n" );
+ }
+ static void print()             /* print a line of traces */
+ {
+    printf("\n");
+    /* printf("... chi square reduced to ... %20.10e\n", fx); */
+    /* printf("... after %u function calls ...\n", nf); */
+    /* printf("... including %u linear searches ...\n", nl); */
+    printf("%10d    %10d%14.7g",nl, nf, fx);
+    vecprint("... current values of x ...", x, n);
+ }
+ /* static void print2(int n, double *x, int prin, double fx, int nf, int nl) */ /* print a line of traces */
+ static void print2() /* print a line of traces */
+ {
+   int i; double fmin=0.;
+    /* printf("\n"); */
+    /* printf("... chi square reduced to ... %20.10e\n", fx); */
+    /* printf("... after %u function calls ...\n", nf); */
+    /* printf("... including %u linear searches ...\n", nl); */
+    /* printf("%10d    %10d%14.7g",nl, nf, fx); */
+   printf ( "\n" );
+   printf ( "  Linear searches      %d", nl );
+   /* printf ( "  Linear searches      %d\n", nl ); */
+   /* printf ( "  Function evaluations %d\n", nf ); */
+   /* printf ( "  Function value FX = %g\n", fx ); */
+   printf ( "  Function evaluations %d", nf );
+   printf ( "  Function value FX = %.12lf\n", fx );
+ #ifdef DEBUGPRAX
+    printf("n=%d prin=%d\n",n,prin);
+ #endif
+    if(fx <= fmin) printf(" UNDEFINED "); else  printf("%14.7g",log(fx-fmin));
+    if ( n <= 4 || 2 < prin )
+    {
+      /* for(i=1;i<=n;i++)printf("%14.7g",x[i-1]); */
+      for(i=1;i<=n;i++)printf("%14.7g",x[i]);
+      /* r8vec_print ( n, x, "  X:" ); */
+    }
+    printf("\n");
+  }
+ /* #ifdef MSDOS */
+ /* static double tflin[N]; */
+ /* #endif */
+ static double flin(double l, int j)
+ /* double l; */
+ {
+    int i;
+    /* #ifndef MSDOS */
+    /*    double tflin[N]; */
+    /* #endif    */
+    /* double *tflin; */ /* Be careful to put tflin on a vector n */
+    /* j is used from 0 to n-1 and can be -1 for parabolic search */
+    /* if (j != -1) {            /\* linear search *\/ */
+    if (j > 0) {         /* linear search */
+      /* for (i=0; i<n; i++){ */
+      for (i=1; i<=n; i++){
+           tflin[i] = x[i] + l *v[i][j];
+ #ifdef DEBUGPRAX
+           /* printf("     flin i=%14d t=%14.7f x=%14.7f l=%14.7f v[%d,%d]=%14.7f nf=%14d\n",i+1, tflin[i],x[i],l,i,j,v[i][j],nf); */
+           printf("     flin i=%14d t=%14.7f x=%14.7f l=%14.7f v[%d,%d]=%14.7f nf=%14d\n",i, tflin[i],x[i],l,i,j,v[i][j],nf);
+ #endif
+      }
+    }
+    else {                       /* search along parabolic space curve */
+       qa = l*(l-qd1)/(qd0*(qd0+qd1));
+       qb = (l+qd0)*(qd1-l)/(qd0*qd1);
+       qc = l*(l+qd0)/(qd1*(qd0+qd1));
+ #ifdef DEBUGPRAX
+       printf("     search along a parabolic space curve. j=%14d nf=%14d l=%14.7f qd0=%14.7f qd1=%14.7f\n",j,nf,l,qd0,qd1);
+ #endif
+       /* for (i=0; i<n; i++){ */
+       for (i=1; i<=n; i++){
+           tflin[i] = qa*q0[i]+qb*x[i]+qc*q1[i];
+ #ifdef DEBUGPRAX
+           /* printf("      parabole i=%14d t(i)=%14.7f q0=%14.7f x=%14.7f q1=%14.7f\n",i+1,tflin[i],q0[i],x[i],q1[i]); */
+           printf("      parabole i=%14d t(i)=%14.7e q0=%14.7e x=%14.7e q1=%14.7e\n",i,tflin[i],q0[i],x[i],q1[i]);
+ #endif
+       }
+    }
+    nf++;
+ #ifdef NR_SHIFT
+       return (*fun)((tflin-1), n);
+ #else
+      /* return (*fun)(tflin, n);*/
+       return (*fun)(tflin);
+ #endif
+ }
+ void minny(int j, int nits, double *d2, double *x1, double f1, int fk)
+ /* double *d2, *x1, f1; */
+ {
+ /* here j is from 0 to n-1 and can be -1 for parabolic search  */
+   /*      MINIMIZES F FROM X IN THE DIRECTION V(*,J) */
+           /*      UNLESS J<1, WHEN A QUADRATIC SEARCH IS DONE */
+           /*      IN THE PLANE DEFINED BY Q0, Q1 AND X. */
+           /*      D2 AN APPROXIMATION TO HALF F'' (OR ZERO), */
+           /*      X1 AN ESTIMATE OF DISTANCE TO MINIMUM, */
+           /*      RETURNED AS THE DISTANCE FOUND. */
+           /*       IF FK = TRUE THEN F1 IS FLIN(X1), OTHERWISE */
+           /*       X1 AND F1 ARE IGNORED ON ENTRY UNLESS FINAL */
+           /*       FX > F1. NITS CONTROLS THE NUMBER OF TIMES */
+           /*       AN ATTEMPT IS MADE TO HALVE THE INTERVAL. */
+           /* SIDE EFFECTS: USES AND ALTERS X, FX, NF, NL. */
+           /*       IF J < 1 USES VARIABLES Q... . */
+           /*       USES H, N, T, M2, M4, LDT, DMIN, MACHEPS; */
+    int k, i, dz;
+    double x2, xm, f0, f2, fm, d1, t2, sf1, sx1;
+    double s;
+    double macheps;
+    macheps=pow(16.0,-13.0);
+    sf1 = f1; sx1 = *x1;
+    k = 0; xm = 0.0; fm = f0 = fx; dz = *d2 < macheps;
+    /* h=1.0;*/ /* To be revised */
+ #ifdef DEBUGPRAX
+    /* printf("min macheps=%14g h=%14g step=%14g t=%14g fx=%14g\n",macheps,h, step,t, fx);  */
+    /* Where is fx coming from */
+    printf("   min macheps=%14g h=%14g  t=%14g fx=%.9lf dirj=%d\n",macheps, h, t, fx, j);
+    matprint("  min vectors:",v,n,n);
+ #endif
+    /* find step size */
+    s = 0.;
+    /* for (i=0; i<n; i++) s += x[i]*x[i]; */
+    for (i=1; i<=n; i++) s += x[i]*x[i];
+    s = sqrt(s);
+    if (dz)
+       t2 = m4*sqrt(fabs(fx)/dmin + s*ldt) + m2*ldt;
+    else
+       t2 = m4*sqrt(fabs(fx)/(*d2) + s*ldt) + m2*ldt;
+    s = s*m4 + t;
+    if (dz && t2 > s) t2 = s;
+    if (t2 < small_windows) t2 = small_windows;
+    if (t2 > 0.01*h) t2 = 0.01 * h;
+    if (fk && f1 <= fm) {
+       xm = *x1;
+       fm = f1;
+    }
+ #ifdef DEBUGPRAX
+    printf("   additional flin X1=%14.7f t2=%14.7f *f1=%14.7f fm=%14.7f fk=%d\n",*x1,t2,f1,fm,fk);
+ #endif
+    if (!fk || fabs(*x1) < t2) {
+      *x1 = (*x1 >= 0 ? t2 : -t2);
+       /* *x1 = (*x1 > 0 ? t2 : -t2); */ /* kind of error */
+ #ifdef DEBUGPRAX
+      printf("    additional flin X1=%16.10e dirj=%d fk=%d\n",*x1, j, fk);
+ #endif
+       f1 = flin(*x1, j);
+ #ifdef DEBUGPRAX
+     printf("    after flin f1=%18.12e dirj=%d fk=%d\n",f1, j,fk);
+ #endif
+    }
+    if (f1 <= fm) {
+       xm = *x1;
+       fm = f1;
+    }
+ L0: /*L0 loop or next */
+ /*
+   Evaluate FLIN at another point and estimate the second derivative.
+ */
+    if (dz) {
+       x2 = (f0 < f1 ? -(*x1) : 2*(*x1));
+ #ifdef DEBUGPRAX
+       printf("     additional second flin x2=%14.8e x1=%14.8e f0=%14.8e f1=%18.12e dirj=%d\n",x2,*x1,f0,f1,j);
+ #endif
+       f2 = flin(x2, j);
+ #ifdef DEBUGPRAX
+       printf("     additional second flin x2=%16.10e x1=%16.10e f1=%18.12e f0=%18.10e f2=%18.10e fm=%18.10e\n",x2, *x1, f1,f0,f2,fm);
+ #endif
+       if (f2 <= fm) {
+          xm = x2;
+          fm = f2;
+       }
+       /* d2 is the curvature or double difference f1 doesn't seem to be accurately computed */
+       *d2 = (x2*(f1-f0) - (*x1)*(f2-f0))/((*x1)*x2*((*x1)-x2));
+ #ifdef DEBUGPRAX
+       double d11,d12;
+       d11=(f1-f0)/(*x1);d12=(f2-f0)/x2;
+       printf(" d11=%18.12e d12=%18.12e d11-d12=%18.12e x1-x2=%18.12e (d11-d12)/(x2-(*x1))=%18.12e\n", d11 ,d12, d11-d12, x2-(*x1), (d11-d12)/(x2-(*x1)));
+       printf(" original computing f1=%18.12e *d2=%16.10e f0=%18.12e f1-f0=%16.10e f2-f0=%16.10e\n",f1,*d2,f0,f1-f0, f2-f0);
+       double ff1=7.783920622852e+04;
+       double f1mf0=9.0344736236e-05;
+       *d2 = (f1mf0)/ (*x1)/((*x1)-x2) - (f2-f0)/x2/((*x1)-x2);
+       /* *d2 = (ff1-f0)/ (*x1)/((*x1)-x2) - (f2-f0)/x2/((*x1)-x2); */
+       printf(" simpliff computing *d2=%16.10e f1mf0=%18.12e,f1=f0+f1mf0=%18.12e\n",*d2,f1mf0,f0+f1mf0);
+       *d2 = ((f1-f0)/ (*x1) - (f2-f0)/x2)/((*x1)-x2);
+       printf(" overlifi computing *d2=%16.10e\n",*d2);
+ #endif
+       *d2 = ((f1-f0)/ (*x1) - (f2-f0)/x2)/((*x1)-x2);
+    }
+ #ifdef DEBUGPRAX
+       printf("    additional second flin xm=%14.8e fm=%14.8e *d2=%14.8e\n",xm, fm,*d2);
+ #endif
+    /*
+      Estimate the first derivative at 0.
+    */
+    d1 = (f1-f0)/(*x1) - *x1**d2; dz = 1;
+    /*
+       Predict the minimum.
+     */
+    if (*d2 <= small_windows) {
+      x2 = (d1 < 0 ? h : -h);
+    }
+    else {
+       x2 = - 0.5*d1/(*d2);
+    }
+ #ifdef DEBUGPRAX
+     printf("   AT d1=%14.8e d2=%14.8e small=%14.8e dz=%d x1=%14.8e x2=%14.8e\n",d1,*d2,small_windows,dz,*x1,x2);
+ #endif
+     if (fabs(x2) > h)
+       x2 = (x2 > 0 ? h : -h);
+ L1:  /* L1 or try loop */
+ #ifdef DEBUGPRAX
+     printf("   AT predicted minimum flin x2=%14.8e x1=%14.8e K=%14d NITS=%14d dirj=%d\n",x2,*x1,k,nits,j);
+ #endif
+    f2 = flin(x2, j); /* x[i]+x2*v[i][j] */
+ #ifdef DEBUGPRAX
+    printf("   after flin f0=%14.8e f1=%14.8e f2=%14.8e fm=%14.8e\n",f0,f1,f2, fm);
+ #endif
+    if ((k < nits) && (f2 > f0)) {
+ #ifdef DEBUGPRAX
+      printf("  NO SUCCESS SO TRY AGAIN;\n");
+ #endif
+      k++;
+      if ((f0 < f1) && (*x1*x2 > 0.0))
+        goto L0; /* or next */
+      x2 *= 0.5;
+      goto L1;
+    }
+    nl++;
+ #ifdef DEBUGPRAX
+    printf(" bebeBE end of min x1=%14.8e x2=%14.8e f1=%14.8e f2=%14.8e f0=%14.8e fm=%14.8e d2=%14.8e\n",*x1, x2, f1, f2, f0, fm, *d2);
+ #endif
+    if (f2 > fm) x2 = xm; else fm = f2;
+    if (fabs(x2*(x2-*x1)) > small_windows) {
+       *d2 = (x2*(f1-f0) - *x1*(fm-f0))/(*x1*x2*(*x1-x2));
+    }
+    else {
+       if (k > 0) *d2 = 0;
+    }
+ #ifdef DEBUGPRAX
+    printf(" bebe end of min x1=%14.8e fx=%14.8e d2=%14.8e\n",*x1, fx, *d2);
+ #endif
+    if (*d2 <= small_windows) *d2 = small_windows;
+    *x1 = x2; fx = fm;
+    if (sf1 < fx) {
+       fx = sf1;
+       *x1 = sx1;
+    }
+   /*
+     Update X for linear search.
+   */
+ #ifdef DEBUGPRAX
+    printf("  end of min x1=%14.8e fx=%14.8e d2=%14.8e\n",*x1, fx, *d2);
+ #endif
+    /* if (j != -1) */
+    /*    for (i=0; i<n; i++) */
+    /*        x[i] += (*x1)*v[i][j]; */
+    if (j > 0)
+       for (i=1; i<=n; i++)
+           x[i] += (*x1)*v[i][j];
+ }
+ void quad()     /* look for a minimum along the curve q0, q1, q2        */
+ {
+    int i;
+    double l, s;
+    s = fx; fx = qf1; qf1 = s; qd1 = 0.0;
+    /* for (i=0; i<n; i++) { */
+    for (i=1; i<=n; i++) {
+        s = x[i]; l = q1[i]; x[i] = l; q1[i] = s;
+        qd1 = qd1 + (s-l)*(s-l);
+    }
+    s = 0.0; qd1 = sqrt(qd1); l = qd1;
+ #ifdef DEBUGPRAX
+   printf("  QUAD after sqrt qd1=%14.8e \n",qd1);
+ #endif
+    if (qd0>0.0 && qd1>0.0 &&nl>=3*n*n) {
+ #ifdef DEBUGPRAX
+      printf(" QUAD before min value=%14.8e \n",qf1);
+ #endif
+       /* min(-1, 2, &s, &l, qf1, 1); */
+       minny(0, 2, &s, &l, qf1, 1);
+       qa = l*(l-qd1)/(qd0*(qd0+qd1));
+       qb = (l+qd0)*(qd1-l)/(qd0*qd1);
+       qc = l*(l+qd0)/(qd1*(qd0+qd1));
+    }
+    else {
+       fx = qf1; qa = qb = 0.0; qc = 1.0;
+    }
+ #ifdef DEBUGPRAX
+   printf("after eventual min qd0=%14.8e qd1=%14.8e nl=%d\n",qd0, qd1,nl);
+ #endif
+    qd0 = qd1;
+    /* for (i=0; i<n; i++) { */
+    for (i=1; i<=n; i++) {
+        s = q0[i]; q0[i] = x[i];
+        x[i] = qa*s + qb*x[i] + qc*q1[i];
+    }
+ #ifdef DEBUGQUAD
+    vecprint ( " X after QUAD:" , x, n );
+ #endif
+ }
+ /* void minfit(int n, double eps, double tol, double ab[N][N], double q[]) */
+ void minfit(int n, double eps, double tol, double **ab, double q[])
+ /* int n; */
+ /* double eps, tol, ab[N][N], q[N]; */
+ {
+    int l, kt, l2, i, j, k;
+    double c, f, g, h, s, x, y, z;
+    /* double eps; */
+ /* #ifndef MSDOS */
+ /*    double e[N];              /\* plenty of stack on a vax *\/ */
+ /* #endif */
+    /* double *e; */
+    /* e=vector(0,n-1); /\* should be freed somewhere but gotos *\/ */
+    /* householder's reduction to bidiagonal form */
+    if(n==1){
+      /* q[1-1]=ab[1-1][1-1]; */
+      /* ab[1-1][1-1]=1.0; */
+      q[1]=ab[1][1];
+      ab[1][1]=1.0;
+      return; /* added from hardt */
+    }
+    /* eps=macheps; */ /* added */
+    x = g = 0.0;
+ #ifdef DEBUGPRAX
+    matprint (" HOUSE holder:", ab, n, n);
+ #endif
+    /* for (i=0; i<n; i++) {  /\* FOR I := 1 UNTIL N DO *\/ */
+    for (i=1; i<=n; i++) {  /* FOR I := 1 UNTIL N DO */
+      e[i] = g; s = 0.0; l = i+1;
+      /* for (j=i; j<n; j++)  /\* FOR J := I UNTIL N DO S := S*AB(J,I)**2; *\/ /\* not correct *\/ */
+      for (j=i; j<=n; j++)  /* FOR J := I UNTIL N DO S := S*AB(J,I)**2; */ /* not correct */
+        s += ab[j][i] * ab[j][i];
+ #ifdef DEBUGPRAXFIN
+      printf("i=%d s=%d %.7g tol=%.7g",i,s,tol);
+ #endif
+      if (s < tol) {
+        g = 0.0;
+      }
+      else {
+        /* f = ab[i][i]; */
+        f = ab[i][i];
+        if (f < 0.0)
+          g = sqrt(s);
+        else
+          g = -sqrt(s);
+        /* h = f*g - s; ab[i][i] = f - g; */
+        h = f*g - s; ab[i][i] = f - g;
+        /* for (j=l; j<n; j++) { */ /* FOR J := L UNTIL N DO */ /* wrong */
+        for (j=l; j<=n; j++) {
+          f = 0.0;
+          /* for (k=i; k<n; k++) /\* FOR K := I UNTIL N DO *\/ /\* wrong *\/ */
+          for (k=i; k<=n; k++) /* FOR K := I UNTIL N DO */
+            /* f += ab[k][i] * ab[k][j]; */
+            f += ab[k][i] * ab[k][j];
+          f /= h;
+          for (k=i; k<=n; k++) /* FOR K := I UNTIL N DO */
+            /* for (k=i; k<n; k++)/\* FOR K := I UNTIL N DO *\/ /\* wrong *\/ */
+            ab[k][j] += f * ab[k][i];
+          /* ab[k][j] += f * ab[k][i]; */
+ #ifdef DEBUGPRAX
+          printf("Holder J=%d F=%.7g",j,f);
+ #endif
+        }
+      } /* end s */
+      /* q[i] = g; s = 0.0; */
+      q[i] = g; s = 0.0;
+ #ifdef DEBUGPRAX
+      printf(" I Q=%d %.7g",i,q[i]);
+ #endif
+      /* if (i < n) */
+      /* if (i <= n)  /\* I is always lower or equal to n wasn't in golub reinsch*\/ */
+      /* for (j=l; j<n; j++) */
+      for (j=l; j<=n; j++)
+        s += ab[i][j] * ab[i][j];
+      /* s += ab[i][j] * ab[i][j]; */
+      if (s < tol) {
+        g = 0.0;
+      }
+      else {
+        if(i<n)
+          /* f = ab[i][i+1]; */ /* Brent golub overflow */
+          f = ab[i][i+1];
+        if (f < 0.0)
+          g = sqrt(s);
+        else
+          g = - sqrt(s);
+        h = f*g - s;
+        /* h = f*g - s; ab[i][i+1] = f - g; */ /* Overflow for i=n Error in Golub too but not Burkardt*/
+        /* for (j=l; j<n; j++) */
+        /*     e[j] = ab[i][j]/h; */
+        if(i<n){
+          ab[i][i+1] = f - g;
+          for (j=l; j<=n; j++)
+            e[j] = ab[i][j]/h;
+          /* for (j=l; j<n; j++) { */
+          for (j=l; j<=n; j++) {
+            s = 0.0;
+            /* for (k=l; k<n; k++) s += ab[j][k]*ab[i][k]; */
+            for (k=l; k<=n; k++) s += ab[j][k]*ab[i][k];
+            /* for (k=l; k<n; k++) ab[j][k] += s * e[k]; */
+            for (k=l; k<=n; k++) ab[j][k] += s * e[k];
+          } /* END J */
+        } /* END i <n */
+      } /* end s */
+        /* y = fabs(q[i]) + fabs(e[i]); */
+      y = fabs(q[i]) + fabs(e[i]);
+      if (y > x) x = y;
+ #ifdef DEBUGPRAX
+      printf(" I Y=%d %.7g",i,y);
+ #endif
+ #ifdef DEBUGPRAX
+      printf(" i=%d e(i) %.7g",i,e[i]);
+ #endif
+    } /* end i */
+    /*
+      Accumulation of right hand transformations */
+    /* for (i=n-1; i >= 0; i--) { */ /* FOR I := N STEP -1 UNTIL 1 DO */
+    /* We should avoid the overflow in Golub */
+    /* ab[n-1][n-1] = 1.0; */
+    /* g = e[n-1]; */
+    ab[n][n] = 1.0;
+    g = e[n];
+    l = n;
+    /* for (i=n; i >= 1; i--) { */
+    for (i=n-1; i >= 1; i--) { /* n-1 loops, different from brent and golub*/
+      if (g != 0.0) {
+        /* h = ab[i-1][i]*g; */
+        h = ab[i][i+1]*g;
+        for (j=l; j<=n; j++) ab[j][i] = ab[i][j] / h;
+        for (j=l; j<=n; j++) {
+          /* h = ab[i][i+1]*g; */
+          /* for (j=l; j<n; j++) ab[j][i] = ab[i][j] / h; */
+          /* for (j=l; j<n; j++) { */
+          s = 0.0;
+          /* for (k=l; k<n; k++) s += ab[i][k] * ab[k][j]; */
+          /* for (k=l; k<n; k++) ab[k][j] += s * ab[k][i]; */
+          for (k=l; k<=n; k++) s += ab[i][k] * ab[k][j];
+          for (k=l; k<=n; k++) ab[k][j] += s * ab[k][i];
+        }/* END J */
+      }/* END G */
+      /* for (j=l; j<n; j++) */
+      /*     ab[i][j] = ab[j][i] = 0.0; */
+      /* ab[i][i] = 1.0; g = e[i]; l = i; */
+      for (j=l; j<=n; j++)
+        ab[i][j] = ab[j][i] = 0.0;
+      ab[i][i] = 1.0; g = e[i]; l = i;
+    }/* END I */
+ #ifdef DEBUGPRAX
+    matprint (" HOUSE accumulation:",ab,n, n );
+ #endif
+    /* diagonalization to bidiagonal form */
+    eps *= x;
+    /* for (k=n-1; k>= 0; k--) { */
+    for (k=n; k>= 1; k--) {
+      kt = 0;
+ TestFsplitting:
+ #ifdef DEBUGPRAX
+      printf(" TestFsplitting: k=%d kt=%d\n",k,kt);
+      /* for(i=1;i<=n;i++)printf(" e(%d)=%.14f",i,e[i]);printf("\n"); */
+ #endif
+      kt = kt+1;
+ /* TestFsplitting: */
+      /* if (++kt > 30) { */
+      if (kt > 30) {
+        e[k] = 0.0;
+        fprintf(stderr, "\n+++ MINFIT - Fatal error\n");
+        fprintf ( stderr, "  The QR algorithm failed to converge.\n" );
+      }
+      /* for (l2=k; l2>=0; l2--) { */
+      for (l2=k; l2>=1; l2--) {
+        l = l2;
+ #ifdef DEBUGPRAX
+        printf(" l e(l)< eps %d %.7g %.7g ",l,e[l], eps);
+ #endif
+        /* if (fabs(e[l]) <= eps) */
+        if (fabs(e[l]) <= eps)
+          goto TestFconvergence;
+        /* if (fabs(q[l-1]) <= eps)*/ /* missing if ( 1 < l ){ *//* printf(" q(l-1)< eps %d %.7g %.7g ",l-1,q[l-2], eps); */
+        if (fabs(q[l-1]) <= eps)
+          break; /* goto Cancellation; */
+      }
+    Cancellation:
+ #ifdef DEBUGPRAX
+      printf(" Cancellation:\n");
+ #endif
+      c = 0.0; s = 1.0;
+      for (i=l; i<=k; i++) {
+        f = s * e[i]; e[i] *= c;
+        /* f = s * e[i]; e[i] *= c; */
+        if (fabs(f) <= eps)
+          goto TestFconvergence;
+        /* g = q[i]; */
+        g = q[i];
+        if (fabs(f) < fabs(g)) {
+          double fg = f/g;
+          h = fabs(g)*sqrt(1.0+fg*fg);
+        }
+        else {
+          double gf = g/f;
+          h = (f!=0.0 ? fabs(f)*sqrt(1.0+gf*gf) : 0.0);
+        }
+        /*    COMMENT: THE ABOVE REPLACES Q(I):=H:=LONGSQRT(G*G+F*F) */
+        /* WHICH MAY GIVE INCORRECT RESULTS IF THE */
+        /* SQUARES UNDERFLOW OR IF F = G = 0; */
+        /* q[i] = h; */
+        q[i] = h;
+        if (h == 0.0) { h = 1.0; g = 1.0; }
+        c = g/h; s = -f/h;
+      }
+ TestFconvergence:
+  #ifdef DEBUGPRAX
+      printf(" TestFconvergence: l=%d k=%d\n",l,k);
+ #endif
+      /* z = q[k]; */
+      z = q[k];
+      if (l == k)
+        goto Convergence;
+      /* shift from bottom 2x2 minor */
+      /* x = q[l]; y = q[k-l]; g = e[k-1]; h = e[k]; */ /* Error */
+      x = q[l]; y = q[k-1]; g = e[k-1]; h = e[k];
+      f = ((y-z)*(y+z) + (g-h)*(g+h)) / (2.0*h*y);
+      g = sqrt(f*f+1.0);
+      if (f <= 0.0)
+        f = ((x-z)*(x+z) + h*(y/(f-g)-h))/x;
+      else
+        f = ((x-z)*(x+z) + h*(y/(f+g)-h))/x;
+      /* next qr transformation */
+      s = c = 1.0;
+      for (i=l+1; i<=k; i++) {
+ #ifdef DEBUGPRAXQR
+        printf(" Before Mid TestFconvergence: l+1=%d i=%d k=%d h=%.6e e(i)=%14.8f e(i-1)=%14.8f\n",l+1,i,k, h, e[i],e[i-1]);
+ #endif
+        /* g = e[i]; y = q[i]; h = s*g; g *= c; */
+        g = e[i]; y = q[i]; h = s*g; g *= c;
+        if (fabs(f) < fabs(h)) {
+          double fh = f/h;
+          z = fabs(h) * sqrt(1.0 + fh*fh);
+        }
+        else {
+          double hf = h/f;
+          z = (f!=0.0 ? fabs(f)*sqrt(1.0+hf*hf) : 0.0);
+        }
+        /* e[i-1] = z; */
+        e[i-1] = z;
+ #ifdef DEBUGPRAXQR
+        printf(" Mid TestFconvergence: l+1=%d i=%d k=%d h=%.6e e(i)=%14.8f e(i-1)=%14.8f\n",l+1,i,k, h, e[i],e[i-1]);
+ #endif
+        if (z == 0.0)
+          f = z = 1.0;
+        c = f/z; s = h/z;
+        f = x*c + g*s; g = - x*s + g*c; h = y*s;
+        y *= c;
+        /* for (j=0; j<n; j++) { */
+        /*     x = ab[j][i-1]; z = ab[j][i]; */
+        /*     ab[j][i-1] = x*c + z*s; */
+        /*     ab[j][i] = - x*s + z*c; */
+        /* } */
+        for (j=1; j<=n; j++) {
+          x = ab[j][i-1]; z = ab[j][i];
+          ab[j][i-1] = x*c + z*s;
+          ab[j][i] = - x*s + z*c;
+        }
+        if (fabs(f) < fabs(h)) {
+          double fh = f/h;
+          z = fabs(h) * sqrt(1.0 + fh*fh);
+        }
+        else {
+          double hf = h/f;
+          z = (f!=0.0 ? fabs(f)*sqrt(1.0+hf*hf) : 0.0);
+        }
+ #ifdef DEBUGPRAXQR
+        printf(" qr transformation z f h=%.7g %.7g %.7g i=%d k=%d\n",z,f,h, i, k);
+ #endif
+        q[i-1] = z;
+        if (z == 0.0)
+          z = f = 1.0;
+        c = f/z; s = h/z;
+        f = c*g + s*y;  /* f can be very small */
+        x = - s*g + c*y;
+      }
+      /* e[l] = 0.0; e[k] = f; q[k] = x; */
+      e[l] = 0.0; e[k] = f; q[k] = x;
+ #ifdef DEBUGPRAXQR
+      printf(" aftermid loop l=%d k=%d e(l)=%7g e(k)=%.7g q(k)=%.7g x=%.7g\n",l,k,e[l],e[k],q[k],x);
+ #endif
+      goto TestFsplitting;
+    Convergence:
+ #ifdef DEBUGPRAX
+      printf(" Convergence:\n");
+ #endif
+      if (z < 0.0) {
+        /* q[k] = - z; */
+        /* for (j=0; j<n; j++) ab[j][k] = - ab[j][k]; */
+        q[k] = - z;
+        for (j=1; j<=n; j++) ab[j][k] = - ab[j][k];
+      }/* END Z */
+    }/* END K */
+ } /* END MINFIT */
+ double praxis(double tol, double macheps, double h0, int _n, int _prin, double *_x, double (*_fun)(double *_x))
+ /* double praxis(double tol, double macheps, double h0, int _n, int _prin, double *_x, double (*_fun)(double *_x, int _n)) */
+ /* double praxis(double (*_fun)(), double _x[], int _n) */
+ /* double (*_fun)(); */
+ /* double _x[N]; */
+ /* double (*_fun)(); */
+ /* double _x[N]; */
+ {
+    /* init global extern variables and parameters */
+    /* double *d, *y, *z, */
+    /*   *q0, *q1, **v; */
+    /* double *tflin; /\* used in flin: return (*fun)(tflin, n); *\/ */
+    /* double *e; /\* used in minfit, don't konw how to free memory and thus made global *\/ */
+   int seed; /* added */
+   int biter=0;
+   double r;
+   double randbrent( int (*));
+   double s, sf;
+    h = h0; /* step; */
+    t = tol;
+    scbd = 1.0;
+    illc = 0;
+    ktm = 1;
+    macheps = DBL_EPSILON;
+    /* prin=4; */
+ #ifdef DEBUGPRAX
+    printf("Praxis macheps=%14g h=%14g step=%14g tol=%14g\n",macheps,h, h0,tol);
+ #endif
+    n = _n;
+    x = _x;
+    prin = _prin;
+    fun = _fun;
+    d=vector(1, n);
+    y=vector(1, n);
+    z=vector(1, n);
+    q0=vector(1, n);
+    q1=vector(1, n);
+    e=vector(1, n);
+    tflin=vector(1, n);
+    v=matrix(1, n, 1, n);
+    for(i=1;i<=n;i++){d[i]=y[i]=z[i]=q0[0]=e[i]=tflin[i]=0.;}
+    small_windows = (macheps) * (macheps); vsmall = small_windows*small_windows;
+    large = 1.0/small_windows; vlarge = 1.0/vsmall;
+    m2 = sqrt(macheps); m4 = sqrt(m2);
+    seed = 123456789; /* added */
+    ldfac = (illc ? 0.1 : 0.01);
+    for(i=1;i<=n;i++) z[i]=0.; /* Was missing in Gegenfurtner as well as Brent's algol or fortran  */
+    nl = kt = 0; nf = 1;
+ #ifdef NR_SHIFT
+    fx = (*fun)((x-1), n);
+ #else
+    fx = (*fun)(x);
+ #endif
+    qf1 = fx;
+    t2 = small_windows + fabs(t); t = t2; dmin = small_windows;
+ #ifdef DEBUGPRAX
+    printf("praxis2 macheps=%14g h=%14g step=%14g small=%14g t=%14g\n",macheps,h, h0,small_windows, t);
+ #endif
+    if (h < 100.0*t) h = 100.0*t;
+ #ifdef DEBUGPRAX
+    printf("praxis3 macheps=%14g h=%14g step=%14g small=%14g t=%14g\n",macheps,h, h0,small_windows, t);
+ #endif
+    ldt = h;
+    /* for (i=0; i<n; i++) for (j=0; j<n; j++) */
+    for (i=1; i<=n; i++) for (j=1; j<=n; j++)
+        v[i][j] = (i == j ? 1.0 : 0.0);
+    d[1] = 0.0; qd0 = 0.0;
+    /* for (i=0; i<n; i++) q1[i] = x[i]; */
+    for (i=1; i<=n; i++) q1[i] = x[i];
+    if (prin > 1) {
+       printf("\n------------- enter function praxis -----------\n");
+       printf("... current parameter settings ...\n");
+       printf("... scaling ... %20.10e\n", scbd);
+       printf("...   tol   ... %20.10e\n", t);
+       printf("... maxstep ... %20.10e\n", h);
+       printf("...   illc  ... %20u\n", illc);
+       printf("...   ktm   ... %20u\n", ktm);
+       printf("... maxfun  ... %20u\n", maxfun);
+    }
+    if (prin) print2();
+ mloop:
+     biter++;  /* Added to count the loops */
+    /* sf = d[0]; */
+    /* s = d[0] = 0.0; */
+     printf("\n Big iteration %d \n",biter);
+     fprintf(ficlog,"\n Big iteration %d \n",biter);
+     sf = d[1];
+    s = d[1] = 0.0;
+    /* minimize along first direction V(*,1) */
+ #ifdef DEBUGPRAX
+    printf("  Minimize along the first direction V(*,1). illc=%d\n",illc);
+    /* fprintf(ficlog,"  Minimize along the first direction V(*,1).\n"); */
+ #endif
+ #ifdef DEBUGPRAX2
+    printf("praxis4 macheps=%14g h=%14g step=%14g small=%14g t=%14g\n",macheps,h, h0,small_windows, t);
+ #endif
+    /* min(0, 2, &d[0], &s, fx, 0); /\* mac heps not global *\/ */
+    minny(1, 2, &d[1], &s, fx, 0); /* mac heps not global */
+ #ifdef DEBUGPRAX
+    printf("praxis5 macheps=%14g h=%14g looks at sign of s=%14g fx=%14g\n",macheps,h, s,fx);
+ #endif
+    if (s <= 0.0)
+       /* for (i=0; i < n; i++) */
+       for (i=1; i <= n; i++)
+           v[i][1] = -v[i][1];
+    /* if ((sf <= (0.9 * d[0])) || ((0.9 * sf) >= d[0])) */
+    if ((sf <= (0.9 * d[1])) || ((0.9 * sf) >= d[1]))
+       /* for (i=1; i<n; i++) */
+       for (i=2; i<=n; i++)
+           d[i] = 0.0;
+    /* for (k=1; k<n; k++) { */
+    for (k=2; k<=n; k++) {
+     /*
+       The inner loop starts here.
+     */
+ #ifdef DEBUGPRAX
+       printf("      The inner loop  here from k=%d to n=%d.\n",k,n);
+       /* fprintf(ficlog,"      The inner loop  here from k=%d to n=%d.\n",k,n); */
+ #endif
+        /* for (i=0; i<n; i++) */
+        for (i=1; i<=n; i++)
+            y[i] = x[i];
+        sf = fx;
+ #ifdef DEBUGPRAX
+        printf(" illc=%d and kt=%d and ktm=%d\n", illc, kt, ktm);
+ #endif
+        illc = illc || (kt > 0);
+ next:
+        kl = k;
+        df = 0.0;
+        if (illc) {        /* random step to get off resolution valley */
+ #ifdef DEBUGPRAX
+           printf("  A random step follows, to avoid resolution valleys.\n");
+           matprint("  before rand, vectors:",v,n,n);
+ #endif
+           for (i=1; i<=n; i++) {
+ #ifdef NOBRENTRAND
+             r = drandom();
+ #else
+             seed=i;
+             /* seed=i+1; */
+ #ifdef DEBUGRAND
+             printf(" Random seed=%d, brent i=%d",seed,i); /* YYYY i=5 j=1 vji= -0.0001170073 */
+ #endif
+             r = randbrent ( &seed );
+ #endif
+ #ifdef DEBUGRAND
+             printf(" Random r=%.7g \n",r);
+ #endif
+             z[i] = (0.1 * ldt + t2 * pow(10.0,(double)kt)) * (r - 0.5);
+             /* z[i] = (0.1 * ldt + t2 * pow(10.0,(double)kt)) * (drandom() - 0.5); */
+             s = z[i];
+               for (j=1; j <= n; j++)
+                   x[j] += s * v[j][i];
+           }
+ #ifdef DEBUGRAND
+           matprint("  after rand, vectors:",v,n,n);
+ #endif
+ #ifdef NR_SHIFT
+           fx = (*fun)((x-1), n);
+ #else
+           fx = (*fun)(x, n);
+ #endif
+           /* fx = (*func) ( (x-1) ); *//* This for func which is computed from x[1] and not from x[0] xm1=(x-1)*/
+           nf++;
+        }
+        /* minimize along non-conjugate directions */
+ #ifdef DEBUGPRAX
+         printf(" Minimize along the 'non-conjugate' directions (dots printed) V(*,%d),...,V(*,%d).\n",k,n);
+         /* fprintf(ficlog," Minimize along the 'non-conjugate' directions  (dots printed) V(*,%d),...,V(*,%d).\n",k,n); */
+ #endif
+         /* for (k2=k; k2<n; k2++) {  /\* Be careful here k2 <=n ? *\/ */
+         for (k2=k; k2<=n; k2++) {  /* Be careful here k2 <=n ? */
+            sl = fx;
+            s = 0.0;
+ #ifdef DEBUGPRAX
+            printf(" Minimize along the 'NON-CONJUGATE' true direction k2=%14d fx=%14.7f\n",k2, fx);
+    matprint("  before min vectors:",v,n,n);
+ #endif
+            /* min(k2, 2, &d[k2], &s, fx, 0); */
+    /*     jsearch=k2-1; */
+    /* min(jsearch, 2, &d[jsearch], &s, fx, 0); */
+    minny(k2, 2, &d[k2], &s, fx, 0);
+ #ifdef DEBUGPRAX
+            printf(" . D(%d)=%14.7f d[k2]=%14.7f z[k2]=%14.7f illc=%14d fx=%14.7f\n",k2,d[k2],d[k2],z[k2],illc,fx);
+ #endif
+           if (illc) {
+               /* double szk = s + z[k2]; */
+               /* s = d[k2] * szk*szk; */
+               double szk = s + z[k2];
+               s = d[k2] * szk*szk;
+            }
+            else
+               s = sl - fx;
+            /* if (df < s) { */
+            if (df <= s) {
+               df = s;
+               kl = k2;
+ #ifdef DEBUGPRAX
+             printf(" df=%.7g and choose kl=%d \n",df,kl); /* UUUU */
+ #endif
+            }
+         } /* end loop k2 */
+         /*
+           If there was not much improvement on the first try, set
+           ILLC = true and start the inner loop again.
+         */
+ #ifdef DEBUGPRAX
+         printf(" If there was not much improvement on the first try, set ILLC = true and start the inner loop again. illc=%d\n",illc);
+         /* fprintf(ficlog,"  If there was not much improvement on the first try, set ILLC = true and start the inner loop again.\n"); */
+ #endif
+         if (!illc && (df < fabs(100.0 * (macheps) * fx))) {
+ #ifdef DEBUGPRAX
+           printf("\n NO SUCCESS because DF is small, starts inner loop with same K(=%d), fabs(  100.0 * machep(=%.10e) * fx(=%.9e) )=%.9e > df(=%.9e) break illc=%d\n", k, macheps, fx, fabs ( 100.0 * macheps * fx ), df, illc);
+ #endif
+           illc = 1;
+           goto next;
+         }
+ #ifdef DEBUGPRAX
+         printf("\n SUCCESS, BREAKS inner loop K(=%d) because DF is big, fabs(  100.0 * machep(=%.10e) * fx(=%.9e) )=%.9e <= df(=%.9e) break illc=%d\n", k, macheps, fx, fabs ( 100.0 * macheps * fx ), df, illc);
+ #endif
+        /* if ((k == 1) && (prin > 1)){ /\* be careful k=2 *\/ */
+        if ((k == 2) && (prin > 1)){ /* be careful k=2 */
+ #ifdef DEBUGPRAX
+         printf("  NEW D The second difference array d:\n" );
+         /* fprintf(ficlog, " NEW D The second difference array d:\n" ); */
+ #endif
+          vecprint(" NEW D The second difference array d:",d,n);
+        }
+        /* minimize along conjugate directions */
+        /*
+          Minimize along the "conjugate" directions V(*,1),...,V(*,K-1).
+        */
+ #ifdef DEBUGPRAX
+       printf("Minimize along the 'conjugate' directions V(*,1),...,V(*,K-1=%d).\n",k-1);
+       /* fprintf(ficlog,"Minimize along the 'conjugate' directions V(*,1),...,V(*,K-1=%d).\n",k-1); */
+ #endif
+       /* for (k2=0; k2<=k-1; k2++) { */
+       for (k2=1; k2<=k-1; k2++) {
+            s = 0.0;
+            /* min(k2-1, 2, &d[k2-1], &s, fx, 0); */
+            minny(k2, 2, &d[k2], &s, fx, 0);
+        }
+        f1 = fx;
+        fx = sf;
+        lds = 0.0;
+        /* for (i=0; i<n; i++) { */
+        for (i=1; i<=n; i++) {
+            sl = x[i];
+            x[i] = y[i];
+            y[i] = sl - y[i];
+            sl = y[i];
+            lds = lds + sl*sl;
+        }
+        lds = sqrt(lds);
+ #ifdef DEBUGPRAX
+        printf("Minimization done 'conjugate', shifted all points, computed lds=%.8f\n",lds);
+ #endif
+       /*
+         Discard direction V(*,kl).
+         If no random step was taken, V(*,KL) is the "non-conjugate"
+         direction along which the greatest improvement was made.
+       */
+        if (lds > small_windows) {
+ #ifdef DEBUGPRAX
+        printf("lds big enough to throw direction  V(*,kl=%d). If no random step was taken, V(*,KL) is the 'non-conjugate' direction along which the greatest improvement was made.\n",kl);
+          matprint("  before shift new conjugate vectors:",v,n,n);
+ #endif
+          for (i=kl-1; i>=k; i--) {
+            /* for (j=0; j < n; j++) */
+            for (j=1; j <= n; j++)
+              /* v[j][i+1] = v[j][i]; */ /* This is v[j][i+1]=v[j][i] i=kl-1 to k */
+              v[j][i+1] = v[j][i]; /* This is v[j][i+1]=v[j][i] i=kl-1 to k */
+            /* v[j][i+1] = v[j][i]; */
+            /* d[i+1] = d[i];*/  /* last  is d[k+1]= d[k] */
+            d[i+1] = d[i];  /* last  is d[k]= d[k-1] */
+          }
+ #ifdef DEBUGPRAX
+          matprint("  after shift new conjugate vectors:",v,n,n);
+ #endif   /* d[k] = 0.0; */
+          d[k] = 0.0;
+          for (i=1; i <= n; i++)
+            v[i][k] = y[i] / lds;
+          /* v[i][k] = y[i] / lds; */
+ #ifdef DEBUGPRAX
+          printf("Minimize along the new 'conjugate' direction V(*,k=%d), which is the normalized vector:  (new x) - (old x). d2=%14.7g lds=%.10f\n",k,d[k],lds);
+          /* fprintf(ficlog,"Minimize along the new 'conjugate' direction V(*,k=%d), which is the normalized vector:  (new x) - (old x).\n",k); */
+     matprint("  before min new conjugate vectors:",v,n,n);
+ #endif
+          /* min(k-1, 4, &d[k-1], &lds, f1, 1); */
+          minny(k, 4, &d[k], &lds, f1, 1);
+ #ifdef DEBUGPRAX
+          printf(" after min d(k)=%d %.7g lds=%14f\n",k,d[k],lds);
+    matprint("  after min vectors:",v,n,n);
+ #endif
+          if (lds <= 0.0) {
+            lds = -lds;
+ #ifdef DEBUGPRAX
+           printf(" lds changed sign lds=%.14f k=%d\n",lds,k);
+ #endif
+            /* for (i=0; i<n; i++) */
+            /*   v[i][k] = -v[i][k]; */
+            for (i=1; i<=n; i++)
+              v[i][k] = -v[i][k];
+          }
+        }
+        ldt = ldfac * ldt;
+        if (ldt < lds)
+           ldt = lds;
+        if (prin > 0){
+ #ifdef DEBUGPRAX
+         printf(" k=%d",k);
+         /* fprintf(ficlog," k=%d",k); */
+ #endif
+         print2();/* n, x, prin, fx, nf, nl ); */
+        }
+        t2 = 0.0;
+        /* for (i=0; i<n; i++) */
+        for (i=1; i<=n; i++)
+            t2 += x[i]*x[i];
+        t2 = m2 * sqrt(t2) + t;
+        /*
+         See whether the length of the step taken since starting the
+         inner loop exceeds half the tolerance.
+       */
+ #ifdef DEBUGPRAX
+        printf("See if step length exceeds half the tolerance.\n"); /* ZZZZZ */
+       /* fprintf(ficlog,"See if step length exceeds half the tolerance.\n"); */
+ #endif
+        if (ldt > (0.5 * t2))
+           kt = 0;
+        else
+           kt++;
+ #ifdef DEBUGPRAX
+        printf("if kt=%d >? ktm=%d gotoL2 loop\n",kt,ktm);
+ #endif
+        if (kt > ktm){
+          if ( 0 < prin ){
+            /* printf("\nr8vec_print\n X:\n"); */
+            /* fprintf(ficlog,"\nr8vec_print\n X:\n"); */
+            vecprint ("END  X:", x, n );
+          }
+            goto fret;
+        }
+ #ifdef DEBUGPRAX
+    matprint("  end of L2 loop vectors:",v,n,n);
+ #endif
+    }
+    /* printf("The inner loop ends here.\n"); */
+    /* fprintf(ficlog,"The inner loop ends here.\n"); */
+    /*
+      The inner loop ends here.
+      Try quadratic extrapolation in case we are in a curved valley.
+    */
+ #ifdef DEBUGPRAX
+    printf("Try QUAD ratic extrapolation in case we are in a curved valley.\n");
+ #endif
+    /*  try quadratic extrapolation in case    */
+    /*  we are stuck in a curved valley        */
+    quad();
+    dn = 0.0;
+    /* for (i=0; i<n; i++) { */
+    for (i=1; i<=n; i++) {
+        d[i] = 1.0 / sqrt(d[i]);
+        if (dn < d[i])
+           dn = d[i];
+    }
+    if (prin > 2)
+      matprint("  NEW DIRECTIONS vectors:",v,n,n);
+    /* for (j=0; j<n; j++) { */
+    for (j=1; j<=n; j++) {
+        s = d[j] / dn;
+        /* for (i=0; i < n; i++) */
+        for (i=1; i <= n; i++)
+            v[i][j] *= s;
+    }
+    if (scbd > 1.0) {       /* scale axis to reduce condition number */
+ #ifdef DEBUGPRAX
+      printf("Scale the axes to try to reduce the condition number.\n");
+ #endif
+      /* fprintf(ficlog,"Scale the axes to try to reduce the condition number.\n"); */
+       s = vlarge;
+       /* for (i=0; i<n; i++) { */
+       for (i=1; i<=n; i++) {
+           sl = 0.0;
+           /* for (j=0; j < n; j++) */
+           for (j=1; j <= n; j++)
+               sl += v[i][j]*v[i][j];
+           z[i] = sqrt(sl);
+           if (z[i] < m4)
+              z[i] = m4;
+           if (s > z[i])
+              s = z[i];
+       }
+       /* for (i=0; i<n; i++) { */
+       for (i=1; i<=n; i++) {
+           sl = s / z[i];
+           z[i] = 1.0 / sl;
+           if (z[i] > scbd) {
+              sl = 1.0 / scbd;
+              z[i] = scbd;
+           }
+       }
+    }
+    for (i=1; i<=n; i++)
+        /* for (j=0; j<=i-1; j++) { */
+        /* for (j=1; j<=i; j++) { */
+        for (j=1; j<=i-1; j++) {
+            s = v[i][j];
+            v[i][j] = v[j][i];
+            v[j][i] = s;
+        }
+ #ifdef DEBUGPRAX
+     printf(" Calculate a new set of orthogonal directions before repeating  the main loop.\n  Transpose V for MINFIT:...\n");
+ #endif
+       /*
+       MINFIT finds the singular value decomposition of V.
+       This gives the principal values and principal directions of the
+       approximating quadratic form without squaring the condition number.
+     */
+  #ifdef DEBUGPRAX
+     printf(" MINFIT finds the singular value decomposition of V. \n This gives the principal values and principal directions of the\n  approximating quadratic form without squaring the condition number...\n");
+ #endif
+    minfit(n, macheps, vsmall, v, d);
+     /* for(i=0; i<n;i++)printf(" %14.7g",d[i]); */
+     /* v is overwritten with R. */
+     /*
+       Unscale the axes.
+     */
+    if (scbd > 1.0) {
+ #ifdef DEBUGPRAX
+       printf(" Unscale the axes.\n");
+ #endif
+       /* for (i=0; i<n; i++) { */
+       for (i=1; i<=n; i++) {
+           s = z[i];
+           /* for (j=0; j<n; j++) */
+           for (j=1; j<=n; j++)
+               v[i][j] *= s;
+       }
+       /* for (i=0; i<n; i++) { */
+       for (i=1; i<=n; i++) {
+           s = 0.0;
+           /* for (j=0; j<n; j++) */
+           for (j=1; j<=n; j++)
+               s += v[j][i]*v[j][i];
+           s = sqrt(s);
+           d[i] *= s;
+           s = 1.0 / s;
+           /* for (j=0; j<n; j++) */
+           for (j=1; j<=n; j++)
+               v[j][i] *= s;
+       }
+    }
+    /* for (i=0; i<n; i++) { */
+    double dni; /* added for compatibility with buckhardt but not brent */
+    for (i=1; i<=n; i++) {
+      dni=dn*d[i]; /* added for compatibility with buckhardt but not brent */
+        if ((dn * d[i]) > large)
+           d[i] = vsmall;
+        else if ((dn * d[i]) < small_windows)
+           d[i] = vlarge;
+        else
+         d[i] = 1.0 / dni / dni; /* added for compatibility with buckhardt but not brent */
+           /* d[i] = pow(dn * d[i],-2.0); */
+    }
+ #ifdef DEBUGPRAX
+    vecprint ("\n Before sort Eigenvalues of a:",d,n );
+ #endif
+    sort();               /* the new eigenvalues and eigenvectors */
+ #ifdef DEBUGPRAX
+    vecprint( " After sort the eigenvalues ....\n", d, n);
+    matprint( " After sort the eigenvectors....\n", v, n,n);
+ #endif
+ #ifdef DEBUGPRAX
+     printf("  Determine the smallest eigenvalue.\n");
+ #endif
+    /* dmin = d[n-1]; */
+    dmin = d[n];
+    if (dmin < small_windows)
+       dmin = small_windows;
+     /*
+      The ratio of the smallest to largest eigenvalue determines whether
+      the system is ill conditioned.
+    */
+    /* illc = (m2 * d[0]) > dmin; */
+    illc = (m2 * d[1]) > dmin;
+ #ifdef DEBUGPRAX
+     printf("  The ratio of the smallest to largest eigenvalue determines whether\n  the system is ill conditioned=%d . dmin=%.10lf < m2=%.10lf * d[1]=%.10lf \n",illc, dmin,m2, d[1]);
+ #endif
+    if ((prin > 2) && (scbd > 1.0))
+       vecprint("\n The scale factors:",z,n);
+    if (prin > 2)
+       vecprint("  Principal values (EIGEN VALUES OF A) of the quadratic form:",d,n);
+    if (prin > 2)
+      matprint("  The principal axes (EIGEN VECTORS OF A:",v,n, n);
+    if ((maxfun > 0) && (nf > maxfun)) {
+       if (prin)
+          printf("\n... maximum number of function calls reached ...\n");
+       goto fret;
+    }
+ #ifdef DEBUGPRAX
+    printf("Goto main loop\n");
+ #endif
+    goto mloop;   /* back to main loop */
+ fret:
+    if (prin > 0) {
+          vecprint("\n  X:", x, n);
+          /* printf("\n... ChiSq reduced to %20.10e ...\n", fx); */
+          /* printf("... after %20u function calls.\n", nf); */
+    }
+    free_vector(d, 1, n);
+    free_vector(y, 1, n);
+    free_vector(z, 1, n);
+    free_vector(q0, 1, n);
+    free_vector(q1, 1, n);
+    free_matrix(v, 1, n, 1, n);
+    /*   double *d, *y, *z, */
+    /* *q0, *q1, **v; */
+    free_vector(tflin, 1, n);
+    /* double *tflin; /\* used in flin: return (*fun)(tflin, n); *\/ */
+    free_vector(e, 1, n);
+    /* double *e; /\* used in minfit, don't konw how to free memory and thus made global *\/ */
+    return(fx);
+ }
+ /* end praxis gegen */
  /*************** powell ************************/
  /*
- Minimization of a function func of n variables. Input consists of an initial starting point
+ Minimization of a function func of n variables. Input consists in an initial starting point
- p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
+ p[1..n] ; an initial matrix xi[1..n][1..n]  whose columns contain the initial set of di-
- rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
+ rections (usually the n unit vectors); and ftol, the fractional tolerance in the function value
- such that failure to decrease by more than this amount on one iteration signals doneness. On
+ such that failure to decrease by more than this amount in one iteration signals doneness. On
  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
  function value at p , and iter is the number of iterations taken. The routine linmin is used.
   */
- Line 2173  void powell(double p[], double **xi, int
+ Line 4167  void powell(double p[], double **xi, int
    double fp,fptt;
    double *xits;
    int niterf, itmp;
- #ifdef LINMINORIGINAL
+   int Bigter=0, nBigterf=1;
- #else
-   flatdir=ivector(1,n);
-   for (j=1;j<=n;j++) flatdir[j]=0;
- #endif
    pt=vector(1,n);
    ptt=vector(1,n);
    xit=vector(1,n);
    xits=vector(1,n);
    *fret=(*func)(p);
    for (j=1;j<=n;j++) pt[j]=p[j];
    rcurr_time = time(NULL);
+   fp=(*fret); /* Initialisation */
    for (*iter=1;;++(*iter)) {
-     fp=(*fret); /* From former iteration or initial value */
      ibig=0;
      del=0.0;
      rlast_time=rcurr_time;
+     rlast_btime=rcurr_time;
      /* (void) gettimeofday(&curr_time,&tzp); */
      rcurr_time = time(NULL);
      curr_time = *localtime(&rcurr_time);
-     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
+     /* printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); */
-     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
+     /* fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*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); */
+     /* Bigter=(*iter - *iter % ncovmodel)/ncovmodel +1; /\* Big iteration, i.e on ncovmodel cycle *\/ */
+     Bigter=(*iter - (*iter-1) % n)/n +1; /* Big iteration, i.e on ncovmodel cycle */
+     printf("\nPowell iter=%d Big Iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,Bigter,*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
+     fprintf(ficlog,"\nPowell iter=%d Big Iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,Bigter,*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
+     fprintf(ficrespow,"%d %d %.12f %d",*iter,Bigter, *fret,curr_time.tm_sec-start_time.tm_sec);
+     fp=(*fret); /* From former iteration or initial value */
      for (i=1;i<=n;i++) {
        fprintf(ficrespow," %.12lf", p[i]);
      }
- Line 2218  void powell(double p[], double **xi, int
+ Line 4213  void powell(double p[], double **xi, int
        }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]);
+       }else if(Typevar[j]==3) {
+         printf("  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(ficlog,"  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
        }
      }
      printf("\n");
- Line 2248  void powell(double p[], double **xi, int
+ Line 4246  void powell(double p[], double **xi, int
          strcurr[itmp-1]='\0';
        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-       for(niterf=10;niterf<=30;niterf+=10){
+       for(nBigterf=1;nBigterf<=31;nBigterf+=10){
+         niterf=nBigterf*ncovmodel;
+         /* rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); */
          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
          forecast_time = *localtime(&rforecast_time);
          strcpy(strfor,asctime(&forecast_time));
          itmp = strlen(strfor);
          if(strfor[itmp-1]=='\n')
            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 BIG iterations (%d iterations) to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",nBigterf, 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 BIG iterations  (%d iterations) to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",nBigterf, niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
        }
      }
-     for (i=1;i<=n;i++) { /* For each direction i */
+     for (i=1;i<=n;i++) { /* For each direction i, maximisation after loading directions */
-       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
+       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales. xi is not changed but one dim xit  */
-       fptt=(*fret);
+       fptt=(*fret); /* Computes likelihood for parameters xit */
  #ifdef DEBUG
        printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
        fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
- Line 2269  void powell(double p[], double **xi, int
+ Line 4270  void powell(double p[], double **xi, int
        printf("%d",i);fflush(stdout); /* print direction (parameter) i */
        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); /* New point i minimizing in direction xit, i has coordinates p[j].*/
+       /* xit[j] gives the n coordinates of direction i as input.*/
+       /* *fret gives the maximum value on direction xit */
  #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 */
+       flatdir[i]=flat; /* Function is vanishing in that direction i */
  #endif
-                         /* Outputs are fret(new point p) p is updated and xit rescaled */
+       /* Outputs are fret(new point p) p is updated and xit rescaled */
        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
-                                 /* because that direction will be replaced unless the gain del is small */
+         /* 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
        printf("%d %.12e",i,(*fret));
        fprintf(ficlog,"%d %.12e",i,(*fret));
        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++) {
-                                 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");
        fprintf(ficlog,"\n");
  #endif
      } /* end loop on each direction i */
-     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
+     /* Convergence test will use last linmin estimation (fret) and compare to former iteration (fp) */
      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
      /* New value of last point Pn is not computed, P(n-1) */
-       for(j=1;j<=n;j++) {
+     for(j=1;j<=n;j++) {
-                                 if(flatdir[j] >0){
+       if(flatdir[j] >0){
-                                         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
+         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
-                                         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
+         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
-                                 }
+       }
-                                 /* printf("\n"); */
+       /* printf("\n"); */
-                                 /* fprintf(ficlog,"\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 */
- Line 2347  void powell(double p[], double **xi, int
+ Line 4350  void powell(double p[], double **xi, int
        }
  #endif
- #ifdef LINMINORIGINAL
- #else
-       free_ivector(flatdir,1,n);
- #endif
        free_vector(xit,1,n);
        free_vector(xits,1,n);
        free_vector(ptt,1,n);
- Line 2358  void powell(double p[], double **xi, int
+ Line 4357  void powell(double p[], double **xi, int
        return;
      } /* enough precision */
      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 and value f3, P_0 + 2 (P_n-P_0)=2Pn-P0 and xit is direction Pn-P0 */
        ptt[j]=2.0*p[j]-pt[j];
-       xit[j]=p[j]-pt[j];
+       xit[j]=p[j]-pt[j]; /* Coordinate j of last direction xi_n=P_n-P_0 */
-       pt[j]=p[j];
+ #ifdef DEBUG
-     }
+       printf("\n %d xit=%12.7g p=%12.7g pt=%12.7g ",j,xit[j],p[j],pt[j]);
+ #endif
+       pt[j]=p[j]; /* New P0 is Pn */
+     }
+ #ifdef DEBUG
+     printf("\n");
+ #endif
      fptt=(*func)(ptt); /* f_3 */
- #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in directions until some iterations are done */
                  if (*iter <=4) {
  #else
  #endif
- Line 2383  void powell(double p[], double **xi, int
+ Line 4388  void powell(double p[], double **xi, int
        /* 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 < del <= lambda^2 both test are equivalent */
-                         /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
+       /* 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 < mu^2 < del then t is negative and directest >0  */
-                         /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
+       /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
  #ifdef NRCORIGINAL
        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
  #else
- Line 2408  void powell(double p[], double **xi, int
+ Line 4413  void powell(double p[], double **xi, int
        if (t < 0.0) { /* Then we use it for new direction */
  #else
        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);
          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);
- Line 2464  void powell(double p[], double **xi, int
+ Line 4469  void powell(double p[], double **xi, int
            }
            printf("\n");
            fprintf(ficlog,"\n");
+ #ifdef FLATSUP
+           free_vector(xit,1,n);
+           free_vector(xits,1,n);
+           free_vector(ptt,1,n);
+           free_vector(pt,1,n);
+           return;
+ #endif
          }
  #endif
          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
- Line 2480  void powell(double p[], double **xi, int
+ Line 4492  void powell(double p[], double **xi, int
          fprintf(ficlog,"\n");
  #endif
        } /* end of t or directest negative */
+       printf(" Directest is positive, P_n-P_0 does not increase the conjugacy. n=%d\n",n);
+       fprintf(ficlog," Directest is positive, P_n-P_0 does not increase the conjugacy. n=%d\n",n);
  #ifdef POWELLNOF3INFF1TEST
  #else
        } /* end if (fptt < fp)  */
- Line 2495  void powell(double p[], double **xi, int
+ Line 4509  void powell(double p[], double **xi, int
    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 combination ij
+     /**< Computes the prevalence limit in each live state at age x and for covariate combination ij . Nicely done
-        (and selected quantitative values in nres)
+      *   (and selected quantitative values in nres)
-        by left multiplying the unit
+      *  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
-   /* or prevalence in state 1, prevalence in state 2, 0 */
+      * or prevalence in state 1, prevalence in state 2, 0
-   /* newm is the matrix after multiplications, its rows are identical at a factor */
+      * newm is the matrix after multiplications, its rows are identical at a factor.
-   /* Initial matrix pimij */
+      * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
+      * Output is prlim.
+      * Initial matrix pimij
+      */
    /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
    /*  0,                   0                  , 1} */
- Line 2517  void powell(double p[], double **xi, int
+ Line 4534  void powell(double p[], double **xi, int
    /*  0.51326036147820708, 0.48673963852179264} */
    /* If we start from prlim again, prlim tends to a constant matrix */
-   int i, ii,j,k;
+     int i, ii,j,k, k1;
    double *min, *max, *meandiff, maxmax,sumnew=0.;
    /* double **matprod2(); */ /* test */
    double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
    double **newm;
    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
    int ncvloop=0;
+   int first=0;
    min=vector(1,nlstate);
    max=vector(1,nlstate);
- Line 2544  void powell(double p[], double **xi, int
+ Line 4562  void powell(double p[], double **xi, int
      newm=savm;
      /* Covariates have to be included here again */
      cov[2]=agefin;
-     if(nagesqr==1)
+      if(nagesqr==1){
-       cov[3]= agefin*agefin;;
+       cov[3]= agefin*agefin;
-     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
+      }
-                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
+      /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
-       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
+      /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
-       /* 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)); */
+      for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
-     }
+        if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
-     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
+          cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
-                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
+        }else{
-       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
+          cov[2+nagesqr+k1]=precov[nres][k1];
-       /* 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]); */
+        }
-     }
+      }/* End of loop on model equation */
-     for (k=1; k<=cptcovage;k++){  /* For product with age */
-       if(Dummy[Tvar[Tage[k]]]){
+ /* Start of old code (replaced by a loop on position in the model equation */
-         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+     /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only of the model *\/ */
-       } else{
+     /*                  /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */
-         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
+     /*   /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; *\/ */
-       }
+     /*   cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[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]); */
+     /*   /\* model = 1 +age + V1*V3 + age*V1 + V2 + V1 + age*V2 + V3 + V3*age + V1*V2  */
-     }
+     /*    * k                  1        2      3    4      5      6     7        8 */
-     for (k=1; k<=cptcovprod;k++){ /* For product without age */
+     /*    *cov[]   1    2      3        4      5    6      7      8     9       10 */
-       /* 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]); */
+     /*    *TypeVar[k]          2        1      0    0      1      0     1        2 */
-       if(Dummy[Tvard[k][1]==0]){
+     /*    *Dummy[k]            0        2      0    0      2      0     2        0 */
-         if(Dummy[Tvard[k][2]==0]){
+     /*    *Tvar[k]             4        1      2    1      2      3     3        5 */
-           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+     /*    *nsd=3                              (1)  (2)           (3) */
-         }else{
+     /*    *TvarsD[nsd]                      [1]=2    1             3 */
-           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
+     /*    *TnsdVar                          [2]=2 [1]=1         [3]=3 */
-         }
+     /*    *TvarsDind[nsd](=k)               [1]=3 [2]=4         [3]=6 */
-       }else{
+     /*    *Tage[]                  [1]=1                  [2]=2      [3]=3 */
-         if(Dummy[Tvard[k][2]==0]){
+     /*    *Tvard[]       [1][1]=1                                           [2][1]=1 */
-           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
+     /*    *                   [1][2]=3                                           [2][2]=2 */
-         }else{
+     /*    *Tprod[](=k)     [1]=1                                              [2]=8 */
-           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
+     /*    *TvarsDp(=Tvar)   [1]=1            [2]=2             [3]=3          [4]=5 */
-         }
+     /*    *TvarD (=k)       [1]=1            [2]=3 [3]=4       [3]=6          [4]=6 */
-       }
+     /*    *TvarsDpType */
-     }
+     /*    *si model= 1 + age + V3 + V2*age + V2 + V3*age */
+     /*    * nsd=1              (1)           (2) */
+     /*    *TvarsD[nsd]          3             2 */
+     /*    *TnsdVar           (3)=1          (2)=2 */
+     /*    *TvarsDind[nsd](=k)  [1]=1        [2]=3 */
+     /*    *Tage[]                  [1]=2           [2]= 3    */
+     /*    *\/ */
+     /*   /\* cov[++k1]=nbcode[TvarsD[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)); *\/ */
+     /* } */
+     /* for (k=1; k<=nsq;k++) { /\* For single quantitative varying covariates only of the model *\/ */
+     /*                  /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
+     /*   /\* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 *\/ */
+     /*   /\* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; *\/ */
+     /*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][resultmodel[nres][k1]] */
+     /*   /\* cov[++k1]=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++){  /\* For product with age *\/ */
+     /*   if(Dummy[Tage[k]]==2){ /\* dummy with age *\/ */
+     /*  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+     /*  /\* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
+     /*   } else if(Dummy[Tage[k]]==3){ /\* quantitative with age *\/ */
+     /*  cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
+     /*  /\* cov[++k1]=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,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+     /*    /\* cov[++k1]=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,Tvard[k][1])] * Tqresult[nres][k]; */
+     /*    /\* cov[++k1]=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,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
+     /*    /\* cov[++k1]=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]]; */
+     /*    /\* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\/ */
+     /*  } */
+     /*   } */
+     /* } /\* End product without age *\/ */
+ /* ENd of old code */
      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-                 /* age and covariate values of ij are in 'cov' */
+     /* age and covariate values of ij are in 'cov' */
      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      savm=oldm;
- Line 2620  void powell(double p[], double **xi, int
+ Line 4686  void powell(double p[], double **xi, int
        free_vector(meandiff,1,nlstate);
        return prlim;
      }
-   } /* age loop */
+   } /* agefin loop */
      /* After some age loop it doesn't converge */
-   printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
+   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;
-   /* 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); */
+     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);
+   }else if (first >=1 && first <10){
+     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);
+     first++;
+   }else if (first ==10){
+     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);
+     printf("Warning: the stable prevalence dit not converge. This warning came too often, IMaCh will stop notifying, even in its log file. Look at the graphs to appreciate the non convergence.\n");
+     fprintf(ficlog,"Warning: the stable prevalence no convergence; too many cases, giving up noticing, even in log file\n");
+     first++;
+   }
+   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl,
+    * (int)age, (int)delaymax, (int)agefin, ncvloop,
+    * (int)age-(int)agefin); */
    free_vector(min,1,nlstate);
    free_vector(max,1,nlstate);
    free_vector(meandiff,1,nlstate);
- Line 2659  Earliest age to start was %d-%d=%d, ncvl
+ Line 4739  Earliest age to start was %d-%d=%d, ncvl
    /*  0.51326036147820708, 0.48673963852179264} */
    /* If we start from prlim again, prlim tends to a constant matrix */
-   int i, ii,j,k;
+   int i, ii,j, k1;
    int first=0;
    double *min, *max, *meandiff, maxmax,sumnew=0.;
    /* double **matprod2(); */ /* test */
- Line 2689  Earliest age to start was %d-%d=%d, ncvl
+ Line 4769  Earliest age to start was %d-%d=%d, ncvl
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
    /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
    /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
-   for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
+   /* 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++;
      newm=savm; /* oldm should be kept from previous iteration or unity at start */
                  /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
      /* Covariates have to be included here again */
      cov[2]=agefin;
-     if(nagesqr==1)
+     if(nagesqr==1){
        cov[3]= agefin*agefin;;
-     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
+     }
-                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
+     for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
-       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
+       if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
-       /* 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)); */
+         cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
-     }
-     /* for (k=1; k<=cptcovn;k++) { */
-     /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
-     /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
-     /*   /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */
-     /* } */
-     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+k1]=precov[nres][k1];
-           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]];
-         }
        }
-     }
+     }/* End of loop on model equation */
+ /* Old code */
+     /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only *\/ */
+     /*                  /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */
+     /*   cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[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)); *\/ */
+     /* } */
+     /* /\* for (k=1; k<=cptcovn;k++) { *\/ */
+     /* /\*   /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\\/ *\/ */
+     /* /\*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; *\/ */
+     /* /\*   /\\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\\/ *\/ */
+     /* /\* } *\/ */
+     /* 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]]]== 2){ /\\* dummy with age *\\/ ERROR ???*\/ */
+     /*   if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */
+     /*  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+     /*   } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age *\/ */
+     /*  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,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+     /*  }else{ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
+     /*  } */
+     /*   }else{ */
+     /*  if(Dummy[Tvard[k][2]]==0){ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * 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 cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
- Line 2790  Earliest age to start was %d-%d=%d, ncvl
+ Line 4883  Earliest age to start was %d-%d=%d, ncvl
      maxmax=0.;
      for(i=1; i<=nlstate; i++){
-       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, could be nan! */
        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); */
      } /* i loop */
- Line 2803  Earliest age to start was %d-%d=%d, ncvl
+ Line 4896  Earliest age to start was %d-%d=%d, ncvl
        free_vector(meandiff,1,nlstate);
        return bprlim;
      }
-   } /* age loop */
+   } /* agefin loop */
      /* After some age loop it doesn't converge */
-   if(first){
+   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);
- Line 2850  double **pmij(double **ps, double *cov,
+ Line 4943  double **pmij(double **ps, double *cov,
          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
        }
        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+       /* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
      }
      for(j=i+1; j<=nlstate+ndeath;j++){
        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
- Line 2859  double **pmij(double **ps, double *cov,
+ Line 4952  double **pmij(double **ps, double *cov,
          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
        }
        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       /* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
      }
    }
    for(i=1; i<= nlstate; i++){
      s1=0;
      for(j=1; j<i; j++){
+       /* printf("debug1 %d %d ps=%lf exp(ps)=%lf \n",i,j,ps[i][j],exp(ps[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++){
+       /* printf("debug2 %d %d ps=%lf exp(ps)=%lf \n",i,j,ps[i][j],exp(ps[i][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];
+       ps[i][j]= exp(ps[i][j])*ps[i][i];/* Bug valgrind */
      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 */
- Line 2888  double **pmij(double **ps, double *cov,
+ Line 4982  double **pmij(double **ps, double *cov,
        ps[ii][ii]=1;
      }
    }
    /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
    /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
- Line 2909  double **pmij(double **ps, double *cov,
+ Line 5003  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, int ij )
  {
-   /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
+   /* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
     * 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 ii, j;
-   double **out, **pmij();
+   double  **pmij();
    double sumnew=0.;
    double agefin;
-   double k3=0.; /* constant of the w_x diagonal matrixe (in order for B to sum to 1 even for death state) */
+   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 **bbmij;
    doldm=ddoldms; /* global pointers */
    dnewm=ddnewms;
    dsavm=ddsavms;
+   /* Debug */
+   /* printf("Bmij ij=%d, cov[2}=%f\n", ij, cov[2]); */
    agefin=cov[2];
    /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
    /* bmij *//* age is cov[2], ij is included in cov, but we need for
- Line 2932  double **pmij(double **ps, double *cov,
+ Line 5028  double **pmij(double **ps, double *cov,
    /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
    /* P_x */
-   pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
+   pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm *//* Bug valgrind */
    /* outputs pmmij which is a stochastic matrix in row */
    /* Diag(w_x) */
-   /* Problem with prevacurrent which can be zero */
+   /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
    sumnew=0.;
    /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
    for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
-     /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]);  */
+     /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
      sumnew+=prevacurrent[(int)agefin][ii][ij];
    }
    if(sumnew >0.01){  /* At least some value in the prevalence */
- Line 2963  double **pmij(double **ps, double *cov,
+ Line 5059  double **pmij(double **ps, double *cov,
    }
    /* End doldm, At the end doldm is diag[(w_i)] */
-   /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */
+   /* 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); /* Bug Valgrind */
+   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 */
+   /* 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.;
- Line 2984  double **pmij(double **ps, double *cov,
+ Line 5080  double **pmij(double **ps, double *cov,
      } /*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); /* Bug Valgrind */
+   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 */
- Line 3056  double **bpmij(double **ps, double *cov,
+ Line 5152  double **bpmij(double **ps, double *cov,
        ps[ii][ii]=1;
      }
    }
-   /* Added for backcast */ /* Transposed matrix too */
+   /* Added for prevbcast */ /* Transposed matrix too */
    for(jj=1; jj<= nlstate+ndeath; jj++){
      s1=0.;
      for(ii=1; ii<= nlstate+ndeath; ii++){
- Line 3112  double **matprod2(double **out, double *
+ Line 5208  double **matprod2(double **out, double *
  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
  {
-   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
+   /* Already optimized with precov.
+      Computes the transition matrix starting at age 'age' and dummies values in each resultline (loop on ij to find the corresponding combination) to over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
       nhstepm*hstepm matrices.
- Line 3124  double ***hpxij(double ***po, int nhstep
+ Line 5221  double ***hpxij(double ***po, int nhstep
       */
-   int i, j, d, h, k;
+   int i, j, d, h, k1;
    double **out, cov[NCOVMAX+1];
    double **newm;
    double agexact;
-   double agebegin, ageend;
+   /*double agebegin, ageend;*/
    /* Hstepm could be zero and should return the unit matrix */
    for (i=1;i<=nlstate+ndeath;i++)
- Line 3144  double ***hpxij(double ***po, int nhstep
+ Line 5241  double ***hpxij(double ***po, int nhstep
        cov[1]=1.;
        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
        cov[2]=agexact;
-       if(nagesqr==1)
+       if(nagesqr==1){
          cov[3]= agexact*agexact;
-       for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
-                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
-         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
-         /* 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)); */
-       }
-       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("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++){
-         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)];
        }
+       /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
+       /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
+       for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
+         if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
+           cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
+         }else{
+           cov[2+nagesqr+k1]=precov[nres][k1];
+         }
+       }/* End of loop on model equation */
+         /* Old code */
+ /*      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /\* Single dummy  *\/ */
+ /* /\*     V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) *\/ */
+ /* /\*       for (k=1; k<=nsd;k++) { /\\* For single dummy covariates only *\\/ *\/ */
+ /* /\* /\\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\\/ *\/ */
+ /*      /\* codtabm(ij,k)  (1 & (ij-1) >> (k-1))+1 *\/ */
+ /* /\*             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 *\/ */
+ /* /\*    nsd         1   2                              3 *\/ /\* Counting single dummies covar fixed or tv *\/ */
+ /* /\*TvarsD[nsd]     4   3                              1 *\/ /\* ID of single dummy cova fixed or timevary*\/ */
+ /* /\*TvarsDind[k]    2   3                              9 *\/ /\* position K of single dummy cova *\/ */
+ /*        /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];or [codtabm(ij,TnsdVar[TvarsD[k]] *\/ */
+ /*        cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; */
+ /*        /\* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,TnsdVar[TvarsD[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,TnsdVar[TvarsD[k]])); *\/ */
+ /*        printf("hpxij Dummy combi=%d k1=%d Tvar[%d]=V%d cov[2+%d+%d]=%lf resultmodel[nres][%d]=%d nres/nresult=%d/%d \n",ij,k1,k1, Tvar[k1],nagesqr,k1,cov[2+nagesqr+k1],k1,resultmodel[nres][k1],nres,nresult); */
+ /*        printf("hpxij new Dummy precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
+ /*      }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /\* Single quantitative variables  *\/ */
+ /*        /\* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline *\/ */
+ /*        cov[2+nagesqr+k1]=Tqresult[nres][resultmodel[nres][k1]];  */
+ /*        /\* 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("hPxij Quantitative k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
+ /*        printf("hpxij new Quanti precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
+ /*      }else if( Dummy[k1]==2 ){ /\* For dummy with age product *\/ */
+ /*        /\* Tvar[k1] Variable in the age product age*V1 is 1 *\/ */
+ /*        /\* [Tinvresult[nres][V1] is its value in the resultline nres *\/ */
+ /*        cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvar[k1]]*cov[2]; */
+ /*        printf("DhPxij Dummy with age k1=%d Tvar[%d]=%d TinvDoQresult[nres=%d][%d]=%.f age=%.2f,cov[2+%d+%d]=%.3f\n",k1,k1,Tvar[k1],nres,TinvDoQresult[nres][Tvar[k1]],cov[2],nagesqr,k1,cov[2+nagesqr+k1]); */
+ /*        printf("hpxij new Dummy with age product precov[nres=%d][k1=%d]=%.4f * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
+ /*        /\* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];    *\/ */
+ /*        /\* for (k=1; k<=cptcovage;k++){ /\\* For product with age V1+V1*age +V4 +age*V3 *\\/ *\/ */
+ /*        /\* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*\/ */
+ /*        /\* *\/ */
+ /* /\*             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 *\/ */
+ /* /\*cptcovage=2                   1               2      *\/ */
+ /* /\*Tage[k]=                      5               8      *\/   */
+ /*      }else if( Dummy[k1]==3 ){ /\* For quant with age product *\/ */
+ /*        cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];        */
+ /*        printf("QhPxij Quant with age k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
+ /*        printf("hpxij new Quanti with age product precov[nres=%d][k1=%d] * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
+ /*        /\* if(Dummy[Tage[k]]== 2){ /\\* dummy with age *\\/ *\/ */
+ /*        /\* /\\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\\* dummy with age *\\\/ *\\/ *\/ */
+ /*        /\*   /\\* 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,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; *\\/ *\/ */
+ /*        /\*   cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; *\/ */
+ /*        /\*   printf("hPxij Age combi=%d k=%d cptcovage=%d Tage[%d]=%d Tvar[Tage[%d]]=V%d nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]]])]=%d nres=%d\n",ij,k,cptcovage,k,Tage[k],k,Tvar[Tage[k]], nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]])],nres); *\/ */
+ /*        /\* } else if(Dummy[Tage[k]]== 3){ /\\* quantitative with age *\\/ *\/ */
+ /*        /\*   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]); *\/ */
+ /*      }else if(Typevar[k1]==2 ){ /\* For product (not with age) *\/ */
+ /* /\*       for (k=1; k<=cptcovprod;k++){ /\\*  For product without age *\\/ *\/ */
+ /* /\* /\\*             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 *\\/ *\/ */
+ /* /\* /\\*cptcovprod=1            1               2            *\\/ *\/ */
+ /* /\* /\\*Tprod[]=                4               7            *\\/ *\/ */
+ /* /\* /\\*Tvard[][1]             4               1             *\\/ *\/ */
+ /* /\* /\\*Tvard[][2]               3               2           *\\/ *\/ */
+ /*        /\* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]=%d nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]=%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2],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)]; *\/ */
+ /*        cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];     */
+ /*        printf("hPxij Prod ij=%d k1=%d  cov[2+%d+%d]=%.5f Tvard[%d][1]=V%d * Tvard[%d][2]=V%d ; TinvDoQresult[nres][Tvardk[k1][1]]=%.4f * TinvDoQresult[nres][Tvardk[k1][1]]=%.4f\n",ij,k1,nagesqr,k1,cov[2+nagesqr+k1],k1,Tvardk[k1][1], k1,Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][1]], TinvDoQresult[nres][Tvardk[k1][2]]); */
+ /*        printf("hpxij new Product no age product precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
+ /*        /\* if(Dummy[Tvardk[k1][1]]==0){ *\/ */
+ /*        /\*   if(Dummy[Tvardk[k1][2]]==0){ /\\* Product of dummies *\\/ *\/ */
+ /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
+ /*            /\* cov[2+nagesqr+k1]=Tinvresult[nres][Tvardk[k1][1]] * Tinvresult[nres][Tvardk[k1][2]];   *\/ */
+ /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])]; *\/ */
+ /*          /\* }else{ /\\* Product of dummy by quantitative *\\/ *\/ */
+ /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * Tqresult[nres][k]; *\/ */
+ /*            /\* cov[2+nagesqr+k1]=Tresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]; *\/ */
+ /*        /\*   } *\/ */
+ /*        /\* }else{ /\\* Product of quantitative by...*\\/ *\/ */
+ /*        /\*   if(Dummy[Tvard[k][2]]==0){  /\\* quant by dummy *\\/ *\/ */
+ /*        /\*     /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][Tvard[k][1]]; *\\/ *\/ */
+ /*        /\*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
+ /*        /\*   }else{ /\\* Product of two quant *\\/ *\/ */
+ /*        /\*     /\\* cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\\/ *\/ */
+ /*        /\*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
+ /*        /\*   } *\/ */
+ /*        /\* }/\\*end of products quantitative *\\/ *\/ */
+ /*      }/\*end of products *\/ */
+       /* } /\* End of loop on model equation *\/ */
        /* 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 *\/ */
- Line 3178  double ***hpxij(double ***po, int nhstep
+ Line 5354  double ***hpxij(double ***po, int nhstep
        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
        /*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 */
        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
                     pmij(pmmij,cov,ncovmodel,x,nlstate));
        /* if((int)age == 70){ */
- Line 3213  double ***hpxij(double ***po, int nhstep
+ Line 5389  double ***hpxij(double ***po, int nhstep
  /* 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, int nres )
  {
-   /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
+   /* For dummy covariates given in each resultline (for historical, computes the corresponding combination ij),
+      computes the transition matrix starting at age 'age' over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
       nhstepm*hstepm matrices.
- Line 3225  double ***hbxij(double ***po, int nhstep
+ Line 5402  double ***hbxij(double ***po, int nhstep
       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, k1;
    double **out, cov[NCOVMAX+1], **bmij();
    double **newm, ***newmm;
    double agexact;
-   double agebegin, ageend;
+   /*double agebegin, ageend;*/
    double **oldm, **savm;
    newmm=po; /* To be saved */
- Line 3248  double ***hbxij(double ***po, int nhstep
+ Line 5425  double ***hbxij(double ***po, int nhstep
        cov[1]=1.;
        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 *\/ */
+         /* Debug */
+       /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */
        cov[2]=agexact;
-       if(nagesqr==1)
+       if(nagesqr==1){
          cov[3]= agexact*agexact;
-       for (k=1; k<=cptcovn;k++){
+       }
-       /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
+       /** New code */
-       /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
+       for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
-         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
+         if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
-         /* 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+k1]=precov[nres][k1]*cov[2];
-       }
+         }else{
-       for (k=1; k<=nsq;k++) { /* For single varying covariates only */
+           cov[2+nagesqr+k1]=precov[nres][k1];
-         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
+         }
-         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
+       }/* End of loop on model equation */
-         /* 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]); */
+       /** End of new code */
-       }
+   /** This was old code */
-       for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
+       /* for (k=1; k<=nsd;k++){ /\* For single dummy covariates only *\//\* cptcovn error *\/ */
-         if(Dummy[Tvar[Tage[k]]]){
+       /* /\*    cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; *\/ */
-           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+       /* /\* /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\\/ *\/ */
-         } else{
+       /*        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])];/\* Bug valgrind *\/ */
-           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
+       /*   /\* 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)); *\/ */
-         }
+       /* } */
-         /* 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<=nsq;k++) { /\* For single varying covariates only *\/ */
-       }
+       /*        /\* 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]); *\/ */
-       }
+       /* } */
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+       /* for (k=1; k<=cptcovage;k++){ /\* Should start at cptcovn+1 *\//\* For product with age *\/ */
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+       /*        /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age error!!!*\\/ *\/ */
+       /*        if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */
+       /*          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+       /*        } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age *\/ */
+       /*          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,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,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,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]; */
+       /*          }else{ */
+       /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
+       /*          } */
+       /*        }else{ */
+       /*          if(Dummy[Tvard[k][2]]==0){ */
+       /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
+       /*          }else{ */
+       /*            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
+       /*          } */
+       /*        } */
+       /* }                       */
+       /* /\*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*\/ */
+       /* /\*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*\/ */
+ /** End of old code */
        /* Careful transposed matrix */
        /* age is in cov[2], prevacurrent at beginning of transition. */
        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
        /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
        out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
-,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);/* Bug valgrind */
        /* if((int)age == 70){ */
        /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
        /*        for(i=1; i<=nlstate+ndeath; i++) { */
- Line 3335  double ***hbxij(double ***po, int nhstep
+ Line 5540  double ***hbxij(double ***po, int nhstep
  /*************** log-likelihood *************/
  double func( double *x)
  {
-   int i, ii, j, k, mi, d, kk;
+   int i, ii, j, k, mi, d, kk, kf=0;
    int ioffset=0;
+   int ipos=0,iposold=0,ncovv=0;
+   double cotvarv, cotvarvold;
    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double lli; /* Individual log likelihood */
    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;
-   long ipmx;
    double agexact;
+   double agebegin, ageend;
    /*extern weight */
    /* We are differentiating ll according to initial status */
    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
- Line 3367  double func( double *x)
+ Line 5576  double func( double *x)
        */
        ioffset=2+nagesqr ;
     /* Fixed */
-       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
+       for (kf=1; kf<=ncovf;kf++){ /* For each fixed covariate dummy or quant or prod */
-         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)*/
+         /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
+         /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+         /*  TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
+         /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
+         cov[ioffset+TvarFind[kf]]=covar[Tvar[TvarFind[kf]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/
+         /* V1*V2 (7)  TvarFind[2]=7, TvarFind[3]=9 */
        }
        /* 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 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6
           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]
+          And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i] because now is moved after nvocol+nqv
           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++){  /* Varying with waves */
-         for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
+       /* Wave varying (but not age varying) */
-           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
+         /* for(k=1; k <= ncovv ; k++){ /\* Varying  covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3)  Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*\/ */
-           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
+         /*   /\* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? *\/ */
+         /*   cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; */
+         /* } */
+         for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying  covariates (single and product but no age )*/
+           itv=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate */
+           ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
+           if(FixedV[itv]!=0){ /* Not a fixed covariate */
+             cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][i];  /* cotvar[wav][ncovcol+nqv+iv][i] */
+           }else{ /* fixed covariate */
+             cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
+           }
+           if(ipos!=iposold){ /* Not a product or first of a product */
+             cotvarvold=cotvarv;
+           }else{ /* A second product */
+             cotvarv=cotvarv*cotvarvold;
+           }
+           iposold=ipos;
+           cov[ioffset+ipos]=cotvarv;
          }
+         /* for products of time varying to be done */
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              savm[ii][j]=(ii==j ? 1.0 : 0.0);
            }
+         agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
+         ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
            cov[2]=agexact;
            if(nagesqr==1)
              cov[3]= agexact*agexact;  /* Should be changed here */
-           for (kk=1; kk<=cptcovage;kk++) {
+           /* for (kk=1; kk<=cptcovage;kk++) { */
-           if(!FixedV[Tvar[Tage[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
+           /*   else */
-             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
+           /*     cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]*agexact; /\* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) *\/  */
+           /* } */
+           for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying  covariates with age including individual from products, product is computed dynamically */
+             itv=TvarAVVA[ncovva]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product Vn*Vm into Vn and then Vm  */
+             ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
+             if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
+               cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */
+             }else{ /* fixed covariate */
+               cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
+             }
+             if(ipos!=iposold){ /* Not a product or first of a product */
+               cotvarvold=cotvarv;
+             }else{ /* A second product */
+               cotvarv=cotvarv*cotvarvold;
+             }
+             iposold=ipos;
+             cov[ioffset+ipos]=cotvarv*agexact;
+             /* For products */
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
            savm=oldm;
- Line 3482  double func( double *x)
+ Line 5735  double func( double *x)
            /*survp += out[s1][j]; */
            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{
            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=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
          /*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("num[i], i=%d, 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;
          sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- Line 3510  double func( double *x)
+ Line 5763  double func( double *x)
      } /* end of individual */
    }  else if(mle==2){
      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 ;
+       for (k=1; k<=ncovf;k++)
+         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
+         for(k=1; k <= ncovv ; k++){
+           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; /* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
+         }
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- Line 3557  double func( double *x)
+ Line 5815  double func( double *x)
            if(nagesqr==1)
              cov[3]= agexact*agexact;
            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; /* Tage[kk] gives the data-covariate associated with age */
+             else
+               cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]*agexact; /* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 3613  double func( double *x)
+ Line 5874  double func( double *x)
          ipmx +=1;
          sw += weight[i];
          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("num[i]=%09ld, 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",num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
        } /* end of wave */
      } /* end of individual */
    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
- Line 3632  double func( double *x)
+ Line 5893  double func( double *x)
            if(nagesqr==1)
              cov[3]= agexact*agexact;
            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; /* Tage[kk] gives the data-covariate associated with age */
+             else
+               cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]*agexact; /* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- Line 3661  double func( double *x)
+ Line 5925  double func( double *x)
  double funcone( double *x)
  {
    /* 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, kv=0, kf=0;
    int ioffset=0;
+   int ipos=0,iposold=0,ncovv=0;
+   double cotvarv, cotvarvold;
    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double lli; /* Individual log likelihood */
- Line 3684  double funcone( double *x)
+ Line 5951  double funcone( double *x)
    for(k=1; k<=nlstate; k++) ll[k]=0.;
    ioffset=0;
    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     /* Computes the values of the ncovmodel covariates of the model
+        depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
+        Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
+        to be observed in j being in i according to the model.
+     */
      /* ioffset=2+nagesqr+cptcovage; */
      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 */
+     for (kf=1; kf<=ncovf;kf++){ /*  V2  +  V3  +  V4  Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
-       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)*/
+       /* printf("Debug3 TvarFind[%d]=%d",kf, TvarFind[kf]); */
+       /* printf(" Tvar[TvarFind[kf]]=%d", Tvar[TvarFind[kf]]); */
+       /* printf(" i=%d covar[Tvar[TvarFind[kf]]][i]=%f\n",i,covar[Tvar[TvarFind[kf]]][i]); */
+       cov[ioffset+TvarFind[kf]]=covar[Tvar[TvarFind[kf]]][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  */
- Line 3701  double funcone( double *x)
+ Line 5976  double funcone( double *x)
  /*    cov[2+9]=covar[Tvar[9]][i];  */
  /*    cov[2+9]=covar[1][i]; V1  */
      }
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
+          is 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6
+          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 in the DATA is the cotvar[mw[mi+1][i]][ncovcol+nqv+iv][i]
+       */
+     /* This part may be useless now because everythin should be in covar */
      /* 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?)*\/ */
      /* } */
- Line 3710  double funcone( double *x)
+ Line 5996  double funcone( double *x)
      for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
-     /* Wave varying (but not age varying) */
+       /* Wave varying (but not age varying) *//* V1+V3+age*V1+age*V3+V1*V3 with V4 tv and V5 tvq k= 1 to 5 and extra at V(5+1)=6 for V1*V3 */
-       for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
+       /* 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]]][i]; *\/ */
-         cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][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 *\/ */
+       /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
-       /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
+       /* model V1+V3+age*V1+age*V3+V1*V3 */
-       /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
+       /*  Tvar={1, 3, 1, 3, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
-       /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
+       /*  TvarVV[1]=V3 (first time varying in the model equation, TvarVV[2]=V1 (in V1*V3) TvarVV[3]=3(V3)  */
-       /* 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]); */
+       /* We need the position of the time varying or product in the model */
+       /* TvarVVind={2,5,5}, for V3 at position 2 and then the product V1*V3 is decomposed into V1 and V3 but at same position 5 */
+       /* TvarVV gives the variable name */
+       /* Other example V1 + V3 + V5 + age*V1  + age*V3 + age*V5 + V1*V3  + V3*V5  + V1*V5
+       *      k=         1   2     3     4         5        6        7       8        9
+       *  varying            1     2                                 3       4        5
+       *  ncovv              1     2                                3 4     5 6      7 8
+       * TvarVV[ncovv]      V3     5                                1 3     3 5      1 5
+       * TvarVVind           2     3                                7 7     8 8      9 9
+       * TvarFind[k]     1   0     0     0         0        0        0       0        0
+       */
+       /* Other model ncovcol=5 nqv=0 ntv=3 nqtv=0 nlstate=3
+        * V2 V3 V4 are fixed V6 V7 are timevarying so V8 and V5 are not in the model and product column will start at 9 Tvar[(v6*V2)6]=9
+         * FixedV[ncovcol+qv+ntv+nqtv]       V5
+         * 3           V1  V2     V3    V4   V5 V6     V7  V8 V3*V2 V7*V2  V6*V3 V7*V3 V6*V4 V7*V4
+         *             0   0      0      0    0  1      1   1  0, 0, 1,1,   1, 0, 1, 0, 1, 0, 1, 0}
+         * 3           0   0      0      0    0  1      1   1  0,     1      1    1      1    1}
+         * model=          V2  +  V3  +  V4  +  V6  +  V7  +  V6*V2  +  V7*V2  +  V6*V3  +  V7*V3  +  V6*V4  +  V7*V4
+         *                +age*V2 +age*V3 +age*V4 +age*V6 + age*V7
+         *                +age*V6*V2 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
+         * model2=          V2  +  V3  +  V4  +  V6  +  V7  +  V3*V2  +  V7*V2  +  V6*V3  +  V7*V3  +  V6*V4  +  V7*V4
+         *                +age*V2 +age*V3 +age*V4 +age*V6 + age*V7
+         *                +age*V3*V2 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
+         * model3=          V2  +  V3  +  V4  +  V6  +  V7  + age*V3*V2  +  V7*V2  +  V6*V3  +  V7*V3  +  V6*V4  +  V7*V4
+         *                +age*V2 +age*V3 +age*V4 +age*V6 + age*V7
+         *                +V3*V2 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
+         * kmodel           1     2      3      4      5        6         7         8         9        10        11
+         *                  12       13      14      15       16
+         *                    17        18         19        20         21
+         * Tvar[kmodel]     2     3      4      6      7        9        10        11        12        13        14
+         *                   2       3        4       6        7
+         *                     9         11          12        13         14
+         * cptcovage=5+5 total of covariates with age
+         * Tage[cptcovage] age*V2=12      13      14      15       16
+         *1                   17            18         19        20         21 gives the position in model of covariates associated with age
+         *3 Tage[cptcovage] age*V3*V2=6
+         *3                age*V2=12         13      14      15       16
+         *3                age*V6*V3=18      19    20   21
+         * Tvar[Tage[cptcovage]]    Tvar[12]=2      3      4       6         Tvar[16]=7(age*V7)
+         *     Tvar[17]age*V6*V2=9      Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
+         * 2   Tvar[17]age*V3*V2=9      Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
+         * 3 Tvar[Tage[cptcovage]]    Tvar[6]=9      Tvar[12]=2      3     4       6         Tvar[16]=7(age*V7)
+         * 3     Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
+         * 3 Tage[cptcovage] age*V3*V2=6   age*V2=12 age*V3 13    14      15       16
+         *                    age*V6*V3=18         19        20         21 gives the position in model of covariates associated with age
+         * 3   Tvar[17]age*V3*V2=9      Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
+         * Tvar=                {2, 3, 4, 6, 7,
+         *                       9, 10, 11, 12, 13, 14,
+         *              Tvar[12]=2, 3, 4, 6, 7,
+         *              Tvar[17]=9, 11, 12, 13, 14}
+         * Typevar[1]@21 = {0, 0, 0, 0, 0,
+         *                  2, 2, 2, 2, 2, 2,
+         * 3                3, 2, 2, 2, 2, 2,
+         *                  1, 1, 1, 1, 1,
+         *                  3, 3, 3, 3, 3}
+         * 3                 2, 3, 3, 3, 3}
+         * p Tposprod[1]@21 {0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 0, 0, 0, 0, 0, 1, 3, 4, 5, 6} Id of the prod at position k in the model
+         * p Tprod[1]@21 {6, 7, 8, 9, 10, 11, 0 <repeats 15 times>}
+         * 3 Tposprod[1]@21 {0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 0, 0, 0, 0, 0, 1, 3, 4, 5, 6}
+         * 3 Tprod[1]@21 {17, 7, 8, 9, 10, 11, 0 <repeats 15 times>}
+         * cptcovprod=11 (6+5)
+         * FixedV[Tvar[Tage[cptcovage]]]]  FixedV[2]=0      FixedV[3]=0      0      1          (age*V7)Tvar[16]=1 FixedV[absolute] not [kmodel]
+         *   FixedV[Tvar[17]=FixedV[age*V6*V2]=FixedV[9]=1        1         1          1         1
+         * 3 FixedV[Tvar[17]=FixedV[age*V3*V2]=FixedV[9]=0        [11]=1         1          1         1
+         * FixedV[]          V1=0     V2=0   V3=0  v4=0    V5=0  V6=1    V7=1 v8=1  OK then model dependent
+         *                   9=1  [V7*V2]=[10]=1 11=1  12=1  13=1  14=1
+         * 3                 9=0  [V7*V2]=[10]=1 11=1  12=1  13=1  14=1
+         * cptcovdageprod=5  for gnuplot printing
+         * cptcovprodvage=6
+         * ncova=15           1        2       3       4       5
+         *                      6 7        8 9      10 11        12 13     14 15
+         * TvarA              2        3       4       6       7
+         *                      6 2        6 7       7 3          6 4       7 4
+         * TvaAind             12 12      13 13     14 14      15 15       16 16
+         * ncovf            1     2      3
+         *                                    V6       V7      V6*V2     V7*V2     V6*V3     V7*V3     V6*V4     V7*V4
+         * ncovvt=14                            1      2        3 4       5 6       7 8       9 10     11 12     13 14
+         * TvarVV[1]@14 = itv               {V6=6,     7, V6*V2=6, 2,     7, 2,     6, 3,     7, 3,     6, 4,     7, 4}
+         * TvarVVind[1]@14=                    {4,     5,       6, 6,     7, 7,     8, 8,      9, 9,   10, 10,   11, 11}
+         * 3 ncovvt=12                        V6       V7      V7*V2     V6*V3     V7*V3     V6*V4     V7*V4
+         * 3 TvarVV[1]@12 = itv                {6,     7, V7*V2=7, 2,     6, 3,     7, 3,     6, 4,     7, 4}
+         * 3                                    1      2        3  4      5  6      7  8      9 10     11 12
+         * TvarVVind[1]@12=         {V6 is in k=4,     5,  7,(4isV2)=7,   8, 8,      9, 9,   10,10,    11,11}TvarVVind[12]=k=11
+         * TvarV              6, 7, 9, 10, 11, 12, 13, 14
+         * 3 cptcovprodvage=6
+         * 3 ncovta=15    +age*V3*V2+age*V2+agev3+ageV4 +age*V6 + age*V7 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
+         * 3 TvarAVVA[1]@15= itva 3 2    2      3    4        6       7        6 3         7 3         6 4         7 4
+         * 3 ncovta             1 2      3      4    5        6       7        8 9       10 11       12 13        14 15
+         *?TvarAVVAind[1]@15= V3 is in k=2 1 1  2    3        4       5        4,2         5,2,      4,3           5 3}TvarVVAind[]
+         * TvarAVVAind[1]@15= V3 is in k=6 6 12  13   14      15      16       18 18       19,19,     20,20        21,21}TvarVVAind[]
+         * 3 ncovvta=10     +age*V6 + age*V7 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
+         * 3 we want to compute =cotvar[mw[mi][i]][TvarVVA[ncovva]][i] at position TvarVVAind[ncovva]
+         * 3 TvarVVA[1]@10= itva   6       7        6 3         7 3         6 4         7 4
+         * 3 ncovva                1       2        3 4         5 6         7 8         9 10
+         * TvarVVAind[1]@10= V6 is in k=4  5        8,8         9, 9,      10,10        11 11}TvarVVAind[]
+         * TvarVVAind[1]@10=       15       16     18,18        19,19,      20,20        21 21}TvarVVAind[]
+         * TvarVA              V3*V2=6 6 , 1, 2, 11, 12, 13, 14
+         * TvarFind[1]@14= {1,    2,     3,     0 <repeats 12 times>}
+         * Tvar[1]@21=     {2,    3,     4,    6,      7,      9,      10,        11,       12,      13,       14,
+         *                   2, 3, 4, 6, 7,
+         *                     6, 8, 9, 10, 11}
+         * TvarFind[itv]                        0      0       0
+         * FixedV[itv]                          1      1       1  0      1 0       1 0       1 0       0
+         *? FixedV[itv]                          1      1       1  0      1 0       1 0       1 0      1 0     1 0
+         * Tvar[TvarFind[ncovf]]=[1]=2 [2]=3 [4]=4
+         * Tvar[TvarFind[itv]]                [0]=?      ?ncovv 1 à ncovvt]
+         *   Not a fixed cotvar[mw][itv][i]     6       7      6  2      7, 2,     6, 3,     7, 3,     6, 4,     7, 4}
+         *   fixed covar[itv]                  [6]     [7]    [6][2]
+         */
+       for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /*  V6       V7      V7*V2     V6*V3     V7*V3     V6*V4     V7*V4 Time varying  covariates (single and extended product but no age) including individual from products, product is computed dynamically */
+         itv=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, or fixed covariate of a varying product after exploding product Vn*Vm into Vn and then Vm  */
+         ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
+         /* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv *\/ */
+         if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
+           /* printf("DEBUG ncovv=%d, Varying TvarVV[ncovv]=%d\n",ncovv, TvarVV[ncovv]); */
+           cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */
+           /* printf("DEBUG Varying cov[ioffset+ipos=%d]=%g \n",ioffset+ipos,cotvarv); */
+         }else{ /* fixed covariate */
+           /* cotvarv=covar[Tvar[TvarFind[itv]]][i];  /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model *\/ */
+           /* printf("DEBUG ncovv=%d, Fixed TvarVV[ncovv]=%d\n",ncovv, TvarVV[ncovv]); */
+           cotvarv=covar[itv][i];  /* Good: In V6*V3, 3 is fixed at position of the data */
+           /* printf("DEBUG Fixed cov[ioffset+ipos=%d]=%g \n",ioffset+ipos,cotvarv); */
+         }
+         if(ipos!=iposold){ /* Not a product or first of a product */
+           cotvarvold=cotvarv;
+         }else{ /* A second product */
+           cotvarv=cotvarv*cotvarvold;
+         }
+         iposold=ipos;
+         cov[ioffset+ipos]=cotvarv;
+         /* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
+         /* For products */
+       }
+       /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates single *\/ */
+       /*        iv=TvarVDind[itv]; /\* iv, position in the model equation of time varying covariate itv *\/ */
+       /*        /\*         "V1+V3+age*V1+age*V3+V1*V3" with V3 time varying *\/ */
+       /*        /\*           1  2   3      4      5                         *\/ */
+       /*        /\*itv           1                                           *\/ */
+       /*        /\* TvarVInd[1]= 2                                           *\/ */
+       /*        /\* iv= Tvar[Tmodelind[itv]]-ncovcol-nqv;  /\\* Counting the # varying covariate from 1 to ntveff *\\/ *\/ */
+       /*        /\* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; *\/ */
+       /*        /\* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; *\/ */
+       /*        /\* k=ioffset-2-nagesqr-cptcovage+itv; /\\* position in simple model *\\/ *\/ */
+       /*        /\* cov[ioffset+iv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; *\/ */
+       /*        cov[ioffset+iv]=cotvar[mw[mi][i]][itv][i]; */
+       /*        /\* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][itv][i]=%f\n", i, mi, itv, TvarVDind[itv],cotvar[mw[mi][i]][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]); *\/ */
- Line 3743  double funcone( double *x)
+ Line 6176  double funcone( double *x)
          cov[2]=agexact;
          if(nagesqr==1)
            cov[3]= agexact*agexact;
-         for (kk=1; kk<=cptcovage;kk++) {
+         for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying  covariates with age including individual from products, product is computed dynamically */
-           if(!FixedV[Tvar[Tage[kk]]])
+           itv=TvarAVVA[ncovva]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product Vn*Vm into Vn and then Vm  */
-             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+           ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
-           else
+           /* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv *\/ */
-             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
+           if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
+             /* printf("DEBUG  ncovva=%d, Varying TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
+             cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */
+           }else{ /* fixed covariate */
+             /* cotvarv=covar[Tvar[TvarFind[itv]]][i];  /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model *\/ */
+             /* printf("DEBUG ncovva=%d, Fixed TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
+             cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
+           }
+           if(ipos!=iposold){ /* Not a product or first of a product */
+             cotvarvold=cotvarv;
+           }else{ /* A second product */
+             /* printf("DEBUG * \n"); */
+             cotvarv=cotvarv*cotvarvold;
+           }
+           iposold=ipos;
+           /* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
+           cov[ioffset+ipos]=cotvarv*agexact;
+           /* For products */
          }
          /* 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); */
          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- Line 3758  double funcone( double *x)
+ Line 6209  double funcone( double *x)
          savm=oldm;
          oldm=newm;
        } /* end mult */
+         /*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.
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
+          * (in months) between two waves is not a multiple of stepm, we rounded to
+          * the nearest (and in case of equal distance, to the lowest) interval but now
+          * 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
+          * 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
+                                  * -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 less biased than in previous versions.
+                                  */
        s1=s[mw[mi][i]][i];
        s2=s[mw[mi+1][i]][i];
        /* if(s2==-1){ */
- Line 3790  double funcone( double *x)
+ Line 6253  double funcone( double *x)
        ipmx +=1;
        sw += weight[i];
        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]); */
+       /* Printing covariates values for each contribution for checking */
+       /* printf("num[i]=%09ld, 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",num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
        if(globpr){
          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 ", \
                  num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
 *weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
+         /*      printf("%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\ */
+         /* %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, */
+         /*              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++){
            llt +=ll[k]*gipmx/gsw;
            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+           /* printf(" %10.6f",-ll[k]*gipmx/gsw); */
          }
-         fprintf(ficresilk," %10.6f\n", -llt);
+         fprintf(ficresilk," %10.6f ", -llt);
-       }
+         /* printf(" %10.6f\n", -llt); */
-         } /* end of wave */
+         /* if(debugILK){ /\* debugILK is set by a #d in a comment line *\/ */
- } /* end of individual */
+         /* fprintf(ficresilk,"%09ld ", num[i]); */ /* not necessary */
- for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+         for (kf=1; kf<=ncovf;kf++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
+           fprintf(ficresilk," %g",covar[Tvar[TvarFind[kf]]][i]);
+         }
+         for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying  covariates (single and product but no age) including individual from products */
+           ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
+           if(ipos!=iposold){ /* Not a product or first of a product */
+             fprintf(ficresilk," %g",cov[ioffset+ipos]);
+             /* printf(" %g",cov[ioffset+ipos]); */
+           }else{
+             fprintf(ficresilk,"*");
+             /* printf("*"); */
+           }
+           iposold=ipos;
+         }
+         /* for (kk=1; kk<=cptcovage;kk++) { */
+         /*   if(!FixedV[Tvar[Tage[kk]]]){ */
+         /*     fprintf(ficresilk," %g*age",covar[Tvar[Tage[kk]]][i]); */
+         /*     /\* printf(" %g*age",covar[Tvar[Tage[kk]]][i]); *\/ */
+         /*   }else{ */
+         /*     fprintf(ficresilk," %g*age",cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]);/\* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) *\/  */
+         /*     /\* printf(" %g*age",cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]);/\\* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) *\\/  *\/ */
+         /*   } */
+         /* } */
+         for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying  covariates with age including individual from products, product is computed dynamically */
+           itv=TvarAVVA[ncovva]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product Vn*Vm into Vn and then Vm  */
+           ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
+           /* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv *\/ */
+           if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
+             /* printf("DEBUG  ncovva=%d, Varying TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
+             cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */
+           }else{ /* fixed covariate */
+             /* cotvarv=covar[Tvar[TvarFind[itv]]][i];  /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model *\/ */
+             /* printf("DEBUG ncovva=%d, Fixed TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
+             cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
+           }
+           if(ipos!=iposold){ /* Not a product or first of a product */
+             cotvarvold=cotvarv;
+           }else{ /* A second product */
+             /* printf("DEBUG * \n"); */
+             cotvarv=cotvarv*cotvarvold;
+           }
+           cotvarv=cotvarv*agexact;
+           fprintf(ficresilk," %g*age",cotvarv);
+           iposold=ipos;
+           /* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
+           cov[ioffset+ipos]=cotvarv;
+           /* For products */
+         }
+         /* printf("\n"); */
+         /* } /\*  End debugILK *\/ */
+         fprintf(ficresilk,"\n");
+       } /* End if globpr */
+     } /* end of wave */
+   } /* end of individual */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
  /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
- l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   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 ***********/
- 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
       the selection of individuals/waves and
       to check the exact contribution to the likelihood.
       Plotting could be done.
-    */
+   */
-   int k;
+   void pstamp(FILE *ficres);
+   int k, kf, kk, kvar, ncovv, iposold, ipos;
    if(*globpri !=0){ /* Just counts and sums, no printings */
      strcpy(fileresilk,"ILK_");
- Line 3832  void likelione(FILE *ficres,double p[],
+ Line 6356  void likelione(FILE *ficres,double p[],
        printf("Problem with resultfile: %s\n", fileresilk);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
      }
+     pstamp(ficresilk);fprintf(ficresilk,"# model=1+age+%s\n",model);
      fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
      fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
      for(k=1; k<=nlstate; k++)
        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total) ");
-   }
+     /* if(debugILK){ /\* debugILK is set by a #d in a comment line *\/ */
+       for(kf=1;kf <= ncovf; kf++){
+         fprintf(ficresilk,"V%d",Tvar[TvarFind[kf]]);
+         /* printf("V%d",Tvar[TvarFind[kf]]); */
+       }
+       for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){
+         ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
+         if(ipos!=iposold){ /* Not a product or first of a product */
+           /* printf(" %d",ipos); */
+           fprintf(ficresilk," V%d",TvarVV[ncovv]);
+         }else{
+           /* printf("*"); */
+           fprintf(ficresilk,"*");
+         }
+         iposold=ipos;
+       }
+       for (kk=1; kk<=cptcovage;kk++) {
+         if(!FixedV[Tvar[Tage[kk]]]){
+           /* printf(" %d*age(Fixed)",Tvar[Tage[kk]]); */
+           fprintf(ficresilk," %d*age(Fixed)",Tvar[Tage[kk]]);
+         }else{
+           fprintf(ficresilk," %d*age(Varying)",Tvar[Tage[kk]]);/* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
+           /* printf(" %d*age(Varying)",Tvar[Tage[kk]]);/\* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) *\/  */
+         }
+       }
+     /* } /\* End if debugILK *\/ */
+     /* printf("\n"); */
+     fprintf(ficresilk,"\n");
+   } /* End glogpri */
-   *fretone=(*funcone)(p);
+   *fretone=(*func)(p);
    if(*globpri !=0){
      fclose(ficresilk);
      if (mle ==0)
- Line 3848  void likelione(FILE *ficres,double p[],
+ Line 6402  void likelione(FILE *ficres,double p[],
      else if(mle >=1)
        fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
      fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
-     for (k=1; k<= nlstate ; k++) {
-       fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
- <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
-     }
      fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
- <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+ <img src=\"%s-ori.png\">\n",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
      fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
- <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+ <img src=\"%s-dest.png\">\n",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+     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>\n \
+ <img src=\"%s-p%dj.png\">\n",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
+       for(kf=1; kf <= ncovf; kf++){ /* For each simple dummy covariate of the model */
+          kvar=Tvar[TvarFind[kf]];  /* variable */
+          fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored covariate V%d. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): ",k,k,Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],Tvar[TvarFind[kf]]);
+          fprintf(fichtm,"<a href=\"%s-p%dj-%d.png\">%s-p%dj-%d.png</a><br>",subdirf2(optionfilefiname,"ILK_"),k,kvar,subdirf2(optionfilefiname,"ILK_"),k,kvar);
+          fprintf(fichtm,"<img src=\"%s-p%dj-%d.png\">",subdirf2(optionfilefiname,"ILK_"),k,Tvar[TvarFind[kf]]);
+       }
+       for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Loop on the time varying extended covariates (with extension of Vn*Vm */
+         ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
+         kvar=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate */
+         /* printf("DebugILK fichtm ncovv=%d, kvar=TvarVV[ncovv]=V%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); */
+         if(ipos!=iposold){ /* Not a product or first of a product */
+           /* fprintf(ficresilk," V%d",TvarVV[ncovv]); */
+           /* printf(" DebugILK fichtm ipos=%d != iposold=%d\n", ipos, iposold); */
+           if(Dummy[ipos]==0 && Typevar[ipos]==0){ /* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummy*age, 3quant*age) Typevar (0 single, 1=*age,2=Vn*vm)  */
+             fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored time varying dummy covariate V%d. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
+ <img src=\"%s-p%dj-%d.png\">",k,k,kvar,kvar,kvar,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,kvar);
+           } /* End only for dummies time varying (single?) */
+         }else{ /* Useless product */
+           /* printf("*"); */
+           /* fprintf(ficresilk,"*"); */
+         }
+         iposold=ipos;
+       } /* For each time varying covariate */
+     } /* End loop on states */
+ /*     if(debugILK){ */
+ /*       for(kf=1; kf <= ncovf; kf++){ /\* For each simple dummy covariate of the model *\/ */
+ /*      /\* kvar=Tvar[TvarFind[kf]]; *\/ /\* variable *\/ */
+ /*      for (k=1; k<= nlstate ; k++) { */
+ /*        fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored covariate V%. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \ */
+ /* <img src=\"%s-p%dj-%d.png\">",k,k,Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,Tvar[TvarFind[kf]]); */
+ /*      } */
+ /*       } */
+ /*       for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /\* Loop on the time varying extended covariates (with extension of Vn*Vm *\/ */
+ /*      ipos=TvarVVind[ncovv]; /\* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate *\/ */
+ /*      kvar=TvarVV[ncovv]; /\*  TvarVV={3, 1, 3} gives the name of each varying covariate *\/ */
+ /*      /\* printf("DebugILK fichtm ncovv=%d, kvar=TvarVV[ncovv]=V%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); *\/ */
+ /*      if(ipos!=iposold){ /\* Not a product or first of a product *\/ */
+ /*        /\* fprintf(ficresilk," V%d",TvarVV[ncovv]); *\/ */
+ /*        /\* printf(" DebugILK fichtm ipos=%d != iposold=%d\n", ipos, iposold); *\/ */
+ /*        if(Dummy[ipos]==0 && Typevar[ipos]==0){ /\* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummy*age, 3quant*age) Typevar (0 single, 1=*age,2=Vn*vm)  *\/ */
+ /*          for (k=1; k<= nlstate ; k++) { */
+ /*            fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \ */
+ /* <img src=\"%s-p%dj-%d.png\">",k,k,kvar,kvar,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,kvar); */
+ /*          } /\* End state *\/ */
+ /*        } /\* End only for dummies time varying (single?) *\/ */
+ /*      }else{ /\* Useless product *\/ */
+ /*        /\* printf("*"); *\/ */
+ /*        /\* fprintf(ficresilk,"*"); *\/  */
+ /*      } */
+ /*      iposold=ipos; */
+ /*       } /\* For each time varying covariate *\/ */
+ /*     }/\* End debugILK *\/ */
      fflush(fichtm);
-   }
+   }/* End globpri */
    return;
  }
- Line 3868  void likelione(FILE *ficres,double p[],
+ Line 6475  void likelione(FILE *ficres,double p[],
  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
  {
-   int i,j, iter=0;
+   int i,j,  jkk=0, iter=0;
    double **xi;
-   double fret;
+   /*double fret;*/
-   double fretone; /* Only one call to likelihood */
+   /*double fretone;*/ /* Only one call to likelihood */
    /*  char filerespow[FILENAMELENGTH];*/
+   /*double * p1;*/ /* Shifted parameters from 0 instead of 1 */
  #ifdef NLOPT
    int creturn;
    nlopt_opt opt;
    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
    double *lb;
    double minf; /* the minimum objective value, upon return */
-   double * p1; /* Shifted parameters from 0 instead of 1 */
    myfunc_data dinst, *d = &dinst;
  #endif
    xi=matrix(1,npar,1,npar);
-   for (i=1;i<=npar;i++)
+   for (i=1;i<=npar;i++)  /* Starting with canonical directions j=1,n xi[i=1,n][j] */
      for (j=1;j<=npar;j++)
        xi[i][j]=(i==j ? 1.0 : 0.0);
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+   printf("Powell-prax\n");  fprintf(ficlog,"Powell-prax\n");
    strcpy(filerespow,"POW_");
    strcat(filerespow,fileres);
    if((ficrespow=fopen(filerespow,"w"))==NULL) {
- Line 3902  void mlikeli(FILE *ficres,double p[], in
+ Line 6510  void mlikeli(FILE *ficres,double p[], in
        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
    fprintf(ficrespow,"\n");
  #ifdef POWELL
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+ #ifdef LINMINORIGINAL
- #endif
+ #else /* LINMINORIGINAL */
+   flatdir=ivector(1,npar);
+   for (j=1;j<=npar;j++) flatdir[j]=0;
+ #endif /*LINMINORIGINAL */
+ #ifdef FLATSUP
+   powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
+   /* reorganizing p by suppressing flat directions */
+   for(i=1, jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
+         printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
+         if(flatdir[jk]==1){
+           printf(" To be skipped %d%d flatdir[%d]=%d ",i,k,jk, flatdir[jk]);
+         }
+         for(j=1; j <=ncovmodel; j++){
+           printf("%12.7f ",p[jk]);
+           jk++;
+         }
+         printf("\n");
+       }
+     }
+   }
+ /* skipping */
+   /* for(i=1, jk=1, jkk=1;(flatdir[jk]==0)&& (i <=nlstate); i++){ */
+   for(i=1, jk=1, jkk=1;i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
+         printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
+         if(flatdir[jk]==1){
+           printf(" To be skipped %d%d flatdir[%d]=%d jk=%d p[%d] ",i,k,jk, flatdir[jk],jk, jk);
+           for(j=1; j <=ncovmodel;  jk++,j++){
+             printf(" p[%d]=%12.7f",jk, p[jk]);
+             /*q[jjk]=p[jk];*/
+           }
+         }else{
+           printf(" To be kept %d%d flatdir[%d]=%d jk=%d q[%d]=p[%d] ",i,k,jk, flatdir[jk],jk, jkk, jk);
+           for(j=1; j <=ncovmodel;  jk++,jkk++,j++){
+             printf(" p[%d]=%12.7f=q[%d]",jk, p[jk],jkk);
+             /*q[jjk]=p[jk];*/
+           }
+         }
+         printf("\n");
+       }
+       fflush(stdout);
+     }
+   }
+   powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
+ #else  /* FLATSUP */
+ /*  powell(p,xi,npar,ftol,&iter,&fret,func);*/
+ /*   praxis ( t0, h0, n, prin, x, beale_f ); */
+   int prin=1;
+   double h0=0.25;
+   double macheps;
+   double fmin;
+   macheps=pow(16.0,-13.0);
+ /* #include "praxis.h" */
+   /* Be careful that praxis start at x[0] and powell start at p[1] */
+    /* praxis ( ftol, h0, npar, prin, p, func ); */
+ /* p1= (p+1); */ /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
+ printf("Praxis Gegenfurtner \n");
+ fprintf(ficlog, "Praxis  Gegenfurtner\n");fflush(ficlog);
+ /* praxis ( ftol, h0, npar, prin, p1, func ); */
+   /* fmin = praxis(1.e-5,macheps, h, n, prin, x, func); */
+   fmin = praxis(ftol,macheps, h0, npar, prin, p, func);
+ printf("End Praxis\n");
+ #endif  /* FLATSUP */
+ #ifdef LINMINORIGINAL
+ #else
+       free_ivector(flatdir,1,npar);
+ #endif  /* LINMINORIGINAL*/
+ #endif /* POWELL */
  #ifdef NLOPT
  #ifdef NEWUOA
- Line 3931  void mlikeli(FILE *ficres,double p[], in
+ Line 6612  void mlikeli(FILE *ficres,double p[], in
    }
    nlopt_destroy(opt);
  #endif
+ #ifdef FLATSUP
+   /* npared = npar -flatd/ncovmodel; */
+   /* xired= matrix(1,npared,1,npared); */
+   /* paramred= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */
+   /* powell(pred,xired,npared,ftol,&iter,&fret,flatdir,func); */
+   /* free_matrix(xire,1,npared,1,npared); */
+ #else  /* FLATSUP */
+ #endif /* FLATSUP */
    free_matrix(xi,1,npar,1,npar);
    fclose(ficrespow);
    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
- Line 4150  double hessij( double x[], double **hess
+ Line 6839  double hessij( double x[], double **hess
        kmax=kmax+10;
      }
      if(kmax >=10 || firstime ==1){
+       /* What are the thetai and thetaj? thetai/ncovmodel thetai=(thetai-thetai%ncovmodel)/ncovmodel +thetai%ncovmodel=(line,pos)  */
        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 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);
- Line 4315  void pstamp(FILE *fichier)
+ Line 7005  void pstamp(FILE *fichier)
    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 ********************/
- Line 4322  void  freqsummary(char fileres[], double
+ Line 7026  void  freqsummary(char fileres[], double
                    int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
  {  /* Some frequencies as well as proposing some starting values */
+   /* Frequencies of any combination of dummy covariate used in the model equation */
    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 */
- Line 4330  void  freqsummary(char fileres[], double
+ Line 7034  void  freqsummary(char fileres[], double
    double ***freq; /* Frequencies */
    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 */
    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;
+   double *meanq, *stdq, *idq;
    double **meanqt;
    double *pp, **prop, *posprop, *pospropt;
    double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
- Line 4343  void  freqsummary(char fileres[], double
+ Line 7047  void  freqsummary(char fileres[], double
    pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
    /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
    meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
+   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_");
    strcat(fileresp,fileresu);
- Line 4366  void  freqsummary(char fileres[], double
+ Line 7072  void  freqsummary(char fileres[], double
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
              fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);
+   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies (weight=%d) and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm, weightopt);
    strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
    if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
- Line 4376  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7082  Title=%s <br>Datafile=%s Firstpass=%d La
      exit(70);
    } else{
      fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
- <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
+ ,<hr size=\"2\" color=\"#EC5E5E\"> \n                                   \
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
              fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions 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);
+   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>(weight=%d) 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,weightopt);
    y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
    x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
- Line 4388  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7094  Title=%s <br>Datafile=%s Firstpass=%d La
    j1=0;
    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
-   j=cptcoveff;  /* Only dummy covariates of the model */
+   j=cptcoveff;  /* Only simple dummy covariates used in the model */
+   /* j=cptcovn;  /\* Only dummy covariates of the model *\/ */
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
- Line 4396  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7103  Title=%s <br>Datafile=%s Firstpass=%d La
       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
+      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcovn
    */
    dateintsum=0;
    k2cpt=0;
- Line 4433  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7140  Title=%s <br>Datafile=%s Firstpass=%d La
      if(nj==1)
        j=0;  /* First pass for the constant */
      else{
-       j=cptcoveff; /* Other passes for the covariate values */
+       j=cptcoveff; /* Other passes for the covariate values number of simple covariates in the model V2+V1 =2 (simple dummy fixed or time varying) */
      }
      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 */
+     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all dummy covariates combination of the model, ie excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
        posproptt=0.;
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+       /*printf("cptcovn=%d Tvaraff=%d", cptcovn,Tvaraff[1]);
          scanf("%d", i);*/
        for (i=-5; i<=nlstate+ndeath; i++)
          for (s2=-5; s2<=nlstate+ndeath; s2++)
- Line 4451  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7158  Title=%s <br>Datafile=%s Firstpass=%d La
          posprop[i]=0;
          pospropt[i]=0;
        }
-       /* for (z1=1; z1<= nqfveff; z1++) {   */
+       for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
-       /*   meanq[z1]+=0.; */
+         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.; */
+       /*          meanqt[m][z1]=0.; */
-       /*   } */
+       /*        } */
-       /* } */
+       /* }       */
        /* dateintsum=0; */
        /* k2cpt=0; */
- Line 4467  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7177  Title=%s <br>Datafile=%s Firstpass=%d La
          if(j !=0){
            if(anyvaryingduminmodel==0){ /* If All fixed covariates */
              if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-               /* for (z1=1; z1<= nqfveff; z1++) {   */
-               /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
-               /* } */
                for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
                  /* if(Tvaraff[z1] ==-20){ */
                  /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                  /* }else  if(Tvaraff[z1] ==-10){ */
                  /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
-                 /* }else  */
+                 /* }else  */ /* TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/
-                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
+                 /* if( iind >=imx-3) printf("Searching error iind=%d Tvaraff[z1]=%d covar[Tvaraff[z1]][iind]=%.f TnsdVar[Tvaraff[z1]]=%d, cptcoveff=%d, cptcovs=%d \n",iind, Tvaraff[z1], covar[Tvaraff[z1]][iind],TnsdVar[Tvaraff[z1]],cptcoveff, cptcovs); */
+                 if(Tvaraff[z1]<1 || Tvaraff[z1]>=NCOVMAX)
+                   printf("Error Tvaraff[z1]=%d<1 or >=%d, cptcoveff=%d model=1+age+%s\n",Tvaraff[z1],NCOVMAX, cptcoveff, model);
+                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]){ /* for combination j1 of covariates */
                    /* 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 */
-                   /* 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",
+                   /* 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),
+                   /*   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);*/
+                   /*   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 */
+             } /* cptcoveff > 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(mi=1; mi<wav[iind];mi++){ /* For that wave */
+           for(mi=1; mi<wav[iind];mi++){ /* For each wave */
              m=mw[mi][iind];
              if(j!=0){
                if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                  for (z1=1; z1<=cptcoveff; z1++) {
                    if( Fixed[Tmodelind[z1]]==1){
-                     iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
+                     /* iv= Tvar[Tmodelind[z1]]-ncovcol-nqv; /\* Good *\/ */
-                     if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
+                     iv= Tvar[Tmodelind[z1]]; /* Good *//* because cotvar starts now at first at ncovcol+nqv+ntv */
+                     if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality. If covariate's
                                                                                        value is -1, we don't select. It differs from the
                                                                                        constant and age model which counts them. */
                        bool=0; /* not selected */
                    }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
-                     if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
+                     /* i1=Tvaraff[z1]; */
+                     /* i2=TnsdVar[i1]; */
+                     /* i3=nbcode[i1][i2]; */
+                     /* i4=covar[i1][iind]; */
+                     /* if(i4 != i3){ */
+                     if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) { /* Bug valgrind */
                        bool=0;
                      }
                    }
- Line 4510  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7226  Title=%s <br>Datafile=%s Firstpass=%d La
                }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
              } /* end j==0 */
              /* bool =0 we keep that guy which corresponds to the combination of dummy values */
-             if(bool==1){
+             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*/
- Line 4528  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7244  Title=%s <br>Datafile=%s Firstpass=%d La
                    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 on known values only */
+                     if(!isnan(covar[ncovcol+z1][iind])){
+                       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]; *//*error*/
+                       stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][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]; */
- Line 4543  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7267  Title=%s <br>Datafile=%s Firstpass=%d La
                bool=1;
              }/* end bool 2 */
            } /* 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 iind = 1 to imx */
-       /* prop[s][age] is feeded for any initial and valid live state as well as
+       /* prop[s][age] is fed 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 */
- Line 4561  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7290  Title=%s <br>Datafile=%s Firstpass=%d La
          fprintf(ficlog, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++){
            if(!FixedV[Tvaraff[z1]]){
-             printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
-             fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
-             fprintf(ficresphtm, "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,TnsdVar[Tvaraff[z1]])]);
-             fprintf(ficresphtmfr, "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,TnsdVar[Tvaraff[z1]])]);
-             fprintf(ficlog, "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,TnsdVar[Tvaraff[z1]])]);
            }else{
-             printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
-             fprintf(ficresp, "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,TnsdVar[Tvaraff[z1]])]);
-             fprintf(ficresphtm, "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,TnsdVar[Tvaraff[z1]])]);
-             fprintf(ficresphtmfr, "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,TnsdVar[Tvaraff[z1]])]);
-             fprintf(ficlog, "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,TnsdVar[Tvaraff[z1]])]);
            }
          }
          printf( "**********\n#");
- Line 4580  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7309  Title=%s <br>Datafile=%s Firstpass=%d La
          fprintf(ficresphtmfr, "**********</h3>\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 %.3g (weighted) 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");
+         }
+         /* mu = \frac{w x}{\sum w}
+            var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2
+         */
+         printf(" fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
+         fprintf(ficlog," fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
+         fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[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\">");
        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)]);
+       if(nj==2) for (z1=1; z1<=cptcoveff; z1++) {
+           printf(" V%d=%d, z1=%d, Tvaraff[z1]=%d, j1=%d, TnsdVar[Tvaraff[%d]]=%d |",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])], z1, Tvaraff[z1], j1,z1,TnsdVar[Tvaraff[z1]]);
+           fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+         }
        for(i=1; i<=nlstate;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);
- Line 4663  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7419  Title=%s <br>Datafile=%s Firstpass=%d La
          }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 (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
            }
          }
          for(s1=1; s1 <=nlstate ; s1++){
- Line 4740  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7496  Title=%s <br>Datafile=%s Firstpass=%d La
          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);
+         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced (or no resultline).</p>",j1);
          invalidvarcomb[j1]=0;
        }
        fprintf(ficresphtmfr,"</table>\n");
- Line 4814  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7570  Title=%s <br>Datafile=%s Firstpass=%d La
              fprintf(ficlog,"\n");
            }
          }
-       }
+       } /* end of state i */
        printf("#Freqsummary\n");
        fprintf(ficlog,"\n");
        for(s1=-1; s1 <=nlstate+ndeath; s1++){
- Line 4856  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7612  Title=%s <br>Datafile=%s Firstpass=%d La
      }
    } /* end mle=-2 */
    dateintmean=dateintsum/k2cpt;
+   date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
    fclose(ficresp);
    fclose(ficresphtm);
    fclose(ficresphtmfr);
+   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);
- Line 4949  void prevalence(double ***probs, double
+ Line 7708  void prevalence(double ***probs, double
    int i, m, jk, j1, bool, z1,j, iv;
    int mi; /* Effective wave */
    int iage;
-   double agebegin, ageend;
+   double agebegin; /*, ageend;*/
    double **prop;
    double posprop;
- Line 4967  void prevalence(double ***probs, double
+ Line 7726  void prevalence(double ***probs, double
    /*j=cptcoveff;*/
    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 simple dummy covariates */
      for (i=1; i<=nlstate; i++)
        for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
          prop[i][iage]=0.0;
- Line 4985  void prevalence(double ***probs, double
+ Line 7744  void prevalence(double ***probs, double
          /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
          for (z1=1; z1<=cptcoveff; z1++){
            if( Fixed[Tmodelind[z1]]==1){
-             iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
+             iv= Tvar[Tmodelind[z1]];/* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
-             if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
+             if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality */
                bool=0;
            }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) {
                bool=0;
              }
          }
- Line 5025  void prevalence(double ***probs, double
+ Line 7784  void prevalence(double ***probs, double
            if(posprop>=1.e-5){
              probs[i][jk][j1]= prop[jk][i]/posprop;
            } else{
-             if(first==1){
+             if(!first){
-               first=0;
+               first=1;
                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]);
-               fprintf(ficlog,"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\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
+               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]);
              }
            }
          }
- Line 5048  void prevalence(double ***probs, double
+ Line 7806  void prevalence(double ***probs, double
  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).
       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-      and mw[mi+1][i]. dh depends on stepm.
+      and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
    */
    int i=0, mi=0, m=0, mli=0;
- Line 5073  void  concatwav(int wav[], int **dh, int
+ Line 7831  void  concatwav(int wav[], int **dh, int
    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
      mi=0;  /* First valid wave */
      mli=0; /* Last valid wave */
-     m=firstpass;
+     m=firstpass;  /* Loop on waves */
-     while(s[m][i] <= nlstate){  /* a live state */
+     while(s[m][i] <= nlstate){  /* a live state or unknown state  */
        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; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition   */
          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 */
        }
-       else{ /* m >= lastpass, eventual special issue with warning */
+       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){ /* no death date and known date of interview, case -2 (vital status unknown is warned later */
            if(firsthree == 0){
-             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 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);
+             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;
+           }else if(firsthree >=1 && firsthree < 10){
+             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);
+             firsthree++;
+           }else if(firsthree == 10){
+             printf("Information, too many Information flags: no more reported to log either\n");
+             fprintf(ficlog,"Information, too many Information flags: no more reported to log either\n");
+             firsthree++;
+           }else{
+             firsthree++;
            }
-           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; /* Valid transition with unknown status */
-           mw[++mi][i]=m;
            mli=m;
          }
          if(s[m][i]==-2){ /* Vital status is really unknown */
            nbwarn++;
-           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
+           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified?not a transition */
              printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
              fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
            }
- Line 5124  void  concatwav(int wav[], int **dh, int
+ Line 7890  void  concatwav(int wav[], int **dh, int
  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
      else if ((int) andc[i] != 9999) {  /* Date of death is known */
        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
-         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
+         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */
            nbwarn++;
            if(firstfiv==0){
-             printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+             printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %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 );
+             fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %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 */
+             s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
+         }else{ /* Month of Death occured afer last wave month, 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 );
+             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. 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], s[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 at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\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{ /* if date of interview is unknown */
          /* death is known but not confirmed by death status at any wave */
          if(firstfour==0){
-           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+           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 with status %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], s[m][i], i,m );
            firstfour=1;
          }
-         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+         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  with status %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], s[m][i], i,m );
        }
      } /* end if date of death is known */
  #endif
-     wav[i]=mi; /* mi should be the last effective wave (or mli) */
+     wav[i]=mi; /* mi should be the last effective wave (or mli),  */
-     /* wav[i]=mw[mi][i]; */
+     /* wav[i]=mw[mi][i];   */
      if(mi==0){
        nbwarn++;
        if(first==0){
- Line 5165  void  concatwav(int wav[], int **dh, int
+ Line 7932  void  concatwav(int wav[], int **dh, int
    } /* End individuals */
    /* wav and mw are no more changed */
+   printf("Information, you have to check %d informations which haven't been logged!\n",firsthree);
+   fprintf(ficlog,"Information, you have to check %d informations which haven't been logged!\n",firsthree);
    for(i=1; i<=imx; i++){
      for(mi=1; mi<wav[i];mi++){
        if (stepm <=0)
- Line 5177  void  concatwav(int wav[], int **dh, int
+ Line 7947  void  concatwav(int wav[], int **dh, int
              if(j==0) j=1;  /* Survives at least one month after exam */
              else if(j<0){
                nberr++;
-               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld (around line %d) who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                j=1; /* Temporary Dangerous patch */
                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld (around line %d) who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
              }
              k=k+1;
- Line 5214  void  concatwav(int wav[], int **dh, int
+ Line 7984  void  concatwav(int wav[], int **dh, int
            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
            if(j<0){
              nberr++;
-             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld (around line %d) who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld (around line %d) who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
            }
            sum=sum+j;
          }
- Line 5276  void  concatwav(int wav[], int **dh, int
+ Line 8046  void  concatwav(int wav[], int **dh, int
     /* *cptcov=0; */
     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
+    for (k=1; k <= maxncov; k++)
+      for(j=1; j<=2; j++)
+        nbcode[k][j]=0; /* Valgrind */
     /* Loop on covariates without age and products and no quantitative variable */
-    /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
+    for (k=1; k<=cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
-    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
       for (j=-1; (j < maxncov); j++) Ndum[j]=0;
-      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
+      /* printf("Testing k=%d, cptcovt=%d\n",k, cptcovt); */
+      if(Dummy[k]==0 && Typevar[k] !=1 && Typevar[k] != 3  && Typevar[k] != 2){ /* Dummy covariate and not age product nor fixed product */
         switch(Fixed[k]) {
         case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
+          modmaxcovj=0;
+          modmincovj=0;
           for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
+            /* printf("Waiting for error tricode Tvar[%d]=%d i=%d (int)(covar[Tvar[k]][i]=%d\n",k,Tvar[k], i, (int)(covar[Tvar[k]][i])); */
             ij=(int)(covar[Tvar[k]][i]);
             /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
              * If product of Vn*Vm, still boolean *:
- Line 5296  void  concatwav(int wav[], int **dh, int
+ Line 8072  void  concatwav(int wav[], int **dh, int
               modmaxcovj=ij;
             else if (ij < modmincovj)
               modmincovj=ij;
-            if ((ij < -1) && (ij > NCOVMAX)){
+            if (ij <0 || ij >1 ){
+              printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
+              fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
+              fflush(ficlog);
+              exit(1);
+            }
+            if ((ij < -1) || (ij > NCOVMAX)){
               printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
               exit(1);
             }else
- Line 5342  void  concatwav(int wav[], int **dh, int
+ Line 8124  void  concatwav(int wav[], int **dh, int
           /* nbcode[Tvar[j]][3]=2; */
           /* To be continued (not working yet). */
           ij=0; /* ij is similar to i but can jump over null modalities */
-          for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
+          /* 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*/
+          /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
+          /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
+           * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
+          /*, could be restored in the future */
+          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 (Ndum[i] == 0) { /* If nobody responded to this modality k */
               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*/
+            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*/
             cptcode = ij; /* New max modality for covar j */
           } /* end of loop on modality i=-1 to 1 or more */
           break;
- Line 5363  void  concatwav(int wav[], int **dh, int
+ Line 8151  void  concatwav(int wav[], int **dh, int
           break;
         } /* end switch */
       } /* end dummy test */
+      if(Dummy[k]==1 && Typevar[k] !=1 && Typevar[k] !=3 && Fixed ==0){ /* Fixed Quantitative covariate and not age product */
-      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+        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*/
-      /*         /\*recode from 0 *\/ */
+          if(Tvar[k]<=0 || Tvar[k]>=NCOVMAX){
-      /*                                      k is a modality. If we have model=V1+V1*sex  */
+            printf("Error k=%d \n",k);
-      /*                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+            exit(1);
-      /*                                   But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
+          }
-      /*         } */
+          if(isnan(covar[Tvar[k]][i])){
-      /*         /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
+            printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
-      /*         if (ij > ncodemax[j]) { */
+            fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
-      /*           printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+            fflush(ficlog);
-      /*           fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
+            exit(1);
-      /*           break; */
+          }
-      /*         } */
+        }
-      /*   }  /\* end of loop on modality k *\/ */
+      } /* end Quanti */
-    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
+    } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/
     for (k=-1; k< maxncov; k++) Ndum[k]=0;
     /* Look at fixed dummy (single or product) covariates to check empty modalities */
- Line 5390  void  concatwav(int wav[], int **dh, int
+ Line 8178  void  concatwav(int wav[], int **dh, int
     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) */
+    for (k=1; k<=  cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
+      /* 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(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy simple and non empty in the model */
+        /* Typevar[k] =0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
+        /* Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product*/
         /* 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, */
+        ++ij;/*    V5 + V4 + V3 + V4*V3 + V5*age + V2 +  V1*V2 + V1*age + V1, *//* V5 quanti, V2 quanti, V4, V3, V1 dummies */
+        /* k=       1    2   3     4       5       6      7       8        9  */
+        /* Tvar[k]= 5    4    3    6       5       2      7       1        1  */
+        /* ij            1    2                                            3  */
+        /* Tvaraff[ij]=  4    3                                            1  */
+        /* Tmodelind[ij]=2    3                                            9  */
+        /* TmodelInvind[ij]=2 1                                            1  */
         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 */
- Line 5412  void  concatwav(int wav[], int **dh, int
+ Line 8209  void  concatwav(int wav[], int **dh, int
     } /* 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
+    *cptcov=ij; /* cptcov= Number of total real effective simple dummies (fixed or time  arying) effective (used as cptcoveff in other functions)
                  * 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++){
- Line 5433  void  concatwav(int wav[], int **dh, int
+ Line 8230  void  concatwav(int wav[], int **dh, int
  {
    /* Health expectancies, no variances */
+   /* cij is the combination in the list of combination of dummy covariates */
+   /* strstart is a string of time at start of computing */
    int i, j, nhstepm, hstepm, h, nstepm;
    int nhstepma, nstepma; /* Decreasing with age */
    double age, agelim, hf;
- Line 5501  void  concatwav(int wav[], int **dh, int
+ Line 8300  void  concatwav(int wav[], int **dh, int
      /* If stepm=6 months */
      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
+     /* printf("HELLO evsij Entering hpxij age=%d cij=%d hstepm=%d x[1]=%f nres=%d\n",(int) age, cij, hstepm, x[1], nres); */
      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
- Line 5543  void  concatwav(int wav[], int **dh, int
+ Line 8342  void  concatwav(int wav[], int **dh, int
    /* Covariances of health expectancies eij and of total life expectancies according
       to initial status i, ei. .
    */
+   /* Very time consuming function, but already optimized with precov */
    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
    int nhstepma, nstepma; /* Decreasing with age */
    double age, agelim, hf;
- Line 5690  void  concatwav(int wav[], int **dh, int
+ Line 8490  void  concatwav(int wav[], int **dh, int
              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
        }
      }
+     /* if((int)age ==50){ */
+     /*   printf(" age=%d cij=%d nres=%d varhe[%d][%d]=%f ",(int)age, cij, nres, 1,2,varhe[1][2]); */
+     /* } */
      /* Computing expectancies */
      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
      for(i=1; i<=nlstate;i++)
- Line 5751  void  concatwav(int wav[], int **dh, int
+ Line 8553  void  concatwav(int wav[], int **dh, int
  /************ 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[], 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(); */
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
+    int first=0;
     int k;
     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 age,agelim, hf;
     /* double ***mobaverage; */
- Line 5807  void  concatwav(int wav[], int **dh, int
+ Line 8611  void  concatwav(int wav[], int **dh, int
     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,"# 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]);
+    /* We use TinvDoQresult[nres][resultmodel[nres][j] we sort according to the equation model and the resultline: it is a choice */
+    /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ /\* To be done*\/ */
+    /*   fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+    /* } */
+    for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value */ /* To be done*/
+      /* fprintf(ficresprobmorprev," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); */
+      fprintf(ficresprobmorprev," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
     }
-    for(j=1;j<=cptcoveff;j++)
+    /* for(j=1;j<=cptcoveff;j++)  */
-      fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
+    /*   fprintf(ficresprobmorprev," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,TnsdVar[Tvaraff[j]])]); */
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
- Line 5827  void  concatwav(int wav[], int **dh, int
+ Line 8637  void  concatwav(int wav[], int **dh, int
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-    /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
- Line 5882  void  concatwav(int wav[], int **dh, int
+ Line 8692  void  concatwav(int wav[], int **dh, int
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
+        /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
+         * 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(mobilav ==0){
             for(i=1; i<=nlstate;i++)
- Line 5894  void  concatwav(int wav[], int **dh, int
+ Line 8707  void  concatwav(int wav[], int **dh, int
               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,nres);  /* 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(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
-        /* Next for computing probability of death (h=1 means
+        /* Next for computing shifted+ probability of death (h=1 means
            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(i=1,gpp[j]=0.; i<= nlstate; i++)
             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 */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
         if (popbased==1) {
- Line 5943  void  concatwav(int wav[], int **dh, int
+ Line 8761  void  concatwav(int wav[], int **dh, int
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
             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(h=0; h<=nhstepm; h++){
             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];
         }
       } /* End theta */
+      /* We got the gradient matrix for each theta and state j */
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       for(h=0; h<=nhstepm; h++) /* veij */
- Line 5966  void  concatwav(int wav[], int **dh, int
+ Line 8788  void  concatwav(int wav[], int **dh, int
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
+      /**< as well as its transposed matrix
+       */
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
+      /* 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(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
- Line 5983  void  concatwav(int wav[], int **dh, int
+ Line 8811  void  concatwav(int wav[], int **dh, int
         }
       }
-      /* 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(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
- Line 6086  void  concatwav(int wav[], int **dh, int
+ Line 8918  void  concatwav(int wav[], int **dh, int
    int theta;
    pstamp(ficresvpl);
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+   fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
    fprintf(ficresvpl,"# Age ");
    if(nresult >=1)
      fprintf(ficresvpl," Result# ");
- Line 6115  void  concatwav(int wav[], int **dh, int
+ Line 8947  void  concatwav(int wav[], int **dh, int
        for(i=1; i<=npar; i++){ /* Computes gradient */
          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,nres);
+       /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
-       else
+       /* else */
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
        for(i=1;i<=nlstate;i++){
          gp[i] = prlim[i][i];
          mgp[theta][i] = prlim[i][i];
        }
        for(i=1; i<=npar; i++) /* Computes gradient */
          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,nres);
+       /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
-       else
+       /* else */
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
        for(i=1;i<=nlstate;i++){
          gm[i] = prlim[i][i];
          mgm[theta][i] = prlim[i][i];
- Line 6177  void  concatwav(int wav[], int **dh, int
+ Line 9009  void  concatwav(int wav[], int **dh, int
      fprintf(ficresvpl,"%.0f ",age );
      if(nresult >=1)
        fprintf(ficresvpl,"%d ",nres );
-     for(i=1; i<=nlstate;i++)
+     for(i=1; i<=nlstate;i++){
        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");
      free_vector(gp,1,nlstate);
      free_vector(gm,1,nlstate);
- Line 6326  void varprob(char optionfilefiname[], do
+ Line 9161  void varprob(char optionfilefiname[], do
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
+    int nres=0; /* New */
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
- Line 6341  void varprob(char optionfilefiname[], do
+ Line 9177  void varprob(char optionfilefiname[], do
     double ***varpij;
     strcpy(fileresprob,"PROB_");
-    strcat(fileresprob,fileres);
+    strcat(fileresprob,fileresu);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
- Line 6395  void varprob(char optionfilefiname[], do
+ Line 9231  void varprob(char optionfilefiname[], do
     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. %s</li>\n",optionfilehtmcov,optionfilehtmcov);
+    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. 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.\
- Line 6413  To be simple, these graphs help to under
+ Line 9249  To be simple, these graphs help to under
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
-    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
+    for(nres=1;nres <=nresult; nres++){ /* For each resultline */
+    for(j1=1; j1<=tj;j1++){ /* For any combination of dummy covariates, fixed and varying */
+      /* printf("Varprob  TKresult[nres]=%d j1=%d, nres=%d, cptcovn=%d, cptcoveff=%d tj=%d cptcovs=%d\n",  TKresult[nres], j1, nres, cptcovn, cptcoveff, tj, cptcovs); */
+      if(tj != 1 && TKresult[nres]!= j1)
+        continue;
+    /* for(j1=1; j1<=tj;j1++){  /\* For each valid combination of covariates or only once*\/ */
+      /* for(nres=1;nres <=1; nres++){ /\* For each resultline *\/ */
+      /* /\* for(nres=1;nres <=nresult; nres++){ /\\* For each resultline *\\/ *\/ */
       if  (cptcovn>0) {
         fprintf(ficresprob, "\n#********** Variable ");
-        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-        fprintf(ficresprob, "**********\n#\n");
         fprintf(ficresprobcov, "\n#********** Variable ");
-        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+        fprintf(ficgp, "\n#********** Variable ");
+        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+        fprintf(ficresprobcor, "\n#********** Variable ");
+        /* Including quantitative variables of the resultline to be done */
+        for (z1=1; z1<=cptcovs; z1++){ /* Loop on each variable of this resultline  */
+          /* printf("Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model); */
+          fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model);
+          /* fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s resultline[%d]=%s \n",nres, z1, modelresult[nres][z1], model, nres, resultline[nres]); */
+          if(Dummy[modelresult[nres][z1]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to z1 in resultline  */
+            if(Fixed[modelresult[nres][z1]]==0){ /* Fixed referenced to model equation */
+              fprintf(ficresprob,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
+              fprintf(ficresprobcov,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
+              fprintf(ficgp,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
+              fprintf(fichtmcov,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
+              fprintf(ficresprobcor,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
+              fprintf(ficresprob,"fixed ");
+              fprintf(ficresprobcov,"fixed ");
+              fprintf(ficgp,"fixed ");
+              fprintf(fichtmcov,"fixed ");
+              fprintf(ficresprobcor,"fixed ");
+            }else{
+              fprintf(ficresprob,"varyi ");
+              fprintf(ficresprobcov,"varyi ");
+              fprintf(ficgp,"varyi ");
+              fprintf(fichtmcov,"varyi ");
+              fprintf(ficresprobcor,"varyi ");
+            }
+          }else if(Dummy[modelresult[nres][z1]]==1){ /* Quanti variable */
+            /* For each selected (single) quantitative value */
+            fprintf(ficresprob," V%d=%lg ",Tvqresult[nres][z1],Tqresult[nres][z1]);
+            if(Fixed[modelresult[nres][z1]]==0){ /* Fixed */
+              fprintf(ficresprob,"fixed ");
+              fprintf(ficresprobcov,"fixed ");
+              fprintf(ficgp,"fixed ");
+              fprintf(fichtmcov,"fixed ");
+              fprintf(ficresprobcor,"fixed ");
+            }else{
+              fprintf(ficresprob,"varyi ");
+              fprintf(ficresprobcov,"varyi ");
+              fprintf(ficgp,"varyi ");
+              fprintf(fichtmcov,"varyi ");
+              fprintf(ficresprobcor,"varyi ");
+            }
+          }else{
+            printf("Error in varprob() Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=V%d cptcovs=%d, cptcoveff=%d \n", nres, z1, Dummy[modelresult[nres][z1]],nres,z1,modelresult[nres][z1],cptcovs, cptcoveff);  /* end if dummy  or quanti */
+            fprintf(ficlog,"Error in varprob() Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=V%d cptcovs=%d, cptcoveff=%d \n", nres, z1, Dummy[modelresult[nres][z1]],nres,z1,modelresult[nres][z1],cptcovs, cptcoveff);  /* end if dummy  or quanti */
+            exit(1);
+          }
+        } /* End loop on variable of this resultline */
+        /* for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); */
+        fprintf(ficresprob, "**********\n#\n");
         fprintf(ficresprobcov, "**********\n#\n");
-        fprintf(ficgp, "\n#********** Variable ");
-        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficgp, "**********\n#\n");
-        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-        fprintf(ficresprobcor, "\n#********** Variable ");
-        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprobcor, "**********\n#");
         if(invalidvarcomb[j1]){
           fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
- Line 6444  To be simple, these graphs help to under
+ Line 9328  To be simple, these graphs help to under
       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       gp=vector(1,(nlstate)*(nlstate+ndeath));
       gm=vector(1,(nlstate)*(nlstate+ndeath));
-      for (age=bage; age<=fage; age ++){
+      for (age=bage; age<=fage; age ++){ /* Fo each age we feed the model equation with covariates, using precov as in hpxij() ? */
         cov[2]=age;
         if(nagesqr==1)
           cov[3]= age*age;
-        for (k=1; k<=cptcovn;k++) {
+        /* New code end of combination but for each resultline */
-          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
+        for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
-          /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
+          if(Typevar[k1]==1 || Typevar[k1] ==3){ /* A product with age */
-                                                                     * 1  1 1 1 1
+            cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
-                                                                     * 2  2 1 1 1
+          }else{
-                                                                     * 3  1 2 1 1
+            cov[2+nagesqr+k1]=precov[nres][k1];
-                                                                     */
+          }
-          /* nbcode[1][1]=0 nbcode[1][2]=1;*/
+        }/* End of loop on model equation */
-        }
+ /* Old code */
-        /* 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+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+        /* /\*    cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; *\/ */
-        for (k=1; k<=cptcovprod;k++)
+        /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only *\/ */
-          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
+        /*        /\* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates *\/ */
+        /*        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,TnsdVar[TvarsD[k]])]; */
+        /*        /\*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*\//\* j1 1 2 3 4 */
+        /*                                                                   * 1  1 1 1 1 */
+        /*                                                                   * 2  2 1 1 1 */
+        /*                                                                   * 3  1 2 1 1 */
+        /*                                                                   *\/ */
+        /*        /\* nbcode[1][1]=0 nbcode[1][2]=1;*\/ */
+        /* } */
+        /* /\* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 *\/ */
+        /* /\* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] *\/ */
+        /* /\*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; *\/ */
+        /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
+        /*        if(Dummy[Tage[k]]==2){ /\* dummy with age *\/ */
+        /*          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,TnsdVar[Tvar[Tage[k]]])]*cov[2]; */
+        /*          /\* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
+        /*        } else if(Dummy[Tage[k]]==3){ /\* quantitative with age *\/ */
+        /*          printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]); */
+        /*          /\* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\\* Using the mean of quantitative variable Tvar[Tage[k]] /\\* Tqresult[nres][k]; *\\/ *\/ */
+        /*          /\* exit(1); *\/ */
+        /*          /\* cov[++k1]=Tqresult[nres][k];  *\/ */
+        /*        } */
+        /*        /\* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
+        /* } */
+        /* for (k=1; k<=cptcovprod;k++){/\* For product without age *\/ */
+        /*        if(Dummy[Tvard[k][1]]==0){ */
+        /*          if(Dummy[Tvard[k][2]]==0){ */
+        /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])]; */
+        /*            /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
+        /*          }else{ /\* Should we use the mean of the quantitative variables? *\/ */
+        /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * Tqresult[nres][resultmodel[nres][k]]; */
+        /*            /\* cov[++k1]=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(j1,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][TnsdVar[Tvard[k][1]]]; */
+        /*            /\* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; *\/ */
+        /*          }else{ */
+        /*            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][TnsdVar[Tvard[k][1]]]*  Tqinvresult[nres][TnsdVar[Tvard[k][2]]]; */
+        /*            /\* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\/ */
+        /*          } */
+        /*        } */
+        /*        /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
+        /* } */
+ /* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/
         for(theta=1; theta <=npar; theta++){
           for(i=1; i<=npar; i++)
             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
- Line 6592  To be simple, these graphs help to under
+ Line 9518  To be simple, these graphs help to under
                   }
                   /* Eigen vectors */
-                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                  if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
+                    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);
+                    v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
+                  }else
+                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                   /*v21=sqrt(1.-v11*v11); *//* error */
                   v21=(lc1-v1)/cv12*v11;
                   v12=-v21;
- Line 6623  To be simple, these graphs help to under
+ Line 9554  To be simple, these graphs help to under
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
-                            mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)),   \
+                            mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
-                            mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2))); /* For gnuplot only */
+                            mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
                   }else{
                     first=0;
                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
- Line 6643  To be simple, these graphs help to under
+ Line 9574  To be simple, these graphs help to under
         } /*l1 */
       }/* k1 */
     }  /* loop on combination of covariates j1 */
+    } /* loop on nres */
     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));
- Line 6660  To be simple, these graphs help to under
+ Line 9592  To be simple, these graphs help to under
  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-                   int popforecast, int mobilav, int prevfcast, int mobilavproj, 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, k4, nres;
+   int jj1, k1, cpt, nres;
+   /* In fact some results are already printed in fichtm which is open */
     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
  </ul>");
-    fprintf(fichtm,"<ul><li> model=1+age+%s\n \
+ /*    fprintf(fichtm,"<ul><li> model=1+age+%s\n \ */
- </ul>", model);
+ /* </ul>", model); */
     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",
             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
-    fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
+    fprintf(fichtm,"<li> - Observed prevalence (cross-sectional prevalence) in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
     fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
     fprintf(fichtm,"\
- Line 6683  void printinghtml(char fileresu[], char
+ Line 9615  void printinghtml(char fileresu[], char
   - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
             stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
     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_"));
     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_"));
     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): \
- Line 6702  void printinghtml(char fileresu[], char
+ Line 9634  void printinghtml(char fileresu[], char
     m=pow(2,cptcoveff);
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+    fprintf(fichtm," \n<ul><li><b>Graphs (first order)</b></li><p>");
     jj1=0;
     fprintf(fichtm," \n<ul>");
-    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+      /* k1=nres; */
-      if(m != 1 && TKresult[nres]!= k1)
+      k1=TKresult[nres];
-        continue;
+      if(TKresult[nres]==0)k1=1; /* To be checked for no result */
+    /* 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++){
+        for (cpt=1; cpt<=cptcovs;cpt++){ /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
-          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+          fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[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]);
         }
+        /* 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++){
+        for (cpt=1; cpt<=cptcovs;cpt++){
-          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+          fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[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,"************ 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;
- Line 6737  void printinghtml(char fileresu[], char
+ Line 9679  void printinghtml(char fileresu[], char
         fprintf(fichtm,"</a></li>");
       } /* cptcovn >0 */
     }
-      fprintf(fichtm," \n</ul>");
+    fprintf(fichtm," \n</ul>");
     jj1=0;
-    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+      /* k1=nres; */
-      if(m != 1 && TKresult[nres]!= k1)
+      k1=TKresult[nres];
-        continue;
+      if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
+    /* for(k1=1; k1<=m;k1++){ /\* For each combination of covariate *\/ */
+    /*   if(m != 1 && TKresult[nres]!= k1) */
+    /*     continue; */
       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
         fprintf(fichtm,"\n<p><a name=\"rescov");
-        for (cpt=1; cpt<=cptcoveff;cpt++){
+        for (cpt=1; cpt<=cptcovs;cpt++){
-          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+          fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[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]);
         }
+        /* 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");
-        for (cpt=1; cpt<=cptcoveff;cpt++){
+        for (cpt=1; cpt<=cptcovs;cpt++){
-          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+          fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
-          printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
+          printf(" V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
           /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
           /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
         }
-        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," (model=1+age+%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
         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);
- Line 6792  divided by h: <sub>h</sub>P<sub>ij</sub>
+ Line 9732  divided by h: <sub>h</sub>P<sub>ij</sub>
  <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 */
       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-%d.svg\">%s_%d-%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. Mean times spent in state (or Life Expectancy or Health Expectancy etc.) are the areas under each curve. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
- <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);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
       }
       /* State specific survival functions (period) */
       for(cpt=1; cpt<=nlstate;cpt++){
-        fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
+        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.  Mean times spent in state (or Life Expectancy or Health Expectancy etc.) are the areas under each curve. \
-  <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);
+  <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> ", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",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++){
-        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> \
+        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 alive in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
- <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);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
+       fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,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++){
-          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> \
+          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>", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
- <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);
+          fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJB_"),subdirf2(optionfilefiname,"PIJB_"));
+          fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
         }
       }
       if(prevfcast==1){
-        /* Projection of prevalence up to period (stable) prevalence in each health state */
+        /* Projection of prevalence up to period (forward stable) prevalence in each health state */
         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) up to period (stable) 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 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>", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
- <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+          fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
+          fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",
+                  subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
         }
       }
-      if(backcast==1){
+      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) up to stable (mixed) back prevalence in state %d. 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> \
+          fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
- <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+  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>", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+          fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
+          fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
         }
       }
       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-%d.svg\">%s_%d-%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>",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
- <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);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\"> %s.txt</a>)\n<br>",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
       }
       /* } /\* end i1 *\/ */
-    }/* End k1 */
+    }/* End k1=nres */
     fprintf(fichtm,"</ul>");
     fprintf(fichtm,"\
- Line 6866  See page 'Matrix of variance-covariance
+ Line 9818  See page 'Matrix of variance-covariance
     <a href=\"%s\">%s</a> <br>\n</li>",
             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
     fprintf(fichtm,"\
-  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+  - 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_"));
     fprintf(fichtm,"\
   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
             estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
     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_"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
- Line 6880  See page 'Matrix of variance-covariance
+ Line 9832  See page 'Matrix of variance-covariance
  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
  /*      <br>",fileres,fileres,fileres,fileres); */
  /*  else  */
- /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=1+age+%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
     fflush(fichtm);
-    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     m=pow(2,cptcoveff);
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    fprintf(fichtm," <ul><li><b>Graphs (second order)</b></li><p>");
+   jj1=0;
+    fprintf(fichtm," \n<ul>");
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+      /* k1=nres; */
+      k1=TKresult[nres];
+      /* 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=\"#rescovsecond");
+        for (cpt=1; cpt<=cptcovs;cpt++){
+          fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
+        }
+        fprintf(fichtm,"\">");
+        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
+        fprintf(fichtm,"************ Results for covariates");
+        for (cpt=1; cpt<=cptcovs;cpt++){
+          fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
+        }
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
+          continue;
+        }
+        fprintf(fichtm,"</a></li>");
+      } /* cptcovn >0 */
+    } /* End nres */
+    fprintf(fichtm," \n</ul>");
     jj1=0;
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-    for(k1=1; k1<=m;k1++){
+      /* k1=nres; */
-      if(m != 1 && TKresult[nres]!= k1)
+      k1=TKresult[nres];
-        continue;
+      if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
+      /* for(k1=1; k1<=m;k1++){ */
+      /* if(m != 1 && TKresult[nres]!= k1) */
+      /*   continue; */
       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
+        fprintf(fichtm,"\n<p><a name=\"rescovsecond");
+        for (cpt=1; cpt<=cptcovs;cpt++){
+          fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
+        }
+        fprintf(fichtm,"\"</a>");
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-        for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
+        for (cpt=1; cpt<=cptcovs;cpt++){  /**< cptcoveff number of variables */
-          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
+          fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
+          printf(" V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[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," (model=1+age+%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
         if(invalidvarcomb[k1]){
           fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
           continue;
         }
-      }
+      } /* If cptcovn >0 */
       for(cpt=1; cpt<=nlstate;cpt++) {
         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-%d.svg\"> %s_%d-%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>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
- <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," (data from text file  <a href=\"%s\">%s</a>)\n <br>",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
       }
       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 each live states (1 to %d). If popbased=1 the smooth (due to the model) \
  true period expectancies (those weighted with period prevalences are also\
   drawn in addition to the population based expectancies computed using\
-  observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
+  observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
- <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
+      fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
+      fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);
       /* } /\* end i1 *\/ */
-    }/* End k1 */
    }/* End nres */
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
  }
  /******************* Gnuplot file **************/
- void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){
+ 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[256],optfileres[256];
-   char gplotcondition[132], gplotlabel[132];
+   char gplotcondition[256], gplotlabel[256];
-   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 cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,kf=0,kvar=0,kk=0,ipos=0,iposold=0,ij=0, ijp=0, l=0;
    int lv=0, vlv=0, kl=0;
    int ng=0;
    int vpopbased;
- Line 6954  void printinggnuplot(char fileresu[], ch
+ Line 9947  void printinggnuplot(char fileresu[], ch
    /*#endif */
    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] for [j=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,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 */
    /* 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");
- Line 6983  void printinggnuplot(char fileresu[], ch
+ Line 9990  void printinggnuplot(char fileresu[], ch
    fprintf(ficgp,"\nset out;unset log\n");
    /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
+   /* Plot the probability implied in the likelihood by covariate value */
+   fprintf(ficgp,"\nset ter pngcairo size 640, 480");
+   /* if(debugILK==1){ */
+   for(kf=1; kf <= ncovf; kf++){ /* For each simple dummy covariate of the model */
+     kvar=Tvar[TvarFind[kf]]; /* variable name */
+     /* k=18+Tvar[TvarFind[kf]];/\*offset because there are 18 columns in the ILK_ file but could be placed else where *\/ */
+     /* k=18+kf;/\*offset because there are 18 columns in the ILK_ file *\/ */
+     /* k=19+kf;/\*offset because there are 19 columns in the ILK_ file *\/ */
+     k=16+nlstate+kf;/*offset because there are 19 columns in the ILK_ file, first cov Vn on col 21 with 4 living states */
+     for (i=1; i<= nlstate ; i ++) {
+       fprintf(ficgp,"\nset out \"%s-p%dj-%d.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i,kvar);
+       fprintf(ficgp,"unset log;\n# For each simple dummy covariate of the model \n plot  \"%s\"",subdirf(fileresilk));
+       if(gnuplotversion >=5.2){ /* Former gnuplot versions do not have variable pointsize!! */
+         fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable \\\n",i,1,k,k,i,1,kvar);
+         for (j=2; j<= nlstate+ndeath ; j ++) {
+           fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable ",i,j,k,k,i,j,kvar);
+         }
+       }else{
+         fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable \\\n",i,1,k,i,1,kvar);
+         for (j=2; j<= nlstate+ndeath ; j ++) {
+           fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable ",i,j,k,i,j,kvar);
+         }
+       }
+       fprintf(ficgp,";\nset out; unset ylabel;\n");
+     }
+   } /* End of each covariate dummy */
+   for(ncovv=1, iposold=0, kk=0; ncovv <= ncovvt ; ncovv++){
+     /* Other example        V1 + V3 + V5 + age*V1  + age*V3 + age*V5 + V1*V3  + V3*V5  + V1*V5
+      *     kmodel       =     1   2     3     4         5        6        7       8        9
+      *  varying                   1     2                                 3       4        5
+      *  ncovv                     1     2                                3 4     5 6      7 8
+      * TvarVV[ncovv]             V3     5                                1 3     3 5      1 5
+      * TvarVVind[ncovv]=kmodel    2     3                                7 7     8 8      9 9
+      * TvarFind[kmodel]       1   0     0     0         0        0        0       0        0
+      * kdata     ncovcol=[V1 V2] nqv=0 ntv=[V3 V4] nqtv=V5
+      * Dummy[kmodel]          0   0     1     2         2        3        1       1        1
+      */
+     ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
+     kvar=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate */
+     /* printf("DebugILK ficgp ncovv=%d, kvar=TvarVV[ncovv]=%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); */
+     if(ipos!=iposold){ /* Not a product or first of a product */
+       /* printf(" %d",ipos); */
+       /* fprintf(ficresilk," V%d",TvarVV[ncovv]); */
+       /* printf(" DebugILK ficgp suite ipos=%d != iposold=%d\n", ipos, iposold); */
+       kk++; /* Position of the ncovv column in ILK_ */
+       k=18+ncovf+kk; /*offset because there are 18 columns in the ILK_ file plus ncovf fixed covariate */
+       if(Dummy[ipos]==0 && Typevar[ipos]==0){ /* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummy*age, 3quant*age) Typevar (0 single, 1=*age,2=Vn*vm)  */
+         for (i=1; i<= nlstate ; i ++) {
+           fprintf(ficgp,"\nset out \"%s-p%dj-%d.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i,kvar);
+           fprintf(ficgp,"unset log;\n# For each simple dummy covariate of the model \n plot  \"%s\"",subdirf(fileresilk));
+             /* printf("Before DebugILK gnuplotversion=%g >=5.2\n",gnuplotversion); */
+           if(gnuplotversion >=5.2){ /* Former gnuplot versions do not have variable pointsize!! */
+             /* printf("DebugILK gnuplotversion=%g >=5.2\n",gnuplotversion); */
+             fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable \\\n",i,1,k,k,i,1,kvar);
+             for (j=2; j<= nlstate+ndeath ; j ++) {
+               fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable ",i,j,k,k,i,j,kvar);
+             }
+           }else{
+             /* printf("DebugILK gnuplotversion=%g <5.2\n",gnuplotversion); */
+             fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable \\\n",i,1,k,i,1,kvar);
+             for (j=2; j<= nlstate+ndeath ; j ++) {
+               fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable ",i,j,k,i,j,kvar);
+             }
+           }
+           fprintf(ficgp,";\nset out; unset ylabel;\n");
+         }
+       }/* End if dummy varying */
+     }else{ /*Product */
+       /* printf("*"); */
+       /* fprintf(ficresilk,"*"); */
+     }
+     iposold=ipos;
+   } /* For each time varying covariate */
+   /* } /\* debugILK==1 *\/ */
+   /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
+   /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
+   /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
+   fprintf(ficgp,"\nset out;unset log\n");
+   /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
    /* 1eme*/
    for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
-     for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
+     /* for (k1=1; k1<= m ; k1 ++){ /\* For each valid combination of covariate *\/ */
        for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+         k1=TKresult[nres];
+         if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
          /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-         if(m != 1 && TKresult[nres]!= k1)
+         /* if(m != 1 && TKresult[nres]!= k1) */
-           continue;
+         /*   continue; */
          /* We are interested in selected combination by the resultline */
          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
-         fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
+         fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
          strcpy(gplotlabel,"(");
-         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-           lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* 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 */
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate k get corresponding value lv for combination k1 *\/ */
-           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the value of the covariate corresponding to k1 combination *\\/ *\/ */
-           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
+         /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
-           /* printf(" V%d=%d ",Tvaraff[k],vlv); */
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
-           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* 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 (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         /*   /\* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv *\/ */
-           /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+         /*   /\* printf(" V%d=%d ",Tvaraff[k],vlv); *\/ */
-           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   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"); */
- Line 7023  void printinggnuplot(char fileresu[], ch
+ Line 10120  void printinggnuplot(char fileresu[], ch
          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 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 model=1+age+%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
          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*/
- Line 7031  void printinggnuplot(char fileresu[], ch
+ Line 10129  void printinggnuplot(char fileresu[], ch
            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
            else        fprintf(ficgp," %%*lf (%%*lf)");
          }
-         fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
+         fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
          for (i=1; i<= nlstate ; i ++) {
            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
            else fprintf(ficgp," %%*lf (%%*lf)");
- Line 7049  void printinggnuplot(char fileresu[], ch
+ Line 10147  void printinggnuplot(char fileresu[], ch
          }else{
            kl=0;
            for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
-             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+             /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
+             lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
- Line 7069  void printinggnuplot(char fileresu[], ch
+ Line 10168  void printinggnuplot(char fileresu[], ch
            } /* end covariate */
          } /* end if no covariate */
-         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+         if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
            /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
            fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
            if(cptcoveff ==0){
- Line 7077  void printinggnuplot(char fileresu[], ch
+ Line 10176  void printinggnuplot(char fileresu[], ch
            }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 */
+               /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
+               lv=codtabm(k1,TnsdVar[Tvaraff[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];
+               /* vlv= nbcode[Tvaraff[k]][lv]; */
+               vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
                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 */
- Line 7091  void printinggnuplot(char fileresu[], ch
+ Line 10192  void printinggnuplot(char fileresu[], ch
                  fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
 +cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
                }else{
-                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
+                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]);
                  kl++;
                }
              } /* end covariate */
            } /* end if no covariate */
-           if(backcast == 1){
+           if(prevbcast == 1){
              fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
              /* k1-1 error should be nres-1*/
              for (i=1; i<= nlstate ; i ++) {
- Line 7108  void printinggnuplot(char fileresu[], ch
+ Line 10209  void printinggnuplot(char fileresu[], ch
                if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                else fprintf(ficgp," %%*lf (%%*lf)");
              }
-             fprintf(ficgp,"\" t\"95%% CI\" w l lt 6,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+             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);
              for (i=1; i<= nlstate ; i ++) {
                if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                else fprintf(ficgp," %%*lf (%%*lf)");
              }
-             fprintf(ficgp,"\" t\"\" w l lt 6");
+             fprintf(ficgp,"\" t\"\" w l lt 4");
            } /* end if backprojcast */
-         } /* end if backcast */
+         } /* end if prevbcast */
-         fprintf(ficgp,"\nset out ;unset label;\n");
+         /* fprintf(ficgp,"\nset out ;unset label;\n"); */
+         fprintf(ficgp,"\nset out ;unset title;\n");
        } /* nres */
-     } /* k1 */
+     /* } /\* k1 *\/ */
    } /* cpt */
    /*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)
+       k1=TKresult[nres];
-         continue;
+       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
+       /* if(m != 1 && TKresult[nres]!= k1) */
+       /*        continue; */
        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<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+       /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+       /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
-         vlv= nbcode[Tvaraff[k]][lv];
+       /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
-         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+       /*        /\* 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 *\/ */
-       /* for(k=1; k <= ncovds; k++){ */
+       /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
-       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+       /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
-         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
-         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
-         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       /* } */
+       /* /\* 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");
- Line 7184  void printinggnuplot(char fileresu[], ch
+ Line 10293  void printinggnuplot(char fileresu[], ch
        } /* vpopbased */
        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*/
+   /* } /\* k1 end 2 eme*\/ */
    /*3eme*/
-   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)
+       k1=TKresult[nres];
-         continue;
+       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
+       /* if(m != 1 && TKresult[nres]!= k1) */
+       /*        continue; */
-       for (cpt=1; cpt<= nlstate ; cpt ++) {
+       for (cpt=1; cpt<= nlstate ; cpt ++) { /* Fragile no verification of covariate values */
          fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
          strcpy(gplotlabel,"(");
-         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
-           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
-           vlv= nbcode[Tvaraff[k]][lv];
+         /*   lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
-           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* 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 *\/ */
-         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
-           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   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][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]); */
+         }
          strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
          if(invalidvarcomb[k1]){
- Line 7239  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 10355  plot [%.f:%.f] \"%s\" every :::%d::%d u
        }
        fprintf(ficgp,"\nunset label;\n");
      } /* end nres */
-   } /* end kl 3eme */
+   /* } /\* end kl 3eme *\/ */
    /* 4eme */
    /* Survival functions (period) from state i in state j by initial state i */
-   for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
+   /* for (k1=1; k1<=m; k1++){    /\* For each covariate and each value *\/ */
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(m != 1 && TKresult[nres]!= k1)
+       k1=TKresult[nres];
-         continue;
+       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
+       /* if(m != 1 && TKresult[nres]!= k1) */
+       /*        continue; */
        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
          strcpy(gplotlabel,"(");
-         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
+         fprintf(ficgp,"\n#\n#\n# Survival functions in state %d : 'LIJ_' files, cov=%d state=%d", cpt, k1, cpt);
-         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
-           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
-           vlv= nbcode[Tvaraff[k]][lv];
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
-           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* 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 *\/ */
-         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
-           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   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][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
          }
          strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
- Line 7290  set ter svg size 640, 480\nunset log y\n
+ Line 10413  set ter svg size 640, 480\nunset log y\n
          fprintf(ficgp,"\nset out; unset label;\n");
        } /* end cpt state*/
      } /* end nres */
-   } /* end covariate k1 */
+   /* } /\* end covariate k1 *\/   */
  /* 5eme */
    /* Survival functions (period) from state i in state j by final state j */
-   for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
+   /* 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)
+       k1=TKresult[nres];
-         continue;
+       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
+       /* if(m != 1 && TKresult[nres]!= k1) */
+       /*        continue; */
        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
          strcpy(gplotlabel,"(");
          fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
-         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
-           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
-           vlv= nbcode[Tvaraff[k]][lv];
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
-           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* 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 *\/ */
-         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
-           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   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][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
          }
          strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
- Line 7348  set ter svg size 640, 480\nunset log y\n
+ Line 10478  set ter svg size 640, 480\nunset log y\n
          }
          fprintf(ficgp,"\nset out; unset label;\n");
        } /* end cpt state*/
-     } /* end covariate */
+     /* } /\* end covariate *\/   */
    } /* end nres */
  /* 6eme */
    /* CV preval stable (period) for each covariate */
-   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+   /* 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)
+      k1=TKresult[nres];
-       continue;
+      if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
+      /* 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 (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
+       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<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+       /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+       /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
-         vlv= nbcode[Tvaraff[k]][lv];
+       /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
-         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+       /*        /\* 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 *\/ */
-       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+       /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
-         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
-         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       /*        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][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+       /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
        }
        strcpy(gplotlabel+strlen(gplotlabel),")");
        fprintf(ficgp,"\n#\n");
- Line 7402  set ter svg size 640, 480\nunset log y\n
+ Line 10539  set ter svg size 640, 480\nunset log y\n
  /* 7eme */
-   if(backcast == 1){
+   if(prevbcast == 1){
-     /* CV back preval stable (period) for each covariate */
+     /* CV backward prevalence  for each covariate */
-     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+     /* 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)
+       k1=TKresult[nres];
-         continue;
+       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
+       /* 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 Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
+         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<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
-           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
-           vlv= nbcode[Tvaraff[k]][lv];
+         /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
-           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* 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 *\/ */
-         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
-           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   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][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
          }
          strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
- Line 7443  set ter svg size 640, 480\nunset log y\n
+ Line 10587  set ter svg size 640, 480\nunset log y\n
              fprintf(ficgp,", '' ");
            /* l=(nlstate+ndeath)*(i-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+i-1); /* To be verified */
            /* for (j=2; j<= nlstate ; j ++) */
            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
- Line 7454  set ter svg size 640, 480\nunset log y\n
+ Line 10598  set ter svg size 640, 480\nunset log y\n
          fprintf(ficgp,"\nset out; unset label;\n");
        } /* end cpt state*/
      } /* end covariate */
-   } /* End if backcast */
+   } /* End if prevbcast */
    /* 8eme */
    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 if any */
+     /* 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)
+       k1=TKresult[nres];
-         continue;
+       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
+       /* if(m != 1 && TKresult[nres]!= k1) */
+       /*        continue; */
        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
          strcpy(gplotlabel,"(");
-         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
+         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
-         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
-           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
-           vlv= nbcode[Tvaraff[k]][lv];
+         /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
-           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* 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 *\/ */
-         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
-           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   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][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
          }
          strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
- Line 7533  set ter svg size 640, 480\nunset log y\n
+ Line 10684  set ter svg size 640, 480\nunset log y\n
              fprintf(ficgp," u %d:(",ioffset);
              kl=0;
              strcpy(gplotcondition,"(");
-             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
+             /* 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 */
+               /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
+             for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+               /* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
+               lv=Tvresult[nres][k];
+               vlv=TinvDoQresult[nres][Tvresult[nres][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] */
+               /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
+               /* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
                kl++;
-               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+               /* sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); */
+               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,lv, kl+1, vlv );
                kl++;
-               if(k <cptcoveff && cptcoveff>1)
+               if(k <cptcovs && cptcovs>1)
                  sprintf(gplotcondition+strlen(gplotcondition)," && ");
              }
              strcpy(gplotcondition+strlen(gplotcondition),")");
- Line 7570  set ter svg size 640, 480\nunset log y\n
+ Line 10727  set ter svg size 640, 480\nunset log y\n
      } /* end covariate */
    } /* End if prevfcast */
-   if(backcast==1){
+   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 (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)
+      k1=TKresult[nres];
-         continue;
+      if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
+        /* 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  */
+         for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+           fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
-           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
-           vlv= nbcode[Tvaraff[k]][lv];
+         /*   lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
-           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         /*   /\* 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 *\/ */
-         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
-           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
-           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         /*   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][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+         /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
          }
          strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
- Line 7619  set ter svg size 640, 480\nunset log y\n
+ Line 10783  set ter svg size 640, 480\nunset log y\n
            }else{
              fprintf(ficgp,",\\\n '' ");
            }
-           if(cptcoveff ==0){ /* No covariate */
+           /* if(cptcoveff ==0){ /\* No covariate *\/ */
+           if(cptcovs ==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 */
- Line 7646  set ter svg size 640, 480\nunset log y\n
+ Line 10811  set ter svg size 640, 480\nunset log y\n
              fprintf(ficgp," u %d:(",ioffset);
              kl=0;
              strcpy(gplotcondition,"(");
-             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
+             for (k=1; k<=cptcovs; k++){    /* For each covariate k of the resultline, get corresponding value lv for combination k1 */
-               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
+               if(Dummy[modelresult[nres][k]]==0){  /* To be verified */
-               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+                 /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate writing the chain of conditions *\/ */
-               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+                 /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
-               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+                 /* lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
-               vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
+                 lv=Tvresult[nres][k];
-               kl++;
+                 vlv=TinvDoQresult[nres][Tvresult[nres][k]];
-               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-               kl++;
+                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-               if(k <cptcoveff && cptcoveff>1)
+                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
+                 /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
+                 /* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
+                 kl++;
+                 /* sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); */
+                 sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%lg " ,kl,Tvresult[nres][k], kl+1,TinvDoQresult[nres][Tvresult[nres][k]]);
+                 kl++;
+                 if(k <cptcovs && cptcovs>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 *\/ */
- Line 7683  set ter svg size 640, 480\nunset log y\n
+ Line 10856  set ter svg size 640, 480\nunset log y\n
          fprintf(ficgp,"\nset out; unset label;\n");
        } /* end cpt state*/
      } /* end covariate */
-   } /* End if backcast */
+   } /* End if prevbcast */
    /* 9eme writing MLE parameters */
- Line 7721  set ter svg size 640, 480\nunset log y\n
+ Line 10894  set ter svg size 640, 480\nunset log y\n
    fprintf(ficgp,"#\n");
    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
      fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
-     fprintf(ficgp,"#model=%s \n",model);
+     fprintf(ficgp,"#model=1+age+%s \n",model);
      fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
-     fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
+     /* fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/\* to be checked *\/ */
-     for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */
+     fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcovs,m);/* to be checked */
+     /* for(k1=1; k1 <=m; k1++)  /\* For each combination of covariate *\/ */
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(m != 1 && TKresult[nres]!= k1)
+      /* k1=nres; */
-         continue;
+       k1=TKresult[nres];
-       fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);
+       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
+       fprintf(ficgp,"\n\n# Resultline k1=%d ",k1);
        strcpy(gplotlabel,"(");
-       sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);
+       /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
-       for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
+       for (k=1; k<=cptcovs; k++){  /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+         /* for each resultline nres, and position k, Tvresult[nres][k] gives the name of the variable and
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+            TinvDoQresult[nres][Tvresult[nres][k]] gives its value double or integer) */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
-         vlv= nbcode[Tvaraff[k]][lv];
+       }
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       /* if(m != 1 && TKresult[nres]!= k1) */
-         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+       /*        continue; */
-       }
+       /* fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1); */
-       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+       /* strcpy(gplotlabel,"("); */
-         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       /* /\*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*\/ */
-         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       /* 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 *\\/ *\/ */
+       /*        lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* 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]; *\/ */
+       /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
+       /*        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][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+       /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
+       /* }       */
        strcpy(gplotlabel+strlen(gplotlabel),")");
        fprintf(ficgp,"\n#\n");
        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
-       fprintf(ficgp,"\nset label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
+       fprintf(ficgp,"\nset key outside ");
+       /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
+       fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
        fprintf(ficgp,"\nset ter svg size 640, 480 ");
        if (ng==1){
          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
- Line 7791  set ter svg size 640, 480\nunset log y\n
+ Line 10981  set ter svg size 640, 480\nunset log y\n
              /* 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 */
+               switch(Typevar[j]){
-                 if(j==Tage[ij]) { /* Product by age  To be looked at!!*/
+               case 1:
-                   if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
+                 if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
-                     if(DummyV[j]==0){
+                   if(j==Tage[ij]) { /* Product by age  To be looked at!!*//* Bug valgrind */
-                       fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
+                     if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
-                     }else{ /* quantitative */
+                       if(DummyV[j]==0){/* Bug valgrind */
-                       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+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
-                       /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                       }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++;
                      }
-                     ij++;
                    }
                  }
-               }else if(cptcovprod >0){
+                 break;
-                 if(j==Tprod[ijp]) { /* */
+               case 2:
-                   /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
+                 if(cptcovprod >0){
-                   if(ijp <=cptcovprod) { /* Product */
+                   if(j==Tprod[ijp]) { /* */
-                     if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
+                     /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
-                       if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
+                     if(ijp <=cptcovprod) { /* Product */
-                         /* 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)]); */
+                       if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
-                         fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
+                         if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
-                       }else{ /* Vn is dummy and Vm is quanti */
+                           /* 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*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
+                           fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[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 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]]);
+                         }
                        }
-                     }else{ /* Vn*Vm Vn is quanti */
+                       ijp++;
-                       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]]);
+                   } /* end Tprod */
-                       }else{ /* Both quanti */
+                 }
-                         fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                 break;
+               case 3:
+                 if(cptcovdageprod >0){
+                   /* if(j==Tprod[ijp]) { */ /* not necessary */
+                     /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
+                     if(ijp <=cptcovprod) { /* Product Vn*Vm and age*VN*Vm*/
+                       if(DummyV[Tvardk[ijp][1]]==0){/* Vn is dummy */
+                         if(DummyV[Tvardk[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*x",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*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
+                         }
+                       }else{ /* age* Vn*Vm Vn is quanti HERE */
+                         if(DummyV[Tvard[ijp][2]]==0){
+                           fprintf(ficgp,"+p%d*%d*%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvardk[ijp][2]],Tqinvresult[nres][Tvardk[ijp][1]]);
+                         }else{ /* Both quanti */
+                           fprintf(ficgp,"+p%d*%f*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
+                         }
                        }
+                       ijp++;
                      }
-                     ijp++;
+                     /* } */ /* end Tprod */
-                   }
+                 }
-                 } /* end Tprod */
+                 break;
-               } else{  /* simple covariate */
+               case 0:
+                 /* 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]]); /*  */
- Line 7833  set ter svg size 640, 480\nunset log y\n
+ Line 11056  set ter svg size 640, 480\nunset log y\n
                    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 simple */
+                 break;
+               default:
+                 break;
+               } /* end switch */
              } /* end j */
-           }else{
+           }else{ /* k=k2 */
-             i=i-ncovmodel;
+             if(ng !=1 ){ /* For logit formula of log p11 is more difficult to get */
-             if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
+               fprintf(ficgp," (1.");i=i-ncovmodel;
-               fprintf(ficgp," (1.");
+             }else
+               i=i-ncovmodel;
            }
            if(ng != 1){
- Line 7851  set ter svg size 640, 480\nunset log y\n
+ Line 11079  set ter svg size 640, 480\nunset log y\n
                  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;
-               for(j=3; j <=ncovmodel-nagesqr; j++){
+               ijp=1;
-                  if(cptcovage >0){
+               /* for(j=3; j <=ncovmodel-nagesqr; j++){ */
-                    if((j-2)==Tage[ij]) { /* Bug valgrind */
+               for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
-                      if(ij <=cptcovage) { /* Bug valgrind */
+                 switch(Typevar[j]){
-                        fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
+                 case 1:
-                        /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                   if(cptcovage >0){
-                        ij++;
+                     if(j==Tage[ij]) { /* Bug valgrind */
-                      }
+                       if(ij <=cptcovage) { /* Bug valgrind */
-                    }
+                         if(DummyV[j]==0){/* Bug valgrind */
-                  }else
+                           /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); */
-                    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*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,nbcode[Tvar[j]][codtabm(k1,j)]); */
+                           fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]);
+                           /* fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; */
+                           /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                         }else{ /* quantitative */
+                           /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */
+                           fprintf(ficgp,"+p%d*%f*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
+                           /* 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++;
+                       }
+                     }
+                   }
+                   break;
+                 case 2:
+                   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",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
+                             /* 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",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],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",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
+                             /* 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",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                             /* fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
+                           }
+                         }
+                         ijp++;
+                       }
+                     } /* end Tprod */
+                   } /* end if */
+                   break;
+                 case 3:
+                   if(cptcovdageprod >0){
+                     /* if(j==Tprod[ijp]) { /\* *\/  */
+                       /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
+                       if(ijp <=cptcovprod) { /* Product */
+                         if(DummyV[Tvardk[ijp][1]]==0){/* Vn is dummy */
+                           if(DummyV[Tvardk[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*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][1]],Tinvresult[nres][Tvardk[ijp][2]]);
+                             /* 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*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
+                             /* fprintf(ficgp,"+p%d*%d*%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
+                           }
+                         }else{ /* Vn*Vm Vn is quanti */
+                           if(DummyV[Tvardk[ijp][2]]==0){
+                             fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][2]],Tqinvresult[nres][Tvardk[ijp][1]]);
+                             /* fprintf(ficgp,"+p%d*%d*%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); */
+                           }else{ /* Both quanti */
+                             fprintf(ficgp,"+p%d*%f*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
+                             /* fprintf(ficgp,"+p%d*%f*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
+                           }
+                         }
+                         ijp++;
+                       }
+                     /* } /\* end Tprod *\/ */
+                   } /* end if */
+                   break;
+                 case 0:
+                   /* 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]]); /\*  *\/ */
+                     fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]); /*  */
+                     /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\*  *\/ */
+                   }else{ /* quantitative */
+                     fprintf(ficgp,"+p%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* */
+                     /* 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 */
+                   /* fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/\* Valgrind bug nbcode *\/ */
+                   break;
+                 default:
+                   break;
+                 } /* end switch */
                }
                fprintf(ficgp,")");
              }
              fprintf(ficgp,")");
              if(ng ==2)
-               fprintf(ficgp," t \"p%d%d\" ", k2,k);
+               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);
              else /* ng= 3 */
-               fprintf(ficgp," t \"i%d%d\" ", k2,k);
+               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);
            }else{ /* end ng <> 1 */
              if( k !=k2) /* logit p11 is hard to draw */
-               fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
+               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);
            }
            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
              fprintf(ficgp,",");
- Line 7881  set ter svg size 640, 480\nunset log y\n
+ Line 11199  set ter svg size 640, 480\nunset log y\n
            i=i+ncovmodel;
          } /* end k */
        } /* end k2 */
-       fprintf(ficgp,"\n set out; unset label;\n");
+       /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
-     } /* end k1 */
+       fprintf(ficgp,"\n set out; unset title;set key default;\n");
+     } /* end resultline */
    } /* end ng */
    /* avoid: */
    fflush(ficgp);
- Line 7897  set ter svg size 640, 480\nunset log y\n
+ Line 11216  set ter svg size 640, 480\nunset log y\n
     int modcovmax =1;
     int mobilavrange, mob;
     int iage=0;
+    int firstA1=0, firstA2=0;
     double sum=0., sumr=0.;
     double age;
- Line 7905  set ter svg size 640, 480\nunset log y\n
+ Line 11225  set ter svg size 640, 480\nunset log y\n
     double *agemingoodr, *agemaxgoodr;
-    /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
+    /* modcovmax=2*cptcoveff;  Max number of modalities. We suppose  */
-    /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
+    /*              a covariate has 2 modalities, should be equal to ncovcombmax   */
     sumnewp = vector(1,ncovcombmax);
     sumnewm = vector(1,ncovcombmax);
- Line 7994  set ter svg size 640, 480\nunset log y\n
+ Line 11314  set ter svg size 640, 480\nunset log y\n
       } /* 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.;
- Line 8026  set ter svg size 640, 480\nunset log y\n
+ Line 11347  set ter svg size 640, 480\nunset log y\n
           sumr+=probs[(int)age][i][cptcod];
         }
         if(fabs(sum - 1.) > 1.e-3) { /* bad */
-          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\n",cptcod,sumr, (int)age, (int)bage);
+          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 */
-          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\n",cptcod,sumr, (int)age, (int)bage);
+          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 */
- Line 8118  set ter svg size 640, 480\nunset log y\n
+ Line 11447  set ter svg size 640, 480\nunset log y\n
   }/* End movingaverage */
  /************** Forecasting ******************/
-  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, 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
       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, k4, nres=0;
+   /* double anprojd, mprojd, jprojd; */
+   /* double anprojf, mprojf, jprojf; */
+   int yearp, stepsize, hstepm, nhstepm, j, k, i, h,  nres=0;
    double agec; /* generic age */
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double agelim, ppij;
-   double *popeffectif,*popcount;
+   /*double *popcount;*/
    double ***p3mat;
    /* double ***mobaverage; */
    char fileresf[FILENAMELENGTH];
- Line 8164  set ter svg size 640, 480\nunset log y\n
+ Line 11498  set ter svg size 640, 480\nunset log y\n
    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
-                                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=pow(2,cptcoveff);
-   if (cptcovn < 1){i1=1;}
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
+   /*                              fractional in yp1 *\/ */
+   /* aintmean=yp; */
+   /* yp2=modf((yp1*12),&yp); */
+   /* mintmean=yp; */
+   /* yp1=modf((yp2*30.5),&yp); */
+   /* jintmean=yp; */
+   /* if(jintmean==0) jintmean=1; */
+   /* if(mintmean==0) mintmean=1; */
+   /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
+   /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
+   /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
+   /* i1=pow(2,cptcoveff); */
+   /* if (cptcovn < 1){i1=1;} */
+   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");
  /*            if (h==(int)(YEARM*yearp)){ */
-   for(nres=1; nres <= nresult; nres++) /* For each resultline */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-   for(k=1; k<=i1;k++){
+     k=TKresult[nres];
-     if(i1 != 1 && TKresult[nres]!= k)
+     if(TKresult[nres]==0) k=1; /* To be checked for noresult */
-       continue;
+     /*  for(k=1; k<=i1;k++){ /\* We want to find the combination k corresponding to the values of the dummies given in this resut line (to be cleaned one day) *\/ */
-     if(invalidvarcomb[k]){
+     /* if(i1 != 1 && TKresult[nres]!= k) */
-       printf("\nCombination (%d) projection ignored because no cases \n",k);
+     /*   continue; */
-       continue;
+     /* if(invalidvarcomb[k]){ */
-     }
+     /*   printf("\nCombination (%d) projection ignored because no cases \n",k);  */
+     /*   continue; */
+     /* } */
      fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
-     for(j=1;j<=cptcoveff;j++) {
+     for(j=1;j<=cptcovs;j++){
-       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       /* for(j=1;j<=cptcoveff;j++) { */
-     }
+     /*   /\* fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); *\/ */
-     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+     /*   fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+     /* } */
+     /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+     /*   fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+     /* } */
+       fprintf(ficresf," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
      }
      fprintf(ficresf," yearproj age");
      for(j=1; j<=nlstate+ndeath;j++){
        for(i=1; i<=nlstate;i++)
          fprintf(ficresf," p%d%d",i,j);
        fprintf(ficresf," wp.%d",j);
      }
-     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+     for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
        fprintf(ficresf,"\n");
-       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
        /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
        for (agec=fage; agec>=(bage); agec--){
          nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
- Line 8223  set ter svg size 640, 480\nunset log y\n
+ Line 11569  set ter svg size 640, 480\nunset log y\n
            }
          }
          fprintf(ficresf,"\n");
-         for(j=1;j<=cptcoveff;j++)
+         /* for(j=1;j<=cptcoveff;j++)  */
-           fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         for(j=1;j<=cptcovs;j++)
-         fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+           fprintf(ficresf,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+           /* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Tvaraff not correct *\/ */
+           /* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /\* TnsdVar[Tvaraff]  correct *\/ */
+         fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
          for(j=1; j<=nlstate+ndeath;j++) {
            ppij=0.;
            for(i=1; i<=nlstate;i++) {
-             /* if (mobilav>=1)  */
+             if (mobilav>=1)
-             ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
+              ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
-             /* else { */ /* even if mobilav==-1 we use mobaverage */
+             else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
-             /*  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
+                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
-             /* } */
+             }
              fprintf(ficresf," %.3f", p3mat[i][j][h]);
            } /* end i */
            fprintf(ficresf," %.3f", ppij);
- Line 8253  set ter svg size 640, 480\nunset log y\n
+ Line 11602  set ter svg size 640, 480\nunset log y\n
  }
  /************** Back Forecasting ******************/
-  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){
+  /* 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){
+   /* back1, year, month, day of starting backprojection
       agemin, agemax range of age
       dateprev1 dateprev2 range of dates during which prevalence is computed
       anback2 year of end of backprojection (same day and month as back1).
       prevacurrent and prev are prevalences.
    */
-   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
+   int yearp, stepsize, hstepm, nhstepm, j, k,  i, h, nres=0;
    double agec; /* generic age */
-   double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double agelim, ppij, ppi; /* ,jintmean,mintmean,aintmean;*/
-   double *popeffectif,*popcount;
+   /*double *popcount;*/
    double ***p3mat;
    /* double ***mobaverage; */
    char fileresfb[FILENAMELENGTH];
- Line 8305  set ter svg size 640, 480\nunset log y\n
+ Line 11655  set ter svg size 640, 480\nunset log y\n
    }
    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) jintmean=1; */
-   i1=pow(2,cptcoveff);
+   /* i1=pow(2,cptcoveff); */
-   if (cptcovn < 1){i1=1;}
+   /* if (cptcovn < 1){i1=1;} */
-   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
-   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
    fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
-   for(nres=1; nres <= nresult; nres++) /* For each resultline */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-   for(k=1; k<=i1;k++){
+     k=TKresult[nres];
-     if(i1 != 1 && TKresult[nres]!= k)
+     if(TKresult[nres]==0) k=1; /* To be checked for noresult */
-       continue;
+   /* for(k=1; k<=i1;k++){ */
-     if(invalidvarcomb[k]){
+   /*   if(i1 != 1 && TKresult[nres]!= k) */
-       printf("\nCombination (%d) projection ignored because no cases \n",k);
+   /*     continue; */
-       continue;
+   /*   if(invalidvarcomb[k]){ */
-     }
+   /*     printf("\nCombination (%d) projection ignored because no cases \n",k);  */
+   /*     continue; */
+   /*   } */
      fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
-     for(j=1;j<=cptcoveff;j++) {
+     for(j=1;j<=cptcovs;j++){
-       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     /* for(j=1;j<=cptcoveff;j++) { */
-     }
+     /*   fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+     /* } */
-       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       fprintf(ficresfb," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
      }
+    /*  fprintf(ficrespij,"******\n"); */
+    /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
+    /*    fprintf(ficresfb," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+    /*  } */
      fprintf(ficresfb," yearbproj age");
      for(j=1; j<=nlstate+ndeath;j++){
        for(i=1; i<=nlstate;i++)
          fprintf(ficresfb," b%d%d",i,j);
        fprintf(ficresfb," b.%d",j);
      }
-     for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
+     for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
        /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
        fprintf(ficresfb,"\n");
-       fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
+       fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
-       printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
+       /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
        /* 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;*/
- Line 8368  set ter svg size 640, 480\nunset log y\n
+ Line 11724  set ter svg size 640, 480\nunset log y\n
            }
          }
          fprintf(ficresfb,"\n");
-         for(j=1;j<=cptcoveff;j++)
+         /* for(j=1;j<=cptcoveff;j++) */
-           fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         for(j=1;j<=cptcovs;j++)
-         fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
+           fprintf(ficresfb,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+           /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[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++) {
- Line 8405  set ter svg size 640, 480\nunset log y\n
+ Line 11763  set ter svg size 640, 480\nunset log y\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 period (stable) prevalence------*/
+     /*------- Variance of forward period (stable) prevalence------*/
     char fileresvpl[FILENAMELENGTH];
     FILE *ficresvpl;
- Line 8416  set ter svg size 640, 480\nunset log y\n
+ Line 11774  set ter svg size 640, 480\nunset log y\n
      strcpy(fileresvpl,"VPL_");
      strcat(fileresvpl,fileresu);
      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       printf("Problem with variance of forward period (stable) prevalence  resultfile: %s\n", fileresvpl);
        exit(0);
      }
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
+     printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
-     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
+     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++){*/
- Line 8428  set ter svg size 640, 480\nunset log y\n
+ Line 11786  set ter svg size 640, 480\nunset log y\n
      i1=pow(2,cptcoveff);
      if (cptcovn < 1){i1=1;}
-     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     for(k=1; k<=i1;k++){
+        k=TKresult[nres];
+        if(TKresult[nres]==0) k=1; /* To be checked for noresult */
+      /* for(k=1; k<=i1;k++){ /\* We find the combination equivalent to result line values of dummies *\/ */
        if(i1 != 1 && TKresult[nres]!= k)
          continue;
        fprintf(ficresvpl,"\n#****** ");
        printf("\n#****** ");
        fprintf(ficlog,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++) {
+       for(j=1;j<=cptcovs;j++) {
-         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresvpl,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-       }
+         /* fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         /* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
-         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
-         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
-       }
+       /*        fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+       /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+       /* }       */
        fprintf(ficresvpl,"******\n");
        printf("******\n");
        fprintf(ficlog,"******\n");
- Line 8457  set ter svg size 640, 480\nunset log y\n
+ Line 11819  set ter svg size 640, 480\nunset log y\n
      }
      fclose(ficresvpl);
-     printf("done variance-covariance of period prevalence\n");fflush(stdout);
+     printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
-     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
+     fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
   }
  /* Variance of back prevalence: varbprlim */
- Line 8485  set ter svg size 640, 480\nunset log y\n
+ Line 11847  set ter svg size 640, 480\nunset log y\n
     i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}
-    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-      for(k=1; k<=i1;k++){
+      k=TKresult[nres];
-        if(i1 != 1 && TKresult[nres]!= k)
+      if(TKresult[nres]==0) k=1; /* To be checked for noresult */
-          continue;
+     /* 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++) {
+        for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value */
-          fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+          printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
-          fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+          fprintf(ficresvbl," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
-          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+          fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
-        }
+        /* for(j=1;j<=cptcoveff;j++) { */
-        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+        /*        fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-          printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+        /*        fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-          fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+        /*        printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-          fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+        /* } */
+        /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
+        /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+        /*        fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+        /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         }
         fprintf(ficresvbl,"******\n");
         printf("******\n");
- Line 8818  void prwizard(int ncovmodel, int nlstate
+ Line 12186  void prwizard(int ncovmodel, int nlstate
  /******************* Gompertz Likelihood ******************************/
  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 */
    for (i=1;i<=imx ; i++) {
- Line 8826  double gompertz(double x[])
+ Line 12194  double gompertz(double x[])
      /*    sump=sump+1;*/
      num=num+1;
    }
+   L=0.0;
+   /* agegomp=AGEGOMP; */
    /* for (i=0; i<=imx; i++)
       if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-   for (i=1;i<=imx ; i++)
+   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)))
-              +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 ) { /* ??? */
+        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("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;
  }
- Line 8856  double gompertz(double x[])
+ Line 12230  double gompertz(double x[])
  /******************* Gompertz_f Likelihood ******************************/
  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;
    int i,n=0; /* n is the size of the sample */
- Line 8922  void printinggnuplotmort(char fileresu[]
+ Line 12296  void printinggnuplotmort(char fileresu[]
    char dirfileres[132],optfileres[132];
-   int ng;
+   /*int ng;*/
    /*#ifdef windows */
- Line 8946  int readdata(char datafile[], int firsto
+ Line 12320  int readdata(char datafile[], int firsto
    /*-------- data file ----------*/
    FILE *fic;
    char dummy[]="                         ";
-   int i=0, j=0, n=0, iv=0, v;
+   int i = 0, j = 0, n = 0, iv = 0;/* , v;*/
    int lstra;
    int linei, month, year,iout;
+   int noffset=0; /* This is the offset if BOM data file */
    char line[MAXLINE], linetmp[MAXLINE];
    char stra[MAXLINE], strb[MAXLINE];
    char *stratrunc;
-   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
+   /* DummyV=ivector(-1,NCOVMAX); /\* 1 to 3 *\/ */
-   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
+   /* FixedV=ivector(-1,NCOVMAX); /\* 1 to 3 *\/ */
-   for(v=1; v <=ncovcol;v++){
+   ncovcolt=ncovcol+nqv+ntv+nqtv; /* total of covariates in the data, not in the model equation */
-     DummyV[v]=0;
-     FixedV[v]=0;
+   if((fic=fopen(datafile,"r"))==NULL)    {
-   }
+     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
-   for(v=ncovcol+1; v <=ncovcol+nqv;v++){
+     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
-     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]);
    }
+     /* Is it a BOM UTF-8 Windows file? */
+   /* First data line */
+   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;
-   linei=0;
    while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
      linei=linei+1;
      for(j=strlen(line); j>=0;j--){  /* Untabifies line */
- Line 9009  int readdata(char datafile[], int firsto
+ Line 12410  int readdata(char datafile[], int firsto
          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 */
+           cotvar[j][ncovcol+nqv+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);
- Line 9029  int readdata(char datafile[], int firsto
+ Line 12430  int readdata(char datafile[], int firsto
              return 1;
            }
            cotqvar[j][iv][i]=dval;
-           cotvar[j][ntv+iv][i]=dval;
+           cotvar[j][ncovcol+nqv+ntv+iv][i]=dval; /* because cotvar starts now at first ntv */
          }
          strcpy(line,stra);
        }/* end loop ntqv */
- Line 9050  int readdata(char datafile[], int firsto
+ Line 12451  int readdata(char datafile[], int firsto
          }
          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 \
+  Should be a value of %d(nth) covariate of wave %d (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);
+  Exiting.\n",lval,linei, i,line,iv,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 \
+  Should be a value of %d(nth) covariate of wave %d (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);
+  Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
            return 1;
          }
-         cotvar[j][iv][i]=(double)(lval);
+         cotvar[j][ncovcol+nqv+iv][i]=(double)(lval);
          strcpy(line,stra);
        }/* end loop ntv */
- Line 9081  int readdata(char datafile[], int firsto
+ Line 12482  int readdata(char datafile[], int firsto
          errno=0;
          lval=strtol(strb,&endptr,10);
          /*      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;
+         }else if( lval==0 || lval > nlstate+ndeath){
+           printf("Error in data around '%s' at line number %d for individual %d, '%s'\n Should be a state at wave %d. A state should be 1 to %d and not %ld.\n Fix your data file '%s'!  Exiting.\n", strb, linei,i,line,j,nlstate+ndeath, lval, datafile);fflush(stdout);
+           fprintf(ficlog,"Error in data around '%s' at line number %d for individual %d, '%s'\n Should be a state at wave %d. A state should be 1 to %d and not %ld.\n Fix your data file '%s'!  Exiting.\n", strb, linei,i,line,j,nlstate+ndeath, lval, datafile); fflush(ficlog);
            return 1;
          }
        }
- Line 9104  int readdata(char datafile[], int firsto
+ Line 12509  int readdata(char datafile[], int firsto
          return 1;
        }
        anint[j][i]= (double) year;
        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);
      } /* End loop on waves */
- Line 9143  int readdata(char datafile[], int firsto
+ Line 12552  int readdata(char datafile[], int firsto
      }
      annais[i]=(double)(year);
      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);
      /* Sample weight */
- Line 9163  int readdata(char datafile[], int firsto
+ Line 12579  int readdata(char datafile[], int firsto
        cutv(stra, strb, line, ' ');
        if(strb[0]=='.') { /* Missing value */
          lval=-1;
+         coqvar[iv][i]=NAN;
+         covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */
        }else{
          errno=0;
          /* what_kind_of_number(strb); */
- Line 9256  void removefirstspace(char **stri){/*, c
+ Line 12674  void removefirstspace(char **stri){/*, c
    *stri=p2;
  }
- int decoderesult ( char resultline[], int nres)
+ 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 resultmodel[MAXLINE]; */
-   int modelresult[MAXLINE];
+   /* int modelresult[MAXLINE]; */
    char stra[80], strb[80], strc[80], strd[80],stre[80];
    removefirstspace(&resultline);
    printf("decoderesult:%s\n",resultline);
-   if (strstr(resultline,"v") !=0){
+   strcpy(resultsav,resultline);
-     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
+   /* printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, 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'=' */
+     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' in this resultline */
    }
-   if(j == 0){ /* Resultline but no = */
+   if(j == 0 && cptcovs== 0){ /* Resultline but no =  and no covariate in the model */
      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 variables in the resultline which is %d, differs from the number %d of single variables used in the model line, 1+age+%s.\n",j, cptcovs, model);fflush(ficlog);
-     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);
+     printf("ERROR: the number of variables in the resultline which is %d, differs from the number %d of single variables used in the model line, 1+age+%s.\n",j, cptcovs, model);fflush(stdout);
+     if(j==0)
+       return 1;
    }
-   for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
+   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 ' '
+       cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop *//*     resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */
-                                       resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
+       /* If resultsav= "V4= 1 V5=25.1 V3=0" with a blank then strb="V4=" and stra="1 V5=25.1 V3=0" */
-        cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
+       cutl(strc,strd,strb,'=');  /* strb:"V4=1" strc="1" strd="V4" */
+       /* If a blank, then strc="V4=" and strd='\0' */
+       if(strc[0]=='\0'){
+       printf("Error in resultline, probably a blank after the \"%s\", \"result:%s\", stra=\"%s\" resultsav=\"%s\"\n",strb,resultline, stra, resultsav);
+         fprintf(ficlog,"Error in resultline, probably a blank after the \"V%s=\", resultline=%s\n",strb,resultline);
+         return 1;
+       }
      }else
        cutl(strc,strd,resultsav,'=');
-     Tvalsel[k]=atof(strc); /* 1 */
+     Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */
      cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
-     Tvarsel[k]=atoi(strc);
+     Tvarsel[k]=atoi(strc);  /* 4 */ /* Tvarsel is the id of the kth covariate in the result line Tvarsel[1] in "V4=1.." is 4.*/
      /* 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 */
+   /* Feeds resultmodel[nres][k1]=k2 for k1th product covariate with age in the model equation fed by the index k2 of the resutline*/
+   for(k1=1; k1<= cptcovt ;k1++){ /* Loop on MODEL LINE V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
      if(Typevar[k1]==0){ /* Single covariate in model */
+       /* 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
        match=0;
-       for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
-         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5   */
+         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
-           modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
+           modelresult[nres][k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
-           match=1;
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
            break;
          }
        }
        if(match == 0){
-         printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
+         printf("Error in result line (Dummy single): V%d is missing in result: %s according to model=1+age+%s. Tvar[k1=%d]=%d is different from Tvarsel[k2=%d]=%d.\n",Tvar[k1], resultline, model,k1, Tvar[k1], k2, Tvarsel[k2]);
+         fprintf(ficlog,"Error in result line (Dummy single): V%d is missing in result: %s according to model=1+age+%s\n",Tvar[k1], resultline, model);
+         return 1;
        }
-     }
+     }else if(Typevar[k1]==1){ /* Product with age We want to get the position k2 in the resultline of the product k1 in the model line*/
-   }
+       /* We feed resultmodel[k1]=k2; */
+       match=0;
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline.  jth occurence of = signs in the result line. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
+           modelresult[nres][k2]=k1;/* we found a Vn=1 corrresponding to Vn*age in the model modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
+           resultmodel[nres][k1]=k2; /* Added here */
+           /* printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%d*AGE\n",k2,k1,Tvar[k1]); */
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
+           break;
+         }
+       }
+       if(match == 0){
+         printf("Error in result line (Product with age): V%d is missing in result: %s according to model=1+age+%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
+         fprintf(ficlog,"Error in result line (Product with age): V%d is missing in result: %s according to model=1+age+%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
+       return 1;
+       }
+     }else if(Typevar[k1]==2 || Typevar[k1]==3){ /* Product with or without age. We want to get the position in the resultline of the product in the model line*/
+       /* resultmodel[nres][of such a Vn * Vm product k1] is not unique, so can't exist, we feed Tvard[k1][1] and [2] */
+       match=0;
+       /* printf("Decoderesult very first Product Tvardk[k1=%d][1]=%d Tvardk[k1=%d][2]=%d V%d * V%d\n",k1,Tvardk[k1][1],k1,Tvardk[k1][2],Tvardk[k1][1],Tvardk[k1][2]); */
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvardk[k1][1]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
+           /* modelresult[k2]=k1; */
+           /* printf("Decoderesult first Product modelresult[k2=%d]=%d (k1) V%d * \n",k2,k1,Tvarsel[k2]); */
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
+         }
+       }
+       if(match == 0){
+         printf("Error in result line (Product without age first variable or double product with age): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][1], resultline, model);
+         fprintf(ficlog,"Error in result line (Product without age first variable or double product with age): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][1], resultline, model);
+         return 1;
+       }
+       match=0;
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvardk[k1][2]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
+           /* modelresult[k2]=k1;*/
+           /* printf("Decoderesult second Product modelresult[k2=%d]=%d (k1) * V%d \n ",k2,k1,Tvarsel[k2]); */
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
+           break;
+         }
+       }
+       if(match == 0){
+         printf("Error in result line (Product without age second variable or double product with age): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][2], resultline, model);
+         fprintf(ficlog,"Error in result line (Product without age second variable or double product with age): V%d is missing in result : %s according to model=1+age+%s\n",Tvardk[k1][2], resultline, model);
+         return 1;
+       }
+     }/* End of testing */
+   }/* End loop cptcovt */
    /* 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 */
+   /* Feeds resultmodel[nres][k1]=k2 for single covariate (k1) in the model equation */
+   for(k2=1; k2 <=j;k2++){ /* j or cptcovs is the number of single covariates used either in the model line as well as in the result line (dummy or quantitative)
+                            * Loop on resultline variables: 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 */
+     for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
-       if(Typevar[k1]==0){ /* Single */
+       if(Typevar[k1]==0){ /* Single only */
-         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
+         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4  What if a product?  */
-           resultmodel[k1]=k2;  /* resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
+           resultmodel[nres][k1]=k2;  /* k1th position in the model equation corresponds to k2th position in the result line. resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
+           modelresult[nres][k2]=k1; /* k1th position in the model equation corresponds to k2th position in the result line. modelresult[1]=2 modelresult[2]=1  modelresult[3]=3  remodelresult[4]=6 modelresult[5]=9 */
            ++match;
          }
        }
      }
      if(match == 0){
-       printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
+       printf("Error in result line: variable V%d is missing in model; result: %s, model=1+age+%s\n",Tvarsel[k2], resultline, model);
+       fprintf(ficlog,"Error in result line: variable V%d is missing in model; result: %s, model=1+age+%s\n",Tvarsel[k2], resultline, model);
+       return 1;
      }else if(match > 1){
-       printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
+       printf("Error in result line: %d doubled; result: %s, model=1+age+%s\n",k2, resultline, model);
+       fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=1+age+%s\n",k2, resultline, model);
+       return 1;
      }
    }
+   /* cptcovres=j /\* Number of variables in the resultline is equal to cptcovs and thus useless *\/     */
    /* 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 */
+   /* nres=1st 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*/
+   /* should correspond to the combination 6 of dummy: V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 1*1 + 0*2 + 1*4 = 5 + (1offset) = 6*/
-   /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+   /* nres=2nd 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 */
+   /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 (nres=2)*/
    /*    5 0 0 1 */
-   /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 */
+   /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 (nres=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 */
+   for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* cptcovt number of covariates (excluding 1 and age or age*age) in the MODEL equation.
-     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
+                                                    * loop on position k1 in the MODEL LINE */
-       k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
+     /* k counting number of combination of single dummies in the equation model */
-       k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
+     /* k4 counting single dummies in the equation model */
-       k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */
+     /* k4q counting single quantitatives in the equation model */
-       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */
+     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, fixed or timevarying, k1 is sorting according to MODEL, but k3 to resultline */
-       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
+        /* k4+1= (not always if quant in model) position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */
+       /* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/
+       /* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */
+       /* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline                        */
+       /*      k3 is the position in the nres result line of the k1th variable of the model equation                                  */
+       /* Tvarsel[k3]: Name of the variable at the k3th position in the result line.                                                  */
+       /* Tvalsel[k3]: Value of the variable at the k3th position in the result line.                                                 */
+       /* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline                   */
+       /* Tvresult[nres][result_position]= name of the dummy variable at the result_position in the nres resultline                     */
+       /* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line                                        */
+       /* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line                                                      */
+       k3= resultmodel[nres][k1]; /* From position k1 in model get position k3 in result line */
+       /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
+       k2=(int)Tvarsel[k3]; /* from position k3 in resultline get name k2: nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
+       k+=Tvalsel[k3]*pow(2,k4);  /* nres=1 k1=2 Tvalsel[1]=1 (V4=1); k1=3 k3=2 Tvalsel[2]=0 (V3=0) */
+       TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][Name]=Value; stores the value into the name of the variable. */
+       /* Tinvresult[nres][4]=1 */
+       /* Tresult[nres][k4+1]=Tvalsel[k3];/\* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) *\/ */
+       Tresult[nres][k3]=Tvalsel[k3];/* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) */
+       /* Tvresult[nres][k4+1]=(int)Tvarsel[k3];/\* Tvresult[nres][1]=4 Tvresult[nres][3]=1 *\/ */
+       Tvresult[nres][k3]=(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);
+       precov[nres][k1]=Tvalsel[k3]; /* Value from resultline of the variable at the k1 position in the model */
+       /* printf("Decoderesult Dummy k=%d, k1=%d precov[nres=%d][k1=%d]=%.f V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k1, nres, k1,precov[nres][k1], k2, k3, (int)Tvalsel[k3], k4); */
        k4++;;
-     }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
+     }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */
-       k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
+       /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 */
-       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
+       /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline                                 */
-       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
+       /* Tqinvresult[nres][Name of a quantitative variable]= value of the variable in the result line                                                      */
-       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
+       k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 5 =k3q */
+       k2q=(int)Tvarsel[k3q]; /*  Name of variable at k3q th position in the resultline */
+       /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
+       /* Tqresult[nres][k4q+1]=Tvalsel[k3q]; /\* Tqresult[nres][1]=25.1 *\/ */
+       /* Tvresult[nres][k4q+1]=(int)Tvarsel[k3q];/\* Tvresult[nres][1]=4 Tvresult[nres][3]=1 *\/ */
+       /* Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /\* Tvqresult[nres][1]=5 *\/ */
+       Tqresult[nres][k3q]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
+       Tvresult[nres][k3q]=(int)Tvarsel[k3q];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
+       Tvqresult[nres][k3q]=(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]);
+       TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
+       precov[nres][k1]=Tvalsel[k3q];
+       /* printf("Decoderesult Quantitative nres=%d,precov[nres=%d][k1=%d]=%.f V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, nres, k1,precov[nres][k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); */
        k4q++;;
+     }else if( Dummy[k1]==2 ){ /* For dummy with age product "V2+V3+V4+V6+V7+V6*V2+V7*V2+V6*V3+V7*V3+V6*V4+V7*V4+age*V2+age*V3+age*V4+age*V6+age*V7+age*V6*V2+age*V6*V3+age*V7*V3+age*V6*V4+age*V7*V4\r"*/
+       /* Tvar[k1]; */ /* Age variable */ /* 17 age*V6*V2 ?*/
+       /* Wrong we want the value of variable name Tvar[k1] */
+       if(Typevar[k1]==2 || Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
+         precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];
+       /* printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]); */
+       }else{
+         k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
+         k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
+         TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][4]=1 */
+         precov[nres][k1]=Tvalsel[k3];
+       }
+       /* printf("Decoderesult Dummy with age k=%d, k1=%d precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]); */
+     }else if( Dummy[k1]==3 ){ /* For quant with age product */
+       if(Typevar[k1]==2 || Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
+         precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];
+       /* printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]); */
+       }else{
+         k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
+         k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
+         TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */
+         precov[nres][k1]=Tvalsel[k3q];
+       }
+       /* printf("Decoderesult Quantitative with age nres=%d, k1=%d, precov[nres=%d][k1=%d]=%f Tvar[%d]=V%d V(k2q=%d)= Tvarsel[%d]=%d, Tvalsel[%d]=%f\n",nres, k1, nres, k1,precov[nres][k1], k1,  Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); */
+     }else if(Typevar[k1]==2 || Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
+       precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];
+       /* printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]); */
+     }else{
+       printf("Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
+       fprintf(ficlog,"Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
      }
    }
-   TKresult[nres]=++k; /* Combination for the nresult and the model */
+   TKresult[nres]=++k; /* Number of combinations of dummies for the nresult and the model =Tvalsel[k3]*pow(2,k4) + 1*/
    return (0);
  }
- Line 9387  int decodemodel( char model[], int lasto
+ Line 12927  int decodemodel( char model[], int lasto
          * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
          * - cptcovage number of covariates with age*products =2
          * - cptcovs number of simple covariates
+         * ncovcolt=ncovcol+nqv+ntv+nqtv total of covariates in the data, not in the model equation
          * - 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.
+         *     which is a new column after the 9 (ncovcol+nqv+ntv+nqtv) variables.
-         * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
+         * - 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 .
          */
+ /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
  {
-   int i, j, k, ks, v;
+   int i, j, k, ks;/* , v;*/
-   int  j1, k1, k2, k3, k4;
+   int n,m;
-   char modelsav[80];
+   int  j1, k1, k11, k12, k2, k3, k4;
-   char stra[80], strb[80], strc[80], strd[80],stre[80];
+   char modelsav[300];
+   char stra[300], strb[300], strc[300], strd[300],stre[300],strf[300];
    char *strpt;
+   int  **existcomb;
+   existcomb=imatrix(1,NCOVMAX,1,NCOVMAX);
+   for(i=1;i<=NCOVMAX;i++)
+     for(j=1;j<=NCOVMAX;j++)
+       existcomb[i][j]=0;
    /*removespace(model);*/
    if (strlen(model) >1){ /* If there is at least 1 covariate */
-     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
+     j=0, j1=0, k1=0, k12=0, k2=-1, ks=0, cptcovn=0;
      if (strstr(model,"AGE") !=0){
        printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
        fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
        return 1;
      }
      if (strstr(model,"v") !=0){
-       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
+       printf("Error. 'v' must be in upper case 'V' model=1+age+%s ",model);
-       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
+       fprintf(ficlog,"Error. 'v' must be in upper case model=1+age+%s ",model);fflush(ficlog);
        return 1;
      }
      strcpy(modelsav,model);
      if ((strpt=strstr(model,"age*age")) !=0){
-       printf(" strpt=%s, model=%s\n",strpt, model);
+       printf(" strpt=%s, model=1+age+%s\n",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=1+age+%s'; 'age*age' should in first place before other covariates\n \
   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
   corresponding column of parameters.\n",model);
-         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+         fprintf(ficlog,"Error in model: 'model=1+age+%s'; 'age*age' should in first place before other covariates\n \
   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
   corresponding column of parameters.\n",model); fflush(ficlog);
          return 1;
- Line 9435  int decodemodel( char model[], int lasto
+ Line 12984  int decodemodel( char model[], int lasto
          substrchaine(modelsav, model, "age*age");
      }else
        nagesqr=0;
-     if (strlen(modelsav) >1){
+     if (strlen(modelsav) >1){ /* V2 +V3 +V4 +V6 +V7 +V6*V2 +V7*V2 +V6*V3 +V7*V3 +V6*V4 +V7*V4 +age*V2 +age*V3 +age*V4 +age*V6 +age*V7 +age*V6*V2 +V7*V2 +age*V6*V3 +age*V7*V3 +age*V6*V4 +age*V7*V4 */
        j=nbocc(modelsav,'+'); /**< j=Number of '+' */
        j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
-       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
+       cptcovs=0; /**<  Number of simple covariates V1 +V1*age +V3 +V3*V4 +age*age => V1 + V3 =4+1-3=2  Wrong */
        cptcovt= j+1; /* Number of total covariates in the model, not including
                       * cst, age and age*age
                       * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
        /* including age products which are counted in cptcovage.
         * but the covariates which are products must be treated
         * separately: ncovn=4- 2=2 (V1+V3). */
-       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
+       cptcovprod=0; /**< Number of products  V1*V2 +v3*age = 2 */
+       cptcovdageprod=0; /* Number of doouble products with age age*Vn*VM or Vn*age*Vm or Vn*Vm*age */
        cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
+       cptcovprodage=0;
+       /* cptcovprodage=nboccstr(modelsav,"age");*/
        /*   Design
         *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
- Line 9455  int decodemodel( char model[], int lasto
+ Line 13006  int decodemodel( char model[], int lasto
         * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
         *   k=  1    2      3       4     5       6      7        8
         *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-        *  covar[k,i], value of kth covariate if not including age for individual i:
+        *  covar[k,i], are for fixed covariates, value of kth covariate if not including age for individual i:
         *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
         *  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
         *  Tage[++cptcovage]=k
-        *       if products, new covar are created after ncovcol with k1
+        *       if products, new covar are created after ncovcol + nqv (quanti fixed) with k1
         *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
         *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
         *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
         *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
         *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
         *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-        *  <          ncovcol=8                >
+        *  <          ncovcol=8  8 fixed covariate. Additional starts at 9 (V5*V6) and 10(V7*V8)              >
         *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
         *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
+        *     Tvard[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+        * p Tvar[1]@12={2,   1,     3,      3,   9,     10,     8,       8}
         * p Tprod[1]@2={                         6, 5}
         *p Tvard[1][1]@4= {7, 8, 5, 6}
         * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
         *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-        *How to reorganize?
+        *How to reorganize? Tvars(orted)
         * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
         * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
         *       {2,   1,     4,      8,    5,      6,     3,       7}
- Line 9501  int decodemodel( char model[], int lasto
+ Line 13052  int decodemodel( char model[], int lasto
          Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
        }
        cptcovage=0;
-       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+       /* First loop in order to calculate */
-                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+       /* for age*VN*Vm
-         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+        * Provides, Typevar[k], Tage[cptcovage], existcomb[n][m], FixedV[ncovcolt+k12]
+        * Tprod[k1]=k  Tposprod[k]=k1;    Tvard[k1][1] =m;
+       */
+       /* Needs  FixedV[Tvardk[k][1]] */
+       /* For others:
+        * Sets   Typevar[k];
+        * Tvar[k]=ncovcol+nqv+ntv+nqtv+k11;
+        *        Tposprod[k]=k11;
+        *        Tprod[k11]=k;
+        *        Tvardk[k][1] =m;
+        * Needs FixedV[Tvardk[k][1]] == 0
+       */
+       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
+                                          modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */    /* <model> "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */
+         if (nbocc(modelsav,'+')==0)
+           strcpy(strb,modelsav); /* and analyzes it */
          /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
          /*scanf("%d",i);*/
-         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V5*age+ V4+V3*age strb=V3*age OR double product with age strb=age*V6*V2 or V6*V2*age or V6*age*V2 */
-           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+           cutl(strc,strd,strb,'*'); /**< k=1 strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 OR strb=age*V6*V2 strc=V6*V2 strd=age OR c=V2*age OR c=age*V2  */
-           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+           if(strchr(strc,'*')) { /**< Model with age and DOUBLE product: allowed since 0.99r44, strc=V6*V2 or V2*age or age*V2, strd=age or V6 or V6   */
-             /* covar is not filled and then is empty */
+             Typevar[k]=3;  /* 3 for age and double product age*Vn*Vm varying of fixed */
-             cptcovprod--;
+             if(strstr(strc,"age")!=0) { /* It means that strc=V2*age or age*V2 and thus that strd=Vn */
-             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+               cutl(stre,strf,strc,'*') ; /* strf=age or Vm, stre=Vm or age. If strc=V6*V2 then strf=V6 and stre=V2 */
-             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
+               strcpy(strc,strb); /* save strb(=age*Vn*Vm) into strc */
-             Typevar[k]=1;  /* 1 for age product */
+               /* We want strb=Vn*Vm */
-             cptcovage++; /* Sums the number of covariates which include age as a product */
+               if(strcmp(strf,"age")==0){ /* strf is "age" so that stre=Vm =V2 . */
-             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
+                 strcpy(strb,strd);
-             /*printf("stre=%s ", stre);*/
+                 strcat(strb,"*");
-           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+                 strcat(strb,stre);
-             cptcovprod--;
+               }else{  /* strf=Vm  If strf=V6 then stre=V2 */
-             cutl(stre,strb,strc,'V');
+                 strcpy(strb,strf);
-             Tvar[k]=atoi(stre);
+                 strcat(strb,"*");
-             Typevar[k]=1;  /* 1 for age product */
+                 strcat(strb,stre);
-             cptcovage++;
+                 strcpy(strd,strb); /* in order for strd to not be "age"  for next test (will be Vn*Vm */
-             Tage[cptcovage]=k;
+               }
-           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+               /* printf("DEBUG FIXED k=%d, Tage[k]=%d, Tvar[Tage[k]=%d,FixedV[Tvar[Tage[k]]]=%d\n",k,Tage[k],Tvar[Tage[k]],FixedV[Tvar[Tage[k]]]); */
-             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+               /* FixedV[Tvar[Tage[k]]]=0; /\* HERY not sure if V7*V4*age Fixed might not exist  yet*\/ */
-             cptcovn++;
+             }else{  /* strc=Vn*Vm (and strd=age) and should be strb=Vn*Vm but want to keep original strb double product  */
-             cptcovprodnoage++;k1++;
+               strcpy(stre,strb); /* save full b in stre */
+               strcpy(strb,strc); /* save short c in new short b for next block strb=Vn*Vm*/
+               strcpy(strf,strc); /* save short c in new short f */
+               cutl(strc,strd,strf,'*'); /* We get strd=Vn and strc=Vm for next block (strb=Vn*Vm)*/
+               /* strcpy(strc,stre);*/ /* save full e in c for future */
+             }
+             cptcovdageprod++; /* double product with age  Which product is it? */
+             /* strcpy(strb,strc);  /\* strb was age*V6*V2 or V6*V2*age or V6*age*V2 IS now V6*V2 or V2*age or age*V2 *\/ */
+             /* cutl(strc,strd,strb,'*'); /\* strd=  V6    or   V2     or    age and  strc=  V2 or    age or    V2 *\/ */
              cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-             Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
+             n=atoi(stre);
-                                                 because this model-covariate is a construction we invent a new column
-                                                 which is after existing variables ncovcol+nqv+ntv+nqtv + k1
-                                                 If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-                                                 Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-             Typevar[k]=2;  /* 2 for double fixed dummy covariates */
              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  */
+             m=atoi(strc);
-             Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
+             cptcovage++; /* Counts the number of covariates which include age as a product */
-             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+             Tage[cptcovage]=k; /* For age*V3*V2 gives the position in model of covariates associated with age Tage[1]=6 HERY too*/
-             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+             if(existcomb[n][m] == 0){
-             k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
+               /*  r /home/brouard/Documents/Recherches/REVES/Zachary/Zach-2022/Feinuo_Sun/Feinuo-threeway/femV12V15_3wayintNBe.imach */
-             /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
+               printf("Warning in model combination V%d*V%d should exist in the model before adding V%d*V%d*age !\n",n,m,n,m);
-             /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
+               fprintf(ficlog,"Warning in model combination V%d*V%d should exist in the model before adding V%d*V%d*age !\n",n,m,n,m);
-             /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
+               fflush(ficlog);
-             /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
+               k1++;  /* The combination Vn*Vm will be in the model so we create it at k1 */
-             for (i=1; i<=lastobs;i++){
+               k12++;
-               /* Computes the new covariate which is a product of
+               existcomb[n][m]=k1;
-                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
+               existcomb[m][n]=k1;
-               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+               Tvar[k]=ncovcol+nqv+ntv+nqtv+k1;
+               Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2+ age*V6*V3 Gives the k position of the k1 double product Vn*Vm or age*Vn*Vm*/
+               Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 Gives the k1 double product  Vn*Vm or age*Vn*Vm at the k position */
+               Tvard[k1][1] =m; /* m 1 for V1*/
+               Tvardk[k][1] =m; /* m 1 for V1*/
+               Tvard[k1][2] =n; /* n 4 for V4*/
+               Tvardk[k][2] =n; /* n 4 for V4*/
+ /*            Tvar[Tage[cptcovage]]=k1;*/ /* Tvar[6=age*V3*V2]=9 (new fixed covariate) */ /* We don't know about Fixed yet HERE */
+               if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with Vn*Vm */
+                 for (i=1; i<=lastobs;i++){/* For fixed product */
+                   /* 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[ncovcolt+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+                 }
+                 cptcovprodage++; /* Counting the number of fixed covariate with age */
+                 FixedV[ncovcolt+k12]=0; /* We expand Vn*Vm */
+                 k12++;
+                 FixedV[ncovcolt+k12]=0;
+               }else{ /*End of FixedV */
+                 cptcovprodvage++; /* Counting the number of varying covariate with age */
+                 FixedV[ncovcolt+k12]=1; /* We expand Vn*Vm */
+                 k12++;
+                 FixedV[ncovcolt+k12]=1;
+               }
+             }else{  /* k1 Vn*Vm already exists */
+               k11=existcomb[n][m];
+               Tposprod[k]=k11; /* OK */
+               Tvar[k]=Tvar[Tprod[k11]]; /* HERY */
+               Tvardk[k][1]=m;
+               Tvardk[k][2]=n;
+               if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with Vn*Vm */
+                 /*cptcovage++;*/ /* Counts the number of covariates which include age as a product */
+                 cptcovprodage++; /* Counting the number of fixed covariate with age */
+                 /*Tage[cptcovage]=k;*/ /* For age*V3*V2 Tage[1]=V3*V3=9 HERY too*/
+                 Tvar[Tage[cptcovage]]=k1;
+                 FixedV[ncovcolt+k12]=0; /* We expand Vn*Vm */
+                 k12++;
+                 FixedV[ncovcolt+k12]=0;
+               }else{ /* Already exists but time varying (and age) */
+                 /*cptcovage++;*/ /* Counts the number of covariates which include age as a product */
+                 /*Tage[cptcovage]=k;*/ /* For age*V3*V2 Tage[1]=V3*V3=9 HERY too*/
+                 /* Tvar[Tage[cptcovage]]=k1; */
+                 cptcovprodvage++;
+                 FixedV[ncovcolt+k12]=1; /* We expand Vn*Vm */
+                 k12++;
+                 FixedV[ncovcolt+k12]=1;
+               }
              }
-           } /* End age is not in the model */
+             /* Tage[cptcovage]=k;  /\*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 *\/ */
-         } /* End if model includes a product */
+             /* Tvar[k]=k11; /\* HERY *\/ */
-         else { /* no more sum */
+           } else {/* simple product strb=age*Vn so that c=Vn and d=age, or strb=Vn*age so that c=age and d=Vn, or b=Vn*Vm so that c=Vm and d=Vn */
+             cptcovprod++;
+             if (strcmp(strc,"age")==0) { /**< Model includes age: strb= Vn*age c=age d=Vn*/
+               /* covar is not filled and then is empty */
+               cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+               Tvar[k]=atoi(stre);  /* V2+V1+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
+               Typevar[k]=1;  /* 1 for age product */
+               cptcovage++; /* Counts the number of covariates which include age as a product */
+               Tage[cptcovage]=k;  /*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
+               if( FixedV[Tvar[k]] == 0){
+                 cptcovprodage++; /* Counting the number of fixed covariate with age */
+               }else{
+                 cptcovprodvage++; /* Counting the number of fixedvarying covariate with age */
+               }
+               /*printf("stre=%s ", stre);*/
+             } else if (strcmp(strd,"age")==0) { /* strb= age*Vn c=Vn */
+               cutl(stre,strb,strc,'V');
+               Tvar[k]=atoi(stre);
+               Typevar[k]=1;  /* 1 for age product */
+               cptcovage++;
+               Tage[cptcovage]=k;
+               if( FixedV[Tvar[k]] == 0){
+                 cptcovprodage++; /* Counting the number of fixed covariate with age */
+               }else{
+                 cptcovprodvage++; /* Counting the number of fixedvarying covariate with age */
+               }
+             }else{ /*  for product Vn*Vm */
+               Typevar[k]=2;  /* 2 for product Vn*Vm */
+               cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+               n=atoi(stre);
+               cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+               m=atoi(strc);
+               k1++;
+               cptcovprodnoage++;
+               if(existcomb[n][m] != 0 || existcomb[m][n] != 0){
+                 printf("Warning in model combination V%d*V%d already exists in the model in position k1=%d!\n",n,m,existcomb[n][m]);
+                 fprintf(ficlog,"Warning in model combination V%d*V%d already exists in the model in position k1=%d!\n",n,m,existcomb[n][m]);
+                 fflush(ficlog);
+                 k11=existcomb[n][m];
+                 Tvar[k]=ncovcol+nqv+ntv+nqtv+k11;
+                 Tposprod[k]=k11;
+                 Tprod[k11]=k;
+                 Tvardk[k][1] =m; /* m 1 for V1*/
+                 /* Tvard[k11][1] =m; /\* n 4 for V4*\/ */
+                 Tvardk[k][2] =n; /* n 4 for V4*/
+                 /* Tvard[k11][2] =n; /\* n 4 for V4*\/ */
+               }else{ /* combination Vn*Vm doesn't exist we create it (no age)*/
+                 existcomb[n][m]=k1;
+                 existcomb[m][n]=k1;
+                 Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* ncovcolt+k1; For model-covariate k tells which data-covariate to use but
+                                                     because this model-covariate is a construction we invent a new column
+                                                     which is after existing variables ncovcol+nqv+ntv+nqtv + k1
+                                                     If already ncovcol=4 and model= V2 + V1 + V1*V4 + age*V3 + V3*V2
+                                                     thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
+                                                     Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=3 etc */
+                 /* Please remark that the new variables are model dependent */
+                 /* If we have 4 variable but the model uses only 3, like in
+                  * model= V1 + age*V1 + V2 + V3 + age*V2 + age*V3 + V1*V2 + V1*V3
+                  *  k=     1     2      3   4     5        6        7       8
+                  * Tvar[k]=1     1       2   3     2        3       (5       6) (and not 4 5 because of V4 missing)
+                  * Tage[kk]    [1]= 2           [2]=5      [3]=6                  kk=1 to cptcovage=3
+                  * Tvar[Tage[kk]][1]=2          [2]=2      [3]=3
+                  */
+                 /* We need to feed some variables like TvarVV, but later on next loop because of ncovv (k2) is not correct */
+                 Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 +V6*V2*age  */
+                 Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
+                 Tvard[k1][1] =m; /* m 1 for V1*/
+                 Tvardk[k][1] =m; /* m 1 for V1*/
+                 Tvard[k1][2] =n; /* n 4 for V4*/
+                 Tvardk[k][2] =n; /* n 4 for V4*/
+                 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+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   */
+                 if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with Vn*Vm */
+                   for (i=1; i<=lastobs;i++){/* For fixed product */
+                     /* 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[ncovcolt+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+                   }
+                   /* TvarVV[k2]=n; */
+                   /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
+                   /* TvarVV[k2+1]=m; */
+                   /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
+                 }else{ /* not FixedV */
+                   /* TvarVV[k2]=n; */
+                   /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
+                   /* TvarVV[k2+1]=m; */
+                   /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
+                 }
+               }  /* End of creation of Vn*Vm if not created by age*Vn*Vm earlier  */
+             } /*  End of product Vn*Vm */
+           } /* End of age*double product or simple product */
+         }else { /* not a product */
            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
            /*  scanf("%d",i);*/
            cutl(strd,strc,strb,'V');
- Line 9566  int decodemodel( char model[], int lasto
+ Line 13277  int decodemodel( char model[], int lasto
                                  /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
                                    scanf("%d",i);*/
        } /* end of loop + on total covariates */
      } /* end if strlen(modelsave == 0) age*age might exist */
    } /* end if strlen(model == 0) */
+   cptcovs=cptcovt - cptcovdageprod - cptcovprod;/**<  Number of simple covariates V1 +V1*age +V3 +V3*V4 +age*age + age*v4*V3=> V1 + V3 =4+1-3=2  */
    /*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*/
- Line 9584  int decodemodel( char model[], int lasto
+ Line 13298  int decodemodel( char model[], int lasto
     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
+    Typevar[k]=   0    0   0     2       1       0      2      1        0
     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;
- Line 9593  int decodemodel( char model[], int lasto
+ Line 13307  int decodemodel( char model[], int lasto
    /* 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\
+   printf("Model=1+age+%s\n\
- Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
+ Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product, 3 for double product with age \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\
+   fprintf(ficlog,"Model=1+age+%s\n\
- Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
+ Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product, 3 for double product with age  \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;k<=NCOVMAX; 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 */
+   for(k=1;k<=NCOVMAX; k++){TvarFind[k]=0; TvarVind[k]=0;}
+   /* Second loop for calculating  Fixed[k], Dummy[k]*/
+   for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0,ncovva=0,ncovvta=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0, ncovvt=0;k<=cptcovt; k++){ /* or cptocvt loop on k from model */
      if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
        Fixed[k]= 0;
        Dummy[k]= 0;
- Line 9612  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 13332  Dummy[k] 0=dummy (0 1), 1 quantitative (
        modell[k].maintype= FTYPE;
        TvarsD[nsd]=Tvar[k];
        TvarsDind[nsd]=k;
+       TnsdVar[Tvar[k]]=nsd;
        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 */
+     /* }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /\* Product of fixed dummy (<=ncovcol) covariates For a fixed product k is higher than ncovcol *\/ */
-       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;
- Line 9633  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 13345  Dummy[k] 0=dummy (0 1), 1 quantitative (
        modell[k].maintype= FTYPE;
        modell[k].subtype= FQ;
        nsq++;
-       TvarsQ[nsq]=Tvar[k];
+       TvarsQ[nsq]=Tvar[k]; /* Gives the variable name (extended to products) of first nsq simple quantitative covariates (fixed or time vary see below */
-       TvarsQind[nsq]=k;
+       TvarsQind[nsq]=k;    /* Gives the position in the model equation of the first nsq simple quantitative covariates (fixed or time vary) */
        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 */
+       /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
+       /* model V1+V3+age*V1+age*V3+V1*V3 */
+       /*  Tvar={1, 3, 1, 3, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
+       ncovvt++;
+       TvarVV[ncovvt]=Tvar[k];  /*  TvarVV[1]=V3 (first time varying in the model equation  */
+       TvarVVind[ncovvt]=k;    /*  TvarVVind[1]=2 (second position in the model equation  */
        Fixed[k]= 1;
        Dummy[k]= 0;
        ntveff++; /* Only simple time varying dummy variable */
- Line 9649  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 13368  Dummy[k] 0=dummy (0 1), 1 quantitative (
        nsd++;
        TvarsD[nsd]=Tvar[k];
        TvarsDind[nsd]=k;
+       TnsdVar[Tvar[k]]=nsd; /* To be verified */
        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 */
- Line 9657  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 13377  Dummy[k] 0=dummy (0 1), 1 quantitative (
        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*/
+       /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
+       /* model V1+V3+age*V1+age*V3+V1*V3 */
+       /*  Tvar={1, 3, 1, 3, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
+       ncovvt++;
+       TvarVV[ncovvt]=Tvar[k];  /*  TvarVV[1]=V3 (first time varying in the model equation  */
+       TvarVVind[ncovvt]=k;  /*  TvarVV[1]=V3 (first time varying in the model equation  */
        Fixed[k]= 1;
        Dummy[k]= 1;
        nqtveff++;
- Line 9664  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 13391  Dummy[k] 0=dummy (0 1), 1 quantitative (
        modell[k].subtype= VQ;
        ncovv++; /* Only simple time varying variables */
        nsq++;
-       TvarsQ[nsq]=Tvar[k];
+       TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */ /* Gives the variable name (extended to products) of first nsq simple quantitative covariates (fixed or time vary here) */
-       TvarsQind[nsq]=k;
+       TvarsQind[nsq]=k; /* For single quantitative covariate gives the model position of each single quantitative covariate *//* Gives the position in the model equation of the first nsq simple quantitative covariates (fixed or time vary) */
        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 TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%Ad,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);
+       /* 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;
+       /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
+       /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
        if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
          Fixed[k]= 2;
          Dummy[k]= 2;
          modell[k].maintype= ATYPE;
          modell[k].subtype= APFD;
+         ncovta++;
+         TvarAVVA[ncovta]=Tvar[k]; /*  (2)age*V3 */
+         TvarAVVAind[ncovta]=k;
          /* 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 */
+         ncovta++;
+         TvarAVVA[ncovta]=Tvar[k]; /*   */
+         TvarAVVAind[ncovta]=k;
          /* 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 */
+         ncovva++;
+         TvarVVA[ncovva]=Tvar[k]; /*  (1)+age*V6 + (2)age*V7 */
+         TvarVVAind[ncovva]=k;
+         ncovta++;
+         TvarAVVA[ncovta]=Tvar[k]; /*   */
+         TvarAVVAind[ncovta]=k;
          /* 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 */
+         ncovva++;
+         TvarVVA[ncovva]=Tvar[k]; /*   */
+         TvarVVAind[ncovva]=k;
+         ncovta++;
+         TvarAVVA[ncovta]=Tvar[k]; /*  (1)+age*V6 + (2)age*V7 */
+         TvarAVVAind[ncovta]=k;
          /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
        }
-     }else if (Typevar[k] == 2) {  /* product without age */
+     }else if( Tposprod[k]>0  &&  Typevar[k]==2){  /* Detects if fixed product no age Vm*Vn */
-       k1=Tposprod[k];
+       printf("MEMORY ERRORR k=%d  Tposprod[k]=%d, Typevar[k]=%d\n ",k, Tposprod[k], Typevar[k]);
-       if(Tvard[k1][1] <=ncovcol){
+       if(FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* Needs a fixed product Product of fixed dummy (<=ncovcol) covariates For a fixed product k is higher than ncovcol V3*V2 */
-         if(Tvard[k1][2] <=ncovcol){
+       printf("MEMORY ERRORR k=%d Tvardk[k][1]=%d, Tvardk[k][2]=%d, FixedV[Tvardk[k][1]]=%d,FixedV[Tvardk[k][2]]=%d\n ",k,Tvardk[k][1],Tvardk[k][2],FixedV[Tvardk[k][1]],FixedV[Tvardk[k][2]]);
-           Fixed[k]= 1;
+         Fixed[k]= 0;
-           Dummy[k]= 0;
+         Dummy[k]= 0;
+         ncoveff++;
+         ncovf++;
+         /* ncovv++; */
+         /* TvarVV[ncovv]=Tvardk[k][1]; */
+         /* FixedV[ncovcolt+ncovv]=0; /\* or FixedV[TvarVV[ncovv]]=0 HERE *\/ */
+         /* ncovv++; */
+         /* TvarVV[ncovv]=Tvardk[k][2]; */
+         /* FixedV[ncovcolt+ncovv]=0; /\* or FixedV[TvarVV[ncovv]]=0 HERE *\/ */
+         modell[k].maintype= FTYPE;
+         TvarF[ncovf]=Tvar[k];
+         /* TnsdVar[Tvar[k]]=nsd; */ /* To be done */
+         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{/* product varying Vn * Vm without age, V1+V3+age*V1+age*V3+V1*V3 looking at V1*V3, Typevar={0, 0, 1, 1, 2}, k=5, V1 is fixed, V3 is timevary, V5 is a product  */
+         /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
+         /* model V1+V3+age*V1+age*V3+V1*V3 + V1*V3*age*/
+         /*  Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
+         k1=Tposprod[k];  /* Position in the products of product k, Tposprod={0, 0, 0, 0, 1, 1} k1=1 first product but second time varying because of V3 */
+         ncovvt++;
+         TvarVV[ncovvt]=Tvard[k1][1];  /*  TvarVV[2]=V1 (because TvarVV[1] was V3, first time varying covariates */
+         TvarVVind[ncovvt]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
+         ncovvt++;
+         TvarVV[ncovvt]=Tvard[k1][2];  /*  TvarVV[3]=V3 */
+         TvarVVind[ncovvt]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
+         /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
+         /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
+         if(Tvard[k1][1] <=ncovcol){ /* Vn is dummy fixed, (Tvard[1][1]=V1), (Tvard[1][1]=V3 time varying) */
+           if(Tvard[k1][2] <=ncovcol){ /* Vm is dummy fixed */
+             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){ /* Vm is quanti fixed */
+             Fixed[k]= 0;  /* Fixed product */
+             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){ /* Vm is a time varying dummy covariate */
+             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];  /* TvarV[1]=Tvar[5]=5 because there is a V4 */
+             TvarVind[ncovv]=k;/* TvarVind[1]=5 */
+           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is a time varying quantitative covariate */
+             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){ /* Vn is fixed quanti  */
+           if(Tvard[k1][2] <=ncovcol){ /* Vm is fixed dummy */
+             Fixed[k]= 0;  /*  Fixed product */
+             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){ /* Vm is time varying */
+             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){ /* Vm is time varying quanti */
+             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){ /* Vn is time varying dummy */
+           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){ /* Vn is time varying quanti */
+           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 if(Typevar[k] == 3){  /* product Vn * Vm with age, V1+V3+age*V1+age*V3+V1*V3 looking at V1*V3, Typevar={0, 0, 1, 1, 2}, k=5, V1 is fixed, V3 is timevary, V5 is a product  */
+       /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
+       /* model V1+V3+age*V1+age*V3+V1*V3 + V1*V3*age*/
+       /*  Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
+       k1=Tposprod[k];  /* Position in the products of product k, Tposprod={0, 0, 0, 0, 1, 1} k1=1 first product but second time varying because of V3 */
+       ncova++;
+       TvarA[ncova]=Tvard[k1][1];  /*  TvarVV[2]=V1 (because TvarVV[1] was V3, first time varying covariates */
+       TvarAind[ncova]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
+       ncova++;
+       TvarA[ncova]=Tvard[k1][2];  /*  TvarVV[3]=V3 */
+       TvarAind[ncova]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
+       /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
+       /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
+       if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){
+         ncovta++;
+         TvarAVVA[ncovta]=Tvard[k1][1]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
+         TvarAVVAind[ncovta]=k;
+         ncovta++;
+         TvarAVVA[ncovta]=Tvard[k1][2]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
+         TvarAVVAind[ncovta]=k;
+       }else{
+         ncovva++;  /* HERY  reached */
+         TvarVVA[ncovva]=Tvard[k1][1]; /*  age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4  */
+         TvarVVAind[ncovva]=k;
+         ncovva++;
+         TvarVVA[ncovva]=Tvard[k1][2]; /*   */
+         TvarVVAind[ncovva]=k;
+         ncovta++;
+         TvarAVVA[ncovta]=Tvard[k1][1]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
+         TvarAVVAind[ncovta]=k;
+         ncovta++;
+         TvarAVVA[ncovta]=Tvard[k1][2]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
+         TvarAVVAind[ncovta]=k;
+       }
+       if(Tvard[k1][1] <=ncovcol){ /* Vn is dummy fixed, (Tvard[1][1]=V1), (Tvard[1][1]=V3 time varying) */
+         if(Tvard[k1][2] <=ncovcol){ /* Vm is dummy fixed */
+           Fixed[k]= 2;
+           Dummy[k]= 2;
            modell[k].maintype= FTYPE;
            modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
-           ncovf++; /* Fixed variables without age */
+           /* TvarF[ncova]=Tvar[k];   /\* Problem to solve *\/ */
-           TvarF[ncovf]=Tvar[k];
+           /* TvarFind[ncova]=k; */
-           TvarFind[ncovf]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){ /* Vm is quanti fixed */
-         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           Fixed[k]= 2;  /* Fixed product */
-           Fixed[k]= 0;  /* or 2 ?*/
+           Dummy[k]= 3;
-           Dummy[k]= 1;
            modell[k].maintype= FTYPE;
            modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
-           ncovf++; /* Varying variables without age */
+           /* TvarF[ncova]=Tvar[k]; */
-           TvarF[ncovf]=Tvar[k];
+           /* TvarFind[ncova]=k; */
-           TvarFind[ncovf]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is a time varying dummy covariate */
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 3;
-           Fixed[k]= 1;
+           Dummy[k]= 2;
-           Dummy[k]= 0;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
-           ncovv++; /* Varying variables without age */
+           TvarV[ncova]=Tvar[k];  /* TvarV[1]=Tvar[5]=5 because there is a V4 */
-           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncova]=k;/* TvarVind[1]=5 */
-           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is a time varying quantitative covariate */
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 3;
-           Fixed[k]= 1;
+           Dummy[k]= 3;
-           Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
-           ncovv++; /* Varying variables without age */
+           /* ncovv++; /\* Varying variables without age *\/ */
-           TvarV[ncovv]=Tvar[k];
+           /* TvarV[ncovv]=Tvar[k]; */
-           TvarVind[ncovv]=k;
+           /* TvarVind[ncovv]=k; */
          }
-       }else if(Tvard[k1][1] <=ncovcol+nqv){
+       }else if(Tvard[k1][1] <=ncovcol+nqv){ /* Vn is fixed quanti  */
-         if(Tvard[k1][2] <=ncovcol){
+         if(Tvard[k1][2] <=ncovcol){ /* Vm is fixed dummy */
-           Fixed[k]= 0;  /* or 2 ?*/
+           Fixed[k]= 2;  /*  Fixed product */
-           Dummy[k]= 1;
+           Dummy[k]= 2;
            modell[k].maintype= FTYPE;
            modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
-           ncovf++; /* Fixed variables without age */
+           /* ncova++; /\* Fixed variables with age *\/ */
-           TvarF[ncovf]=Tvar[k];
+           /* TvarF[ncovf]=Tvar[k]; */
-           TvarFind[ncovf]=k;
+           /* TvarFind[ncovf]=k; */
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is time varying */
-           Fixed[k]= 1;
+           Fixed[k]= 2;
-           Dummy[k]= 1;
+           Dummy[k]= 3;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
-           ncovv++; /* Varying variables without age */
+           /* ncova++; /\* Varying variables with age *\/ */
-           TvarV[ncovv]=Tvar[k];
+           /* TvarV[ncova]=Tvar[k]; */
-           TvarVind[ncovv]=k;
+           /* TvarVind[ncova]=k; */
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is time varying quanti */
-           Fixed[k]= 1;
+           Fixed[k]= 3;
-           Dummy[k]= 1;
+           Dummy[k]= 2;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
-           ncovv++; /* Varying variables without age */
+           ncova++; /* Varying variables without age */
-           TvarV[ncovv]=Tvar[k];
+           TvarV[ncova]=Tvar[k];
-           TvarVind[ncovv]=k;
+           TvarVind[ncova]=k;
-           ncovv++; /* Varying variables without age */
+           /* ncova++; /\* Varying variables without age *\/ */
-           TvarV[ncovv]=Tvar[k];
+           /* TvarV[ncova]=Tvar[k]; */
-           TvarVind[ncovv]=k;
+           /* TvarVind[ncova]=k; */
          }
-       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
+       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){ /* Vn is time varying dummy */
          if(Tvard[k1][2] <=ncovcol){
-           Fixed[k]= 1;
+           Fixed[k]= 2;
-           Dummy[k]= 1;
+           Dummy[k]= 2;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
-           ncovv++; /* Varying variables without age */
+           /* ncova++; /\* Varying variables with age *\/ */
-           TvarV[ncovv]=Tvar[k];
+           /* TvarV[ncova]=Tvar[k]; */
-           TvarVind[ncovv]=k;
+           /* TvarVind[ncova]=k; */
          }else if(Tvard[k1][2] <=ncovcol+nqv){
-           Fixed[k]= 1;
+           Fixed[k]= 2;
-           Dummy[k]= 1;
+           Dummy[k]= 3;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
-           ncovv++; /* Varying variables without age */
+           /* ncova++; /\* Varying variables with age *\/ */
-           TvarV[ncovv]=Tvar[k];
+           /* TvarV[ncova]=Tvar[k]; */
-           TvarVind[ncovv]=k;
+           /* TvarVind[ncova]=k; */
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
-           Fixed[k]= 1;
+           Fixed[k]= 3;
-           Dummy[k]= 0;
+           Dummy[k]= 2;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
-           ncovv++; /* Varying variables without age */
+           /* ncova++; /\* Varying variables with age *\/ */
-           TvarV[ncovv]=Tvar[k];
+           /* TvarV[ncova]=Tvar[k]; */
-           TvarVind[ncovv]=k;
+           /* TvarVind[ncova]=k; */
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
-           Fixed[k]= 1;
+           Fixed[k]= 3;
-           Dummy[k]= 1;
+           Dummy[k]= 3;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
-           ncovv++; /* Varying variables without age */
+           /* ncova++; /\* Varying variables with age *\/ */
-           TvarV[ncovv]=Tvar[k];
+           /* TvarV[ncova]=Tvar[k]; */
-           TvarVind[ncovv]=k;
+           /* TvarVind[ncova]=k; */
          }
-       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
+       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){ /* Vn is time varying quanti */
          if(Tvard[k1][2] <=ncovcol){
-           Fixed[k]= 1;
+           Fixed[k]= 2;
-           Dummy[k]= 1;
+           Dummy[k]= 2;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
-           ncovv++; /* Varying variables without age */
+           /* ncova++; /\* Varying variables with age *\/ */
-           TvarV[ncovv]=Tvar[k];
+           /* TvarV[ncova]=Tvar[k]; */
-           TvarVind[ncovv]=k;
+           /* TvarVind[ncova]=k; */
          }else if(Tvard[k1][2] <=ncovcol+nqv){
-           Fixed[k]= 1;
+           Fixed[k]= 2;
-           Dummy[k]= 1;
+           Dummy[k]= 3;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
-           ncovv++; /* Varying variables without age */
+           /* ncova++; /\* Varying variables with age *\/ */
-           TvarV[ncovv]=Tvar[k];
+           /* TvarV[ncova]=Tvar[k]; */
-           TvarVind[ncovv]=k;
+           /* TvarVind[ncova]=k; */
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
-           Fixed[k]= 1;
+           Fixed[k]= 3;
-           Dummy[k]= 1;
+           Dummy[k]= 2;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
-           ncovv++; /* Varying variables without age */
+           /* ncova++; /\* Varying variables with age *\/ */
-           TvarV[ncovv]=Tvar[k];
+           /* TvarV[ncova]=Tvar[k]; */
-           TvarVind[ncovv]=k;
+           /* TvarVind[ncova]=k; */
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
-           Fixed[k]= 1;
+           Fixed[k]= 3;
-           Dummy[k]= 1;
+           Dummy[k]= 3;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
-           ncovv++; /* Varying variables without age */
+           /* ncova++; /\* Varying variables with age *\/ */
-           TvarV[ncovv]=Tvar[k];
+           /* TvarV[ncova]=Tvar[k]; */
-           TvarVind[ncovv]=k;
+           /* TvarVind[ncova]=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{
+     } 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("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);
+     /* 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]);
    }
+   ncovvta=ncovva;
    /* 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[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[Tvar[k1]],Dummy[Tvar[k1]]);
+             printf("Error duplication in the model=1+age+%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[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
+             fprintf(ficlog,"Error duplication in the model=1+age+%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]]);
+             printf("Error duplication in the model=1+age+%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);
+             fprintf(ficlog,"Error duplication in the model=1+age+%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);
            }
          }
- Line 9874  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 13824  Dummy[k] 0=dummy (0 1), 1 quantitative (
    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);
+   free_imatrix(existcomb,1,NCOVMAX,1,NCOVMAX);
    return (0); /* with covar[new additional covariate if product] and Tage if age */
    /*endread:*/
    printf("Exiting decodemodel: ");
- Line 10027  BOOL IsWow64()
+ Line 13979  BOOL IsWow64()
  #endif
  void syscompilerinfo(int logged)
-  {
+ {
-    /* #include "syscompilerinfo.h"*/
+ #include <stdint.h>
+   /* #include "syscompilerinfo.h"*/
     /* command line Intel compiler 32bit windows, XP compatible:*/
     /* /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
- Line 10063  void syscompilerinfo(int logged)
+ Line 14017  void syscompilerinfo(int logged)
        /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
        /NOLOGO /TLBID:1
     */
  #if defined __INTEL_COMPILER
  #if defined(__GNUC__)
          struct utsname sysInfo;  /* For Intel on Linux and OS/X */
- Line 10079  void syscompilerinfo(int logged)
+ Line 14035  void syscompilerinfo(int logged)
     }
  #endif
- #include <stdint.h>
     printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
  #if defined(__clang__)
     printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
- Line 10166  void syscompilerinfo(int logged)
+ Line 14120  void syscompilerinfo(int logged)
  #endif
  #endif
-    //   void main()
+    //   void main ()
     //   {
  #if defined(_MSC_VER)
     if (IsWow64()){
- Line 10187  void syscompilerinfo(int logged)
+ Line 14141  void syscompilerinfo(int logged)
  }
  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) --------------*/
+   /* Computes the prevalence limit for each combination of the dummy covariates */
    int i, j, k, i1, k4=0, nres=0 ;
    /* double ftolpl = 1.e-10; */
    double age, agebase, agelim;
- Line 10196  int prevalence_limit(double *p, double *
+ Line 14151  int prevalence_limit(double *p, double *
    strcpy(filerespl,"PL_");
    strcat(filerespl,fileresu);
    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("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
+   printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
    pstamp(ficrespl);
-   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
    fprintf(ficrespl,"#Age ");
    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
    fprintf(ficrespl,"\n");
- Line 10216  int prevalence_limit(double *p, double *
+ Line 14171  int prevalence_limit(double *p, double *
    i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
    if (cptcovn < 1){i1=1;}
-   for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
+   /* for(k=1; k<=i1;k++){ /\* For each combination k of dummy covariates in the model *\/ */
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(i1 != 1 && TKresult[nres]!= k)
+       k=TKresult[nres];
-         continue;
+       if(TKresult[nres]==0) k=1; /* To be checked for noresult */
+       /* if(i1 != 1 && TKresult[nres]!= k) /\* We found the combination k corresponding to the resultline value of dummies *\/ */
+       /*        continue; */
        /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
        /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
        //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        /* k=k+1; */
        /* to clean */
-       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+       /*printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));*/
        fprintf(ficrespl,"#******");
        printf("#******");
        fprintf(ficlog,"#******");
-       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+       for(j=1;j<=cptcovs ;j++) {/**< cptcovs number of SIMPLE covariates in the model or resultline V2+V1 =2 (dummy or quantit or time varying) */
-         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
+         /* fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Here problem for varying dummy*\/ */
-         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         /* printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[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,TnsdVar[Tvaraff[j]])]); */
-       }
+         fprintf(ficrespl," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-         fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
-         fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       /* 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");
- Line 10251  int prevalence_limit(double *p, double *
+ Line 14211  int prevalence_limit(double *p, double *
        }
        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,TnsdVar[Tvaraff[j]])]); */
+       /* } */
+       for(j=1;j<=cptcovs;j++) { /* New the quanti variable is added */
+         fprintf(ficrespl,"V%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
        }
        for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
        fprintf(ficrespl,"Total Years_to_converge\n");
        for (age=agebase; age<=agelim; age++){
          /* for (age=agebase; age<=agebase; age++){ */
-         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
+         /**< Computes the prevalence limit in each live state at age x and for covariate combination (k and) nres */
+         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres); /* Nicely done */
          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,TnsdVar[Tvaraff[j]])]); */
+         for(j=1;j<=cptcovs;j++)
+           fprintf(ficrespl,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
          tot=0.;
          for(i=1; i<=nlstate;i++){
            tot +=  prlim[i][i];
- Line 10271  int prevalence_limit(double *p, double *
+ Line 14237  int prevalence_limit(double *p, double *
          fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
        } /* Age */
        /* was end of cptcod */
-     } /* cptcov */
+     } /* nres */
-   } /* nres */
+   /* } /\* for each combination *\/ */
    return 0;
  }
  int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
-         /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
+         /*--------------- Back Prevalence limit  (backward stable prevalence) --------------*/
          /* Computes the back prevalence limit  for any combination      of covariate values
     * at any age between ageminpar and agemaxpar
- Line 10292  int back_prevalence_limit(double *p, dou
+ Line 14258  int back_prevalence_limit(double *p, dou
    strcpy(fileresplb,"PLB_");
    strcat(fileresplb,fileresu);
    if((ficresplb=fopen(fileresplb,"w"))==NULL) {
-     printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+     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);
-   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 ");
    for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
    fprintf(ficresplb,"\n");
- Line 10314  int back_prevalence_limit(double *p, dou
+ Line 14280  int back_prevalence_limit(double *p, dou
    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 */
+     /* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying *\/ */
-      if(i1 != 1 && TKresult[nres]!= k)
+       k=TKresult[nres];
-         continue;
+       if(TKresult[nres]==0) k=1; /* To be checked for noresult */
-       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+      /* if(i1 != 1 && TKresult[nres]!= k) */
+      /*         continue; */
+      /* /\*printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));*\/ */
        fprintf(ficresplb,"#******");
        printf("#******");
        fprintf(ficlog,"#******");
-       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+       for(j=1;j<=cptcovs ;j++) {/**< cptcovs number of SIMPLE covariates in the model or resultline V2+V1 =2 (dummy or quantit or time varying) */
-         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresplb," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
        }
-       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+       /* for(j=1;j<=cptcoveff ;j++) {/\* all covariates *\/ */
-         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       /*        fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       /*        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       /*        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-       }
+       /* } */
+       /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
+       /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+       /*        fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+       /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+       /* } */
        fprintf(ficresplb,"******\n");
        printf("******\n");
        fprintf(ficlog,"******\n");
- Line 10342  int back_prevalence_limit(double *p, dou
+ Line 14315  int back_prevalence_limit(double *p, dou
        }
        fprintf(ficresplb,"#Age ");
-       for(j=1;j<=cptcoveff;j++) {
+       for(j=1;j<=cptcovs;j++) {
-         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresplb,"V%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
        }
        for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
        fprintf(ficresplb,"Total Years_to_converge\n");
- Line 10366  int back_prevalence_limit(double *p, dou
+ Line 14339  int back_prevalence_limit(double *p, dou
            /* exit(1); */
          }
          fprintf(ficresplb,"%.0f ",age );
-         for(j=1;j<=cptcoveff;j++)
+         for(j=1;j<=cptcovs;j++)
-           fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           fprintf(ficresplb,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
          tot=0.;
          for(i=1; i<=nlstate;i++){
            tot +=  bprlim[i][i];
- Line 10377  int back_prevalence_limit(double *p, dou
+ Line 14350  int back_prevalence_limit(double *p, dou
        } /* 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 any combination *\/ */
    } /* end of nres */
    /* hBijx(p, bage, fage); */
    /* fclose(ficrespijb); */
- Line 10387  int back_prevalence_limit(double *p, dou
+ Line 14360  int back_prevalence_limit(double *p, dou
  int hPijx(double *p, int bage, int fage){
      /*------------- h Pij x at various ages ------------*/
+   /* to be optimized with precov */
    int stepsize;
    int agelim;
    int hstepm;
    int nhstepm;
-   int h, i, i1, j, k, k4, nres=0;
+   int h, i, i1, j, k, nres=0;
    double agedeb;
    double ***p3mat;
-     strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
+   strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+   if((ficrespij=fopen(filerespij,"w"))==NULL) {
-       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
+     printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
+     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
-     }
+   }
-     printf("Computing pij: result on file '%s' \n", filerespij);
+   printf("Computing pij: result on file '%s' \n", filerespij);
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-     /*if (stepm<=24) stepsize=2;*/
+   /*if (stepm<=24) stepsize=2;*/
-     agelim=AGESUP;
+   agelim=AGESUP;
-     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(ficrespij);
+   pstamp(ficrespij);
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-     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(nres=1; nres <= nresult; nres++) /* For each resultline */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     for(k=1; k<=i1;k++){
+     k=TKresult[nres];
-       if(i1 != 1 && TKresult[nres]!= k)
+     if(TKresult[nres]==0) k=1; /* To be checked for noresult */
-         continue;
+     /* for(k=1; k<=i1;k++){ */
-       fprintf(ficrespij,"\n#****** ");
+     /* if(i1 != 1 && TKresult[nres]!= k) */
-       for(j=1;j<=cptcoveff;j++)
+     /*  continue; */
-         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     fprintf(ficrespij,"\n#****** ");
-       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+     for(j=1;j<=cptcovs;j++){
-         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       fprintf(ficrespij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-         fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       /* fprintf(ficrespij,"@wV%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-       }
+       /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
-       fprintf(ficrespij,"******\n");
+       /*        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
+       /*        fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
-       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+     }
-         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     fprintf(ficrespij,"******\n");
-         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-         /*        nhstepm=nhstepm*YEARM; aff par mois*/
+       nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         oldm=oldms;savm=savms;
+       /*          nhstepm=nhstepm*YEARM; aff par mois*/
-         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
-         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       oldm=oldms;savm=savms;
+       hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
+       fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+       for(i=1; i<=nlstate;i++)
+         for(j=1; j<=nlstate+ndeath;j++)
+           fprintf(ficrespij," %1d-%1d",i,j);
+       fprintf(ficrespij,"\n");
+       for (h=0; h<=nhstepm; h++){
+         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+         fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
          for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate+ndeath;j++)
-             fprintf(ficrespij," %1d-%1d",i,j);
+             fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-         fprintf(ficrespij,"\n");
-         for (h=0; h<=nhstepm; h++){
-           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
-           fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
-           for(i=1; i<=nlstate;i++)
-             for(j=1; j<=nlstate+ndeath;j++)
-               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-           fprintf(ficrespij,"\n");
-         }
-         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          fprintf(ficrespij,"\n");
        }
-       /*}*/
+       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       fprintf(ficrespij,"\n");
      }
-     return 0;
+   }
+   /*}*/
+   return 0;
  }
   int hBijx(double *p, int bage, int fage, double ***prevacurrent){
      /*------------- h Bij x at various ages ------------*/
+     /* To be optimized with precov */
    int stepsize;
    /* int agelim; */
          int ageminl;
- Line 10487  int hPijx(double *p, int bage, int fage)
+ Line 14463  int hPijx(double *p, int bage, int fage)
    /*if (stepm<=24) stepsize=2;*/
    /* agelim=AGESUP; */
-   ageminl=30;
+   ageminl=AGEINF; /* was 30 */
    hstepm=stepsize*YEARM; /* Every year of age */
    hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
- Line 10499  int hPijx(double *p, int bage, int fage)
+ Line 14475  int hPijx(double *p, int bage, int fage)
    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
    /*    k=k+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 */
+     k=TKresult[nres];
-       if(i1 != 1 && TKresult[nres]!= k)
+     if(TKresult[nres]==0) k=1; /* To be checked for noresult */
-         continue;
+     /* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying *\/ */
-       fprintf(ficrespijb,"\n#****** ");
+     /*    if(i1 != 1 && TKresult[nres]!= k) */
-       for(j=1;j<=cptcoveff;j++)
+     /*  continue; */
-         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     fprintf(ficrespijb,"\n#****** ");
-       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+     for(j=1;j<=cptcovs;j++){
-         fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       fprintf(ficrespijb," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
-       }
+       /* for(j=1;j<=cptcoveff;j++) */
-       fprintf(ficrespijb,"******\n");
+       /*        fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-       if(invalidvarcomb[k]){  /* Is it necessary here? */
+       /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
-         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
+       /*        fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
-         continue;
+     }
-       }
+     fprintf(ficrespijb,"******\n");
+     if(invalidvarcomb[k]){  /* Is it necessary here? */
+       fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
+       continue;
+     }
+     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
+       /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
+       nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
+       nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
-       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+       /*          nhstepm=nhstepm*YEARM; aff par mois*/
-       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
-         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
+       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
-         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+       /* and memory limitations if stepm is small */
-         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
+       /* oldm=oldms;savm=savms; */
-         /*        nhstepm=nhstepm*YEARM; aff par mois*/
+       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
+       hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */
-         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
+       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
-         /* and memory limitations if stepm is small */
+       fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
+       for(i=1; i<=nlstate;i++)
-         /* oldm=oldms;savm=savms; */
+         for(j=1; j<=nlstate+ndeath;j++)
-         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
+           fprintf(ficrespijb," %1d-%1d",i,j);
-         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
+       fprintf(ficrespijb,"\n");
-         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
+       for (h=0; h<=nhstepm; h++){
-         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
+         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+         fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
+         /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
          for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate+ndeath;j++)
-             fprintf(ficrespijb," %1d-%1d",i,j);
+             fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */
-         fprintf(ficrespijb,"\n");
-         for (h=0; h<=nhstepm; h++){
-           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
-           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
-           /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
-           for(i=1; i<=nlstate;i++)
-             for(j=1; j<=nlstate+ndeath;j++)
-               fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
-           fprintf(ficrespijb,"\n");
-         }
-         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          fprintf(ficrespijb,"\n");
-       } /* end age deb */
+       }
-     } /* end combination */
+       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       fprintf(ficrespijb,"\n");
+     } /* end age deb */
+     /* } /\* end combination *\/ */
    } /* end nres */
    return 0;
   } /*  hBijx */
- Line 10566  int main(int argc, char *argv[])
+ Line 14546  int main(int argc, char *argv[])
    double ssval;
  #endif
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
+   int 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 jj, ll, li, lj, lk;
    int numlinepar=0; /* Current linenumber of parameter file */
- Line 10576  int main(int argc, char *argv[])
+ Line 14557  int main(int argc, char *argv[])
    int vpopbased=0;
    int nres=0;
    int endishere=0;
+   int noffset=0;
+   int ncurrv=0; /* Temporary variable */
    char ca[32], cb[32];
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
- Line 10588  int main(int argc, char *argv[])
+ Line 14571  int main(int argc, char *argv[])
    double fret;
    double dum=0.; /* Dummy variable */
-   double ***p3mat;
+   /* double*** p3mat;*/
    /* double ***mobaverage; */
+   double wald;
-   char line[MAXLINE];
+   char line[MAXLINE], linetmp[MAXLINE];
    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
    char  modeltemp[MAXLINE];
-   char resultline[MAXLINE];
+   char resultline[MAXLINE], resultlineori[MAXLINE];
    char pathr[MAXLINE], pathimach[MAXLINE];
    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; /* c2; */
    int jl=0;
    int i1, j1, jk, stepsize=0;
    int count=0;
    int *tab;
    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-   int 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 hstepm=0, nhstepm=0;
    int agemortsup;
- Line 10619  int main(int argc, char *argv[])
+ Line 14610  int main(int argc, char *argv[])
    double ftolpl=FTOL;
    double **prlim;
    double **bprlim;
-   double ***param; /* Matrix of parameters */
+   double ***param; /* Matrix of parameters, param[i][j][k] param=ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel)
+                     state of origin, state of destination including death, for each covariate: constante, age, and V1 V2 etc. */
    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 */
- Line 10627  int main(int argc, char *argv[])
+ Line 14619  int main(int argc, char *argv[])
    double ***delti3; /* Scale */
    double *delti; /* Scale */
    double ***eij, ***vareij;
-   double **varpl; /* Variances of prevalence limits by age */
+   //double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double 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;
    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
- Line 10683  int main(int argc, char *argv[])
+ Line 14677  int main(int argc, char *argv[])
    getcwd(pathcd, size);
  #endif
    syscompilerinfo(0);
-   printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
+   printf("\nIMaCh prax version %s, %s\n%s",version, copyright, fullversion);
    if(argc <=1){
      printf("\nEnter the parameter file name: ");
      if(!fgets(pathr,FILENAMELENGTH,stdin)){
- Line 10710  int main(int argc, char *argv[])
+ Line 14704  int main(int argc, char *argv[])
        if(pathr[0] == '\0') break; /* Dirty */
      }
    }
+   else if (argc<=2){
+     strcpy(pathtot,argv[1]);
+   }
    else{
      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");*/
    /*cygwin_split_path(pathtot,path,optionfile);
- Line 10789  int main(int argc, char *argv[])
+ Line 14788  int main(int argc, char *argv[])
      exit(70);
    }
    strcpy(filereso,"o");
    strcat(filereso,fileresu);
    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
- Line 10799  int main(int argc, char *argv[])
+ Line 14796  int main(int argc, char *argv[])
      fflush(ficlog);
      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 '#' */
    numlinepar=0;
+   /* Is it a BOM UTF-8 Windows file? */
-     /* First parameter line */
+   /* First parameter line */
    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[0] == '#') {
+     if (line[noffset] == '#') {
        numlinepar++;
        fputs(line,stdout);
        fputs(line,ficparo);
+       fputs(line,ficres);
        fputs(line,ficlog);
        continue;
      }else
- Line 10819  int main(int argc, char *argv[])
+ Line 14852  int main(int argc, char *argv[])
                          title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
      if (num_filled != 5) {
        printf("Should be 5 parameters\n");
+       fprintf(ficlog,"Should be 5 parameters\n");
      }
      numlinepar++;
      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 */
    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] == '#') {
        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;
      }else
        break;
- Line 10840  int main(int argc, char *argv[])
+ Line 14879  int main(int argc, char *argv[])
      if (num_filled != 11) {
        printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
        printf("but line=%s\n",line);
+       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);
+     }
+     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);
+       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.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
- Line 10850  int main(int argc, char *argv[])
+ Line 14900  int main(int argc, char *argv[])
      /* If line starts with a # it is a comment */
      if (line[0] == '#') {
        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;
      }else
        break;
    }
-   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
+   if((num_filled=sscanf(line,"model=%[^.\n]", model)) !=EOF){ /* Every character after model but dot and  return */
-     if (num_filled == 0){
+     if (num_filled != 1){
-       printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
+       printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
-       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
+       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
        model[0]='\0';
        goto end;
-     } else if (num_filled != 1){
+     }else{
-       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+       trimbtab(linetmp,line); /* Trims multiple blanks in line */
-       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+       strcpy(line, linetmp);
+     }
+   }
+   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){ /* Every character after 1+age but dot and  return */
+     if (num_filled != 1){
+       printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
+       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
        model[0]='\0';
        goto end;
      }
- Line 10876  int main(int argc, char *argv[])
+ Line 14933  int main(int argc, char *argv[])
          strcpy(model,modeltemp);
        }
      }
-     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
+     /* printf(" model=1+age%s modeltemp= %s, model=1+age+%s\n",model, modeltemp, 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); */
    /* numlinepar=numlinepar+3; /\* In general *\/ */
    /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
+   /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
+   /* 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);
    /* if(model[0]=='#'|| model[0]== '\0'){ */
    if(model[0]=='#'){
-     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
+     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){
-       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);
      }
    }
- Line 10901  int main(int argc, char *argv[])
+ Line 14961  int main(int argc, char *argv[])
      numlinepar++;
      if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
        z[0]=line[1];
+     }else if(line[1]=='d'){ /* For debugging individual values of covariates in ficresilk */
+       debugILK=1;printf("DebugILK\n");
      }
      /* printf("****line [1] = %c \n",line[1]); */
      fputs(line, stdout);
- Line 10911  int main(int argc, char *argv[])
+ Line 14973  int main(int argc, char *argv[])
    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,1,n);  /**< Fixed quantitative covariate */
+   if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs);  /**< Fixed quantitative covariate */
-   if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying 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,1,n);  /**< Time varying covariate (dummy and quantitative)*/
+   /* if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs);  /\**< Time varying covariate (dummy and quantitative)*\/ */
+   if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,ncovcol+nqv+1,ncovcol+nqv+ntv+nqtv,firstobs,lastobs);  /**< Might be better */
    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
       v1+v2*age+v2*v3 makes cptcovn = 3
- Line 10977  int main(int argc, char *argv[])
+ Line 15040  int main(int argc, char *argv[])
        for(jj=1; jj <=nlstate+ndeath; jj++){
          if(jj==i) continue;
          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);
          if ((i1 != i) || (j1 != jj)){
            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
- Line 11113  Please run with mle=-1 to get a correct
+ Line 15185  Please run with mle=-1 to get a correct
      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 */
    /*  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); */
-   weight=vector(1,n);
+   /* weight=vector(1,n); */
-   agedc=vector(1,n);
+   /* agedc=vector(1,n); */
-   cod=ivector(1,n);
+   /* cod=ivector(1,n); */
-   for(i=1;i<=n;i++){
+   /* for(i=1;i<=n;i++){ */
+   num=lvector(firstobs,lastobs);
+   moisnais=vector(firstobs,lastobs);
+   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;
- Line 11146  Please run with mle=-1 to get a correct
+ Line 15217  Please run with mle=-1 to get a correct
      cod[i]=0;
      weight[i]=1.0; /* Equal weights, 1 by default */
    }
-   mint=matrix(1,maxwav,1,n);
+   mint=matrix(1,maxwav,firstobs,lastobs);
-   anint=matrix(1,maxwav,1,n);
+   anint=matrix(1,maxwav,firstobs,lastobs);
-   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
+   s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
+   /* printf("BUG ncovmodel=%d NCOVMAX=%d 2**ncovmodel=%f BUG\n",ncovmodel,NCOVMAX,pow(2,ncovmodel)); */
    tab=ivector(1,NCOVMAX);
    ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
    ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
- Line 11167  Please run with mle=-1 to get a correct
+ Line 15239  Please run with mle=-1 to get a correct
    Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
    TvarsDind=ivector(1,NCOVMAX); /*  */
+   TnsdVar=ivector(1,NCOVMAX); /*  */
+     /* for(i=1; i<=NCOVMAX;i++) TnsdVar[i]=3; */
    TvarsD=ivector(1,NCOVMAX); /*  */
    TvarsQind=ivector(1,NCOVMAX); /*  */
    TvarsQ=ivector(1,NCOVMAX); /*  */
- Line 11184  Please run with mle=-1 to get a correct
+ Line 15258  Please run with mle=-1 to get a correct
    TvarVDind=ivector(1,NCOVMAX); /*  */
    TvarVQ=ivector(1,NCOVMAX); /*  */
    TvarVQind=ivector(1,NCOVMAX); /*  */
+   TvarVV=ivector(1,NCOVMAX); /*  */
+   TvarVVind=ivector(1,NCOVMAX); /*  */
+   TvarVVA=ivector(1,NCOVMAX); /*  */
+   TvarVVAind=ivector(1,NCOVMAX); /*  */
+   TvarAVVA=ivector(1,NCOVMAX); /*  */
+   TvarAVVAind=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 */
+   DummyV=ivector(-1,NCOVMAX); /* 1 to 3 */
+   FixedV=ivector(-1,NCOVMAX); /* 1 to 3 */
    /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
        For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
        Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
- Line 11209  Please run with mle=-1 to get a correct
+ Line 15292  Please run with mle=-1 to get a correct
    Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                              * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
                              * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
+   Tvardk=imatrix(0,NCOVMAX,1,2);
    Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
 covariates (3 plus signs)
                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
-                       */
+                            */
+   for(i=1;i<NCOVMAX;i++)
+     Tage[i]=0;
    Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
                                  * individual dummy, fixed or varying:
                                  * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
- Line 11226  Please run with mle=-1 to get a correct
+ Line 15312  Please run with mle=-1 to get a correct
                                  * 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*/
+ /* Probably useless zeroes */
+   for(i=1;i<NCOVMAX;i++){
+     DummyV[i]=0;
+     FixedV[i]=0;
+   }
+   for(i=1; i <=ncovcol;i++){
+     DummyV[i]=0;
+     FixedV[i]=0;
+   }
+   for(i=ncovcol+1; i <=ncovcol+nqv;i++){
+     DummyV[i]=1;
+     FixedV[i]=0;
+   }
+   for(i=ncovcol+nqv+1; i <=ncovcol+nqv+ntv;i++){
+     DummyV[i]=0;
+     FixedV[i]=1;
+   }
+   for(i=ncovcol+nqv+ntv+1; i <=ncovcol+nqv+ntv+nqtv;i++){
+     DummyV[i]=1;
+     FixedV[i]=1;
+   }
+   for(i=1; i <=ncovcol+nqv+ntv+nqtv;i++){
+     printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",i,i,DummyV[i],i,FixedV[i]);
+     fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",i,i,DummyV[i],i,FixedV[i]);
+   }
  /* Main decodemodel */
- Line 11250  Please run with mle=-1 to get a correct
+ Line 15366  Please run with mle=-1 to get a correct
    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(anint,1,maxwav,1,n);*/
    /* free_vector(moisdc,1,n); */
- Line 11277  Please run with mle=-1 to get a correct
+ Line 15393  Please run with mle=-1 to get a correct
    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 */
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
- Line 11286  Please run with mle=-1 to get a correct
+ Line 15402  Please run with mle=-1 to get a correct
    Ndum =ivector(-1,NCOVMAX);
    cptcoveff=0;
    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]; */
+     tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; as well as calculate cptcoveff or number of total effective dummy covariates*/
    }
    ncovcombmax=pow(2,cptcoveff);
-   invalidvarcomb=ivector(1, ncovcombmax);
+   invalidvarcomb=ivector(0, ncovcombmax);
-   for(i=1;i<ncovcombmax;i++)
+   for(i=0;i<ncovcombmax;i++)
      invalidvarcomb[i]=0;
    /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
- Line 11316  Please run with mle=-1 to get a correct
+ Line 15432  Please run with mle=-1 to get a correct
             * For k=4 covariates, h goes from 1 to m=2**k
             * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
             * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
-            *     h\k   1     2     3     4
+            *     h\k   1     2     3     4   *  h-1\k-1  4  3  2  1
-            *______________________________
+            *______________________________   *______________________
-            *     1 i=1 1 i=1 1 i=1 1 i=1 1
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1   *     0     0  0  0  0
-            *     2     2     1     1     1
+            *     2     2     1     1     1   *     1     0  0  0  1
-            *     3 i=2 1     2     1     1
+            *     3 i=2 1     2     1     1   *     2     0  0  1  0
-            *     4     2     2     1     1
+            *     4     2     2     1     1   *     3     0  0  1  1
-            *     5 i=3 1 i=2 1     2     1
+            *     5 i=3 1 i=2 1     2     1   *     4     0  1  0  0
-            *     6     2     1     2     1
+            *     6     2     1     2     1   *     5     0  1  0  1
-            *     7 i=4 1     2     2     1
+            *     7 i=4 1     2     2     1   *     6     0  1  1  0
-            *     8     2     2     2     1
+            *     8     2     2     2     1   *     7     0  1  1  1
-            *     9 i=5 1 i=3 1 i=2 1     2
+            *     9 i=5 1 i=3 1 i=2 1     2   *     8     1  0  0  0
-            *    10     2     1     1     2
+            *    10     2     1     1     2   *     9     1  0  0  1
-            *    11 i=6 1     2     1     2
+            *    11 i=6 1     2     1     2   *    10     1  0  1  0
-            *    12     2     2     1     2
+            *    12     2     2     1     2   *    11     1  0  1  1
-            *    13 i=7 1 i=4 1     2     2
+            *    13 i=7 1 i=4 1     2     2   *    12     1  1  0  0
-            *    14     2     1     2     2
+            *    14     2     1     2     2   *    13     1  1  0  1
-            *    15 i=8 1     2     2     2
+            *    15 i=8 1     2     2     2   *    14     1  1  1  0
-            *    16     2     2     2     2
+            *    16     2     2     2     2   *    15     1  1  1  1
             */
    /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
       /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
       * and the value of each covariate?
- Line 11425  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 15541  Title=%s <br>Datafile=%s Firstpass=%d La
            optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \
+   fprintf(fichtm,"<html><head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n\
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ <title>IMaCh %s</title></head>\n\
+  <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n\
+ <font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>\
+ -EUROREVES-Institut de longévité-2013-2022-Japan Society for the Promotion of Sciences 日本学術振興会 \
+ (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - \
+ <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \n", optionfilehtm);
+   fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\"> \n\
  <font size=\"2\">IMaCh-%s <br> %s</font> \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
+ This file: <a href=\"%s\">%s</a></br>Title=%s <br>Datafile=<a href=\"%s\">%s</a> Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
  \n\
  <hr  size=\"2\" color=\"#EC5E5E\">\
   <ul><li><h4>Parameter files</h4>\n\
- Line 11438  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 15561  Title=%s <br>Datafile=%s Firstpass=%d La
   - Log file of the run: <a href=\"%s\">%s</a><br>\n\
   - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
   - Date and time at start: %s</ul>\n",\
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+           version,fullversion,optionfilehtm,optionfilehtm,title,datafile,datafile,firstpass,lastpass,stepm, weightopt, model, \
            optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
            fileres,fileres,\
            filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
- Line 11456  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 15579  Title=%s <br>Datafile=%s Firstpass=%d La
    /* Calculates basic frequencies. Computes observed prevalence at single age
                   and for any valid combination of covariates
       and prints on file fileres'p'. */
-   freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
+   freqsummary(fileres, p, pstart, (double)agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
                firstpass, lastpass,  stepm,  weightopt, model);
    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>Number of (used) observations=%d <br>\n\
  Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-           imx,agemin,agemax,jmin,jmax,jmean);
+   imx,agemin,agemax,jmin,jmax,jmean);
    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
    oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
    newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
- Line 11482  Interval (in months) between two waves:
+ Line 15626  Interval (in months) between two waves:
        for(j=1;j<=NDIM;j++)
          ximort[i][j]=0.;
      /*     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++){
        dcwave[i]=-1;
- Line 11519  Interval (in months) between two waves:
+ Line 15663  Interval (in months) between two waves:
          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
      printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
  #else
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+     printf("Powell-mort\n");  fprintf(ficlog,"Powell-mort\n");
  #endif
      strcpy(filerespow,"POW-MORT_");
      strcat(filerespow,fileresu);
- Line 11629  Interval (in months) between two waves:
+ Line 15773  Interval (in months) between two waves:
      for(i=1; i <=NDIM; i++)
        for(j=i+1;j<=NDIM;j++)
-                                 matcov[i][j]=matcov[j][i];
+         matcov[i][j]=matcov[j][i];
      printf("\nCovariance matrix\n ");
      fprintf(ficlog,"\nCovariance matrix\n ");
- Line 11646  Interval (in months) between two waves:
+ Line 15790  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]));
        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;
      for (k=agegomp;k<=AGESUP;k++) {
- Line 11695  Please run with mle=-1 to get a correct
+ Line 15839  Please run with mle=-1 to get a correct
                       stepm, weightopt,\
                       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);
      free_matrix(ximort,1,NDIM,1,NDIM);
-     free_ivector(cens,1,n);
+     free_ivector(dcwave,firstobs,lastobs);
-     free_vector(agecens,1,n);
+     free_vector(agecens,firstobs,lastobs);
-     free_ivector(dcwave,1,n);
+     free_vector(ageexmed,firstobs,lastobs);
+     free_ivector(cens,firstobs,lastobs);
  #ifdef GSL
  #endif
    } /* Endof if mle==-3 mortality only */
- Line 11730  Please run with mle=-1 to get a correct
+ Line 15875  Please run with mle=-1 to get a correct
      globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
      printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+           /* exit(0); */
      for (k=1; k<=npar;k++)
        printf(" %d %8.5f",k,p[k]);
      printf("\n");
      /*--------- results files --------------*/
-     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,"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");
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); /* Printing model equation */
      fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("#model=  1      +     age ");
+     fprintf(ficres,"#model=  1      +     age ");
+     fprintf(ficlog,"#model=  1      +     age ");
+     fprintf(fichtm,"\n<ul><li> model=1+age+%s\n \
+ </ul>", model);
+     fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">\n");
+     fprintf(fichtm, "<tr><th>Model=</th><th>1</th><th>+ age</th>");
+     if(nagesqr==1){
+       printf("  + age*age  ");
+       fprintf(ficres,"  + age*age  ");
+       fprintf(ficlog,"  + age*age  ");
+       fprintf(fichtm, "<th>+ age*age</th>");
+     }
+     for(j=1;j <=ncovmodel-2;j++){
+       if(Typevar[j]==0) {
+         printf("  +      V%d  ",Tvar[j]);
+         fprintf(ficres,"  +      V%d  ",Tvar[j]);
+         fprintf(ficlog,"  +      V%d  ",Tvar[j]);
+         fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
+       }else if(Typevar[j]==1) {
+         printf("  +    V%d*age ",Tvar[j]);
+         fprintf(ficres,"  +    V%d*age ",Tvar[j]);
+         fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
+         fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
+       }else if(Typevar[j]==2) {
+         printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(ficres,"  +    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]);
+         fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+       }else if(Typevar[j]==3) { /* TO VERIFY */
+         printf("  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(ficres,"  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(ficlog,"  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(fichtm, "<th>+  V%d*V%d*age</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+       }
+     }
+     printf("\n");
+     fprintf(ficres,"\n");
+     fprintf(ficlog,"\n");
+     fprintf(fichtm, "</tr>");
+     fprintf(fichtm, "\n");
      for(i=1,jk=1; i <=nlstate; i++){
        for(k=1; k <=(nlstate+ndeath); k++){
          if (k != i) {
+           fprintf(fichtm, "<tr>");
            printf("%d%d ",i,k);
            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);
+           fprintf(fichtm, "<td>%1d%1d</td>",i,k);
            for(j=1; j <=ncovmodel; j++){
              printf("%12.7f ",p[jk]);
              fprintf(ficlog,"%12.7f ",p[jk]);
              fprintf(ficres,"%12.7f ",p[jk]);
+             fprintf(fichtm, "<td>%12.7f</td>",p[jk]);
              jk++;
            }
            printf("\n");
            fprintf(ficlog,"\n");
            fprintf(ficres,"\n");
+           fprintf(fichtm, "</tr>\n");
          }
        }
      }
+     /* fprintf(fichtm,"</tr>\n"); */
+     fprintf(fichtm,"</table>\n");
+     fprintf(fichtm, "\n");
      if(mle != 0){
        /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
        ftolhess=ftol; /* Usually correct */
        hesscov(matcov, hess, p, npar, delti, ftolhess, func);
        printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
        fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       fprintf(fichtm, "\n<p>The Wald test results are output only if the maximimzation of the Likelihood is performed (mle=1)\n</br>Parameters, Wald tests and Wald-based confidence intervals\n</br> W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n</br> And Wald-based confidence intervals plus and minus 1.96 * W \n </br> It might be better to visualize the covariance matrix. See the page '<a href=\"%s\">Matrix of variance-covariance of one-step probabilities and its graphs</a>'.\n</br>",optionfilehtmcov);
+       fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">");
+       fprintf(fichtm, "\n<tr><th>Model=</th><th>1</th><th>+ age</th>");
+       if(nagesqr==1){
+         printf("  + age*age  ");
+         fprintf(ficres,"  + age*age  ");
+         fprintf(ficlog,"  + age*age  ");
+         fprintf(fichtm, "<th>+ age*age</th>");
+       }
+       for(j=1;j <=ncovmodel-2;j++){
+         if(Typevar[j]==0) {
+           printf("  +      V%d  ",Tvar[j]);
+           fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
+         }else if(Typevar[j]==1) {
+           printf("  +    V%d*age ",Tvar[j]);
+           fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
+         }else if(Typevar[j]==2) {
+           fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         }else if(Typevar[j]==3) { /* TO VERIFY */
+           fprintf(fichtm, "<th>+  V%d*V%d*age</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         }
+       }
+       fprintf(fichtm, "</tr>\n");
        for(i=1,jk=1; i <=nlstate; i++){
          for(k=1; k <=(nlstate+ndeath); k++){
            if (k != i) {
+             fprintf(fichtm, "<tr valign=top>");
              printf("%d%d ",i,k);
              fprintf(ficlog,"%d%d ",i,k);
+             fprintf(fichtm, "<td>%1d%1d</td>",i,k);
              for(j=1; j <=ncovmodel; j++){
-               printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               wald=p[jk]/sqrt(matcov[jk][jk]);
-               fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               printf("%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               fprintf(ficlog,"%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               if(fabs(wald) > 1.96){
+                 fprintf(fichtm, "<td><b>%12.7f</b></br> (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
+               }else{
+                 fprintf(fichtm, "<td>%12.7f (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
+               }
+               fprintf(fichtm,"W=%8.3f</br>",wald);
+               fprintf(fichtm,"[%12.7f;%12.7f]</br></td>", p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                jk++;
              }
              printf("\n");
              fprintf(ficlog,"\n");
+             fprintf(fichtm, "</tr>\n");
            }
          }
        }
      } /* end of hesscov and Wald tests */
+     fprintf(fichtm,"</table>\n");
      /*  */
      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
- Line 11806  Please run with mle=-1 to get a correct
+ Line 16041  Please run with mle=-1 to get a correct
      }
      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-     if(mle >= 1) /* To big for the screen */
+     if(mle >= 1) /* Too big for the screen */
        printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      /* # 121 Var(a12)\n\ */
- Line 11897  Please run with mle=-1 to get a correct
+ Line 16132  Please run with mle=-1 to get a correct
          fputs(line,stdout);
          fputs(line,ficparo);
          fputs(line,ficlog);
+         fputs(line,ficres);
          continue;
        }else
          break;
- Line 11942  Please run with mle=-1 to get a correct
+ Line 16178  Please run with mle=-1 to get a correct
          fputs(line,stdout);
          fputs(line,ficparo);
          fputs(line,ficlog);
+         fputs(line,ficres);
          continue;
        }else
          break;
- Line 11967  Please run with mle=-1 to get a correct
+ Line 16204  Please run with mle=-1 to get a correct
          fputs(line,stdout);
          fputs(line,ficparo);
          fputs(line,ficlog);
+         fputs(line,ficres);
          continue;
        }else
          break;
- Line 11989  Please run with mle=-1 to get a correct
+ Line 16227  Please run with mle=-1 to get a correct
      }
      /* Results */
+     /* Value of covariate in each resultine will be computed (if product) and sorted according to model rank */
+     /* It is precov[] because we need the varying age in order to compute the real cov[] of the model equation */
+     precov=matrix(1,MAXRESULTLINESPONE,1,NCOVMAX+1);
+     endishere=0;
      nresult=0;
+     parameterline=0;
      do{
        if(!fgets(line, MAXLINE, ficpar)){
          endishere=1;
-         parameterline=14;
+         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,"backcast=%[^\n]\n",modeltemp))
+       else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
          parameterline=12;
-       else if(sscanf(line,"result:%[^\n]\n",modeltemp))
+       else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
          parameterline=13;
+       }
        else{
          parameterline=14;
        }
-       switch (parameterline){
+       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){
+         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)){
-           if (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("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\n, your line=%s . Probably you are running 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 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-             goto end;
-           }
-           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=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+           fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+           fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf 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:
-         /*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);*/
+         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)){
-         if((num_filled=sscanf(line,"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)) !=EOF){
+           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);
-           if (num_filled != 8) {
+           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);
-             printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+           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(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+           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);
-             goto end;
+           /* day and month of back2 are not used but only year anback2.*/
-           }
+           dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
-           printf("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);
+           dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
-           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);
+           prvbackcast = 1;
-           fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+         }
-           fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+         else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
-           /* day and month of proj2 are not used but only year anproj2.*/
+           printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+           fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+           fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf 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:
-         if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
+         num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);
-           if (num_filled == 0){
+         nresult++; /* Sum of resultlines */
-             resultline[0]='\0';
+         /* printf("Result %d: result:%s\n",nresult, resultlineori); */
-             printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
+         /* removefirstspace(&resultlineori); */
-             fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
-             break;
+         if(strstr(resultlineori,"v") !=0){
-           } else if (num_filled != 1){
+           printf("Error. 'v' must be in upper case 'V' result: %s ",resultlineori);
-             printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
+           fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultlineori);fflush(ficlog);
-             fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
+           return 1;
-           }
+         }
-           nresult++; /* Sum of resultlines */
+         trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */
-           printf("Result %d: result=%s\n",nresult, resultline);
+         /* printf("Decoderesult resultline=\"%s\" resultlineori=\"%s\"\n", resultline, resultlineori); */
-           if(nresult > MAXRESULTLINES){
+         if(nresult > MAXRESULTLINESPONE-1){
-             printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+           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. ",MAXRESULTLINESPONE-1,nresult,rfileres);
-             fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+           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. ",MAXRESULTLINESPONE-1,nresult,rfileres);
-             goto end;
+           goto end;
-           }
+         }
-           decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
+         if(!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;
+         } else
-         case 14:
+           goto end;
-           if(ncovmodel >2 && nresult==0 ){
+         break;
-             printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
+       case 14:
-             goto end;
+         printf("Error: Unknown command '%s'\n",line);
-           }
+         fprintf(ficlog,"Error: Unknown command '%s'\n",line);
-           break;
+         if(line[0] == ' ' || line[0] == '\n'){
-         default:
+           printf("It should not be an empty line '%s'\n",line);
-           nresult=1;
+           fprintf(ficlog,"It should not be an empty line '%s'\n",line);
-           decoderesult(".",nresult ); /* No covariate */
+         }
+         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 */
- Line 12089  This is probably because your parameter
+ Line 16364  This is probably because your parameter
  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
      }else{
        /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
-       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);
+       /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
+       /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
+       if(prvforecast==1){
+         dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
+         jprojd=jproj1;
+         mprojd=mproj1;
+         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);/* HERE valgrind Tvard*/
      }
      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
-                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
+                  jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
- Line 12102  Please run with mle=-1 to get a correct
+ Line 16410  Please run with mle=-1 to get a correct
      /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
      /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
      /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
-     free_lvector(num,1,n);
+     free_lvector(num,firstobs,lastobs);
-     free_vector(agedc,1,n);
+     free_vector(agedc,firstobs,lastobs);
      /*free_matrix(covar,0,NCOVMAX,1,n);*/
      /*free_matrix(covar,1,NCOVMAX,1,n);*/
      fclose(ficparo);
- Line 12116  Please run with mle=-1 to get a correct
+ Line 16424  Please run with mle=-1 to get a correct
      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
      prlim=matrix(1,nlstate,1,nlstate);
+     /* Computes the prevalence limit for each combination k of the dummy covariates by calling prevalim(k) */
      prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
      fclose(ficrespl);
      /*------------- h Pij x at various ages ------------*/
      /*#include "hpijx.h"*/
+     /** h Pij x Probability to be in state j at age x+h being in i at x, for each combination k of dummies in the model line or to nres?*/
+     /* calls hpxij with combination k */
      hPijx(p, bage, fage);
      fclose(ficrespij);
      /* ncovcombmax=  pow(2,cptcoveff); */
-     /*-------------- Variance of one-step probabilities---*/
+     /*-------------- Variance of one-step probabilities for a combination ij or for nres ?---*/
      k=1;
      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
- Line 12166  Please run with mle=-1 to get a correct
+ Line 16477  Please run with mle=-1 to get a correct
      }/* end if moving average */
      /*---------- Forecasting ------------------*/
      if(prevfcast==1){
-       /*    if(stepm ==1){*/
+       /*   /\*    if(stepm ==1){*\/ */
-       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
+       /*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);
      }
-     /* Backcasting */
+     /* Prevbcasting */
-     if(backcast==1){
+     if(prevbcast==1){
        ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
        ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
        ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
- Line 12187  Please run with mle=-1 to get a correct
+ Line 16508  Please run with mle=-1 to get a correct
        hBijx(p, bage, fage, mobaverage);
        fclose(ficrespijb);
-       prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,
+       /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
-                        mobilavproj, 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);
- Line 12196  Please run with mle=-1 to get a correct
+ Line 16523  Please run with mle=-1 to get a correct
        free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
        free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
        free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
-     }    /* end  Backcasting */
+     }    /* end  Prevbcasting */
      /* ------ Other prevalence ratios------------ */
- Line 12220  Please run with mle=-1 to get a correct
+ Line 16547  Please run with mle=-1 to get a correct
      pstamp(ficreseij);
-     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
+     /* i1=pow(2,cptcoveff); /\* Number of combination of dummy covariates *\/ */
-     if (cptcovn < 1){i1=1;}
+     /* if (cptcovn < 1){i1=1;} */
-     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+     /* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying *\/ */
-       if(i1 != 1 && TKresult[nres]!= k)
+       /* if(i1 != 1 && TKresult[nres]!= k) */
-         continue;
+       /*        continue; */
        fprintf(ficreseij,"\n#****** ");
        printf("\n#****** ");
-       for(j=1;j<=cptcoveff;j++) {
+       for(j=1;j<=cptcovs;j++){
-         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       /* for(j=1;j<=cptcoveff;j++) { */
-         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         /* fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+         fprintf(ficreseij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+         printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
+         /* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
        }
        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         printf(" V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]); /* TvarsQ[j] gives the name of the jth quantitative (fixed or time v) */
-         fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficreseij,"V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]);
        }
        fprintf(ficreseij,"******\n");
        printf("******\n");
        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
+       /* printf("HELLO Entering evsij bage=%d fage=%d k=%d estepm=%d nres=%d\n",(int) bage, (int)fage, k, estepm, nres); */
        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);
- Line 12252  Please run with mle=-1 to get a correct
+ Line 16583  Please run with mle=-1 to get a correct
      /*---------- State-specific expectancies and variances ------------*/
+     /* Should be moved in a function */
      strcpy(filerest,"T_");
      strcat(filerest,fileresu);
      if((ficrest=fopen(filerest,"w"))==NULL) {
- Line 12291  Please run with mle=-1 to get a correct
+ Line 16622  Please run with mle=-1 to get a correct
      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(nres=1; nres <= nresult; nres++) /* For each resultline, find the combination and output results according to the values of dummies and then quanti.  */
-     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying. For each nres and each value at position k
-       if(i1 != 1 && TKresult[nres]!= k)
+                           * we know Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline
+                           * Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline
+                           * and Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
+       /* */
+       if(i1 != 1 && TKresult[nres]!= k) /* TKresult[nres] is the combination of this nres resultline. All the i1 combinations are not output */
          continue;
-       printf("\n#****** Result for:");
+       printf("\n# model=1+age+%s \n#****** Result for:", model);  /* HERE model is empty */
-       fprintf(ficrest,"\n#****** Result for:");
+       fprintf(ficrest,"\n# model=1+age+%s \n#****** Result for:", model);
-       fprintf(ficlog,"\n#****** Result for:");
+       fprintf(ficlog,"\n# model=1+age+%s \n#****** Result for:", model);
-       for(j=1;j<=cptcoveff;j++){
+       /* It might not be a good idea to mix dummies and quantitative */
-         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       /* for(j=1;j<=cptcoveff;j++){ /\* j=resultpos. Could be a loop on cptcovs: number of single dummy covariate in the result line as well as in the model *\/ */
-         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for(j=1;j<=cptcovs;j++){ /* j=resultpos. Could be a loop on cptcovs: number of single covariate (dummy or quantitative) in the result line as well as in the model */
-         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         /* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /\* Output by variables in the resultline *\/ */
-       }
+         /* Tvaraff[j] is the name of the dummy variable in position j in the equation model:
-       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+          * Tvaraff[1]@9={4, 3, 0, 0, 0, 0, 0, 0, 0}, in model=V5+V4+V3+V4*V3+V5*age
-         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+          * (V5 is quanti) V4 and V3 are dummies
-         fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+          * TnsdVar[4] is the position 1 and TnsdVar[3]=2 in codtabm(k,l)(V4  V3)=V4  V3
-         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+          *                                                              l=1 l=2
-       }
+          *                                                           k=1  1   1   0   0
+          *                                                           k=2  2   1   1   0
+          *                                                           k=3 [1] [2]  0   1
+          *                                                           k=4  2   2   1   1
+          * If nres=1 result: V3=1 V4=0 then k=3 and outputs
+          * If nres=2 result: V4=1 V3=0 then k=2 and outputs
+          * nres=1 =>k=3 j=1 V4= nbcode[4][codtabm(3,1)=1)=0; j=2  V3= nbcode[3][codtabm(3,2)=2]=1
+          * nres=2 =>k=2 j=1 V4= nbcode[4][codtabm(2,1)=2)=1; j=2  V3= nbcode[3][codtabm(2,2)=1]=0
+          */
+         /* Tvresult[nres][j] Name of the variable at position j in this resultline */
+         /* Tresult[nres][j] Value of this variable at position j could be a float if quantitative  */
+ /* We give up with the combinations!! */
+         /* if(debugILK) */
+         /*   printf("\n j=%d In computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d Fixed[modelresult[nres][j]]=%d\n", j, nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff,Fixed[modelresult[nres][j]]);  /\* end if dummy  or quanti *\/ */
+         if(Dummy[modelresult[nres][j]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to j in resultline  */
+           /* printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /\* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  *\/ */ /* TinvDoQresult[nres][Name of the variable] */
+           printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordered by the covariate values in the resultline  */
+           fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
+           fprintf(ficrest,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
+           if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
+             printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
+           }else{
+             printf("varyi ");fprintf(ficlog,"varyi ");fprintf(ficrest,"varyi ");
+           }
+           /* fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+           /* fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
+         }else if(Dummy[modelresult[nres][j]]==1){ /* Quanti variable */
+           /* For each selected (single) quantitative value */
+           printf(" V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
+           fprintf(ficlog," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
+           fprintf(ficrest," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
+           if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
+             printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
+           }else{
+             printf("varyi ");fprintf(ficlog,"varyi ");fprintf(ficrest,"varyi ");
+           }
+         }else{
+           printf("Error in computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d \n", nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff);  /* end if dummy  or quanti */
+           fprintf(ficlog,"Error in computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d \n", nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff);  /* end if dummy  or quanti */
+           exit(1);
+         }
+       } /* End loop for each variable in the resultline */
+       /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
+       /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /\* Wrong j is not in the equation model *\/ */
+       /*        fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+       /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
+       /* }       */
        fprintf(ficrest,"******\n");
        fprintf(ficlog,"******\n");
        printf("******\n");
        fprintf(ficresstdeij,"\n#****** ");
        fprintf(ficrescveij,"\n#****** ");
+       /* It could have been: for(j=1;j<=cptcoveff;j++) {printf("V=%d=%lg",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);} */
+       /* But it won't be sorted and depends on how the resultline is ordered */
        for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresstdeij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
-         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         /* fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-       }
+         /* fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
-       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+       }
-         fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value, TvarsQind gives the position of a quantitative in model equation  */
-         fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficresstdeij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
+         fprintf(ficrescveij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
        }
        fprintf(ficresstdeij,"******\n");
        fprintf(ficrescveij,"******\n");
- Line 12328  Please run with mle=-1 to get a correct
+ Line 16713  Please run with mle=-1 to get a correct
        fprintf(ficresvij,"\n#****** ");
        /* pstamp(ficresvij); */
        for(j=1;j<=cptcoveff;j++)
-         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresvij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
+         /* fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[TnsdVar[Tvaraff[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," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); /\* To solve *\/ */
+         fprintf(ficresvij," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */
        }
        fprintf(ficresvij,"******\n");
- Line 12360  Please run with mle=-1 to get a correct
+ Line 16747  Please run with mle=-1 to get a correct
          if(vpopbased==1)
            fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
          else
-           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"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) "); /* Adding covariate values? */
          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
          fprintf(ficrest,"\n");
          /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
-         printf("Computing age specific period (stable) prevalences in each health state \n");
+         printf("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");
+         fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
          for(age=bage; age <=fage ;age++){
            prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
            if (vpopbased==1) {
- Line 12408  Please run with mle=-1 to get a correct
+ Line 16795  Please run with mle=-1 to get a correct
        printf("done selection\n");fflush(stdout);
        fprintf(ficlog,"done selection\n");fflush(ficlog);
-     } /* End k selection */
+     } /* End k selection or end covariate selection for nres */
      printf("done State-specific expectancies\n");fflush(stdout);
      fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
-     /* variance-covariance of period prevalence*/
+     /* variance-covariance of forward period prevalence */
      varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
-     free_vector(weight,1,n);
+     free_vector(weight,firstobs,lastobs);
+     free_imatrix(Tvardk,0,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);
      fclose(ficresstdeij);
      fclose(ficrescveij);
- Line 12439  Please run with mle=-1 to get a correct
+ Line 16827  Please run with mle=-1 to get a correct
      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
    }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
+   if(mle!=-3) free_matrix(precov, 1,MAXRESULTLINESPONE,1,NCOVMAX+1); /* Could be elsewhere ?*/
    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
    free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
    free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
+   /* if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs); */
-   if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
+   if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,ncovcol+nqv+1,ncovcol+nqv+ntv+nqtv,firstobs,lastobs);
-   if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);
+   if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
-   free_matrix(covar,0,NCOVMAX,1,n);
+   if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
+   free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
    free_matrix(matcov,1,npar,1,npar);
    free_matrix(hess,1,npar,1,npar);
    /*free_vector(delti,1,npar);*/
- Line 12458  Please run with mle=-1 to get a correct
+ Line 16848  Please run with mle=-1 to get a correct
    free_ivector(ncodemaxwundef,1,NCOVMAX);
    free_ivector(Dummy,-1,NCOVMAX);
    free_ivector(Fixed,-1,NCOVMAX);
-   free_ivector(DummyV,1,NCOVMAX);
+   free_ivector(DummyV,-1,NCOVMAX);
-   free_ivector(FixedV,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(TnsdVar,1,NCOVMAX);
    free_ivector(TvarsDind,1,NCOVMAX);
    free_ivector(TvarFD,1,NCOVMAX);
    free_ivector(TvarFDind,1,NCOVMAX);
- Line 12480  Please run with mle=-1 to get a correct
+ Line 16871  Please run with mle=-1 to get a correct
    free_ivector(TvarVDind,1,NCOVMAX);
    free_ivector(TvarVQ,1,NCOVMAX);
    free_ivector(TvarVQind,1,NCOVMAX);
+   free_ivector(TvarAVVA,1,NCOVMAX);
+   free_ivector(TvarAVVAind,1,NCOVMAX);
+   free_ivector(TvarVVA,1,NCOVMAX);
+   free_ivector(TvarVVAind,1,NCOVMAX);
+   free_ivector(TvarVV,1,NCOVMAX);
+   free_ivector(TvarVVind,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(invalidvarcomb,0,ncovcombmax);
    free_ivector(Tage,1,NCOVMAX);
    free_ivector(Tmodelind,1,NCOVMAX);
    free_ivector(TmodelInvind,1,NCOVMAX);
    free_ivector(TmodelInvQind,1,NCOVMAX);
+   /* free_matrix(precov, 1,MAXRESULTLINESPONE,1,NCOVMAX+1); /\* Could be elsewhere ?*\/ */
    free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
    /* free_imatrix(codtab,1,100,1,10); */
    fflush(fichtm);
- Line 12528  Please run with mle=-1 to get a correct
+ Line 16928  Please run with mle=-1 to get a correct
    fclose(ficlog);
    /*------ End -----------*/
+ /* Executes gnuplot */
    printf("Before Current directory %s!\n",pathcd);
  #ifdef WIN32
- Line 12563  Please run with mle=-1 to get a correct
+ Line 16965  Please run with mle=-1 to get a correct
    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+   strcpy(pplotcmd,plotcmd);
    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");
      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);
+       strcpy(plotcmd,pplotcmd);
+     }
    }
    printf(" Successful, please wait...");
    while (z[0] != 'q') {
- Line 12596  end:
+ Line 17001  end:
      printf("\nType  q for exiting: "); fflush(stdout);
      scanf("%s",z);
    }
+   printf("End\n");
+   exit(0);
  }

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