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Diff for /imach/src/imach.c between versions 1.286 and 1.349

-version 1.286, 2018/04/27 14:27:04
+version 1.349, 2023/01/31 09:19:37
  Line 1
  /* $Id$
    $State$
    $Log$
+   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
- Line 725
+ Line 1016
    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 904  Important routines
+ Line 1195  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 974  Important routines
+ Line 1265  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 */
  #include <math.h>
  #include <stdio.h>
- Line 1025  typedef struct {
+ Line 1317  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 1067  typedef struct {
+ Line 1362  typedef struct {
  /* $State$ */
  #include "version.h"
  char version[]=__IMACH_VERSION__;
- char copyright[]="April 2018,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[]="January 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 1091  int nqfveff=0; /**< nqfveff Number of Qu
+ Line 1395  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 */
- Line 1167  extern time_t time();
+ Line 1474  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 1229  int *ncodemaxwundef;  /* ncodemax[j]= Nu
+ Line 1537  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 1239  double  **covar; /**< covar[j,i], value
+ Line 1553  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 */
+ /* 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 1292  int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3
+ Line 1646  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 1308  int *TmodelInvQind; /** Tmodelqind[1]=1
+ Line 1672  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 1457  char *trimbb(char *out, char *in)
+ Line 1822  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 1477  char *substrchaine(char *out, char *in,
+ Line 1842  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 1543  int nbocc(char *s, char occ)
+ Line 1908  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 1760  char *subdirf(char fileres[])
+ Line 2147  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 2131  void linmin(double p[], double xi[], int
+ Line 2520  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 2192  void linmin(double p[], double xi[], int
+ Line 2581  void linmin(double p[], double xi[], int
  /*************** 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 2220  void powell(double p[], double **xi, int
+ Line 2609  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 */
+     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 2265  void powell(double p[], double **xi, int
+ Line 2654  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 2295  void powell(double p[], double **xi, int
+ Line 2687  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 */
- Line 2349  void powell(double p[], double **xi, int
+ Line 2743  void powell(double p[], double **xi, int
      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
      /* New value of last point Pn is not computed, P(n-1) */
-       for(j=1;j<=n;j++) {
+     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 2394  void powell(double p[], double **xi, int
+ Line 2788  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 2511  void powell(double p[], double **xi, int
+ Line 2901  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 2542  void powell(double p[], double **xi, int
+ Line 2939  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)
       *  by left multiplying the unit
       *  matrix by transitions matrix until convergence is reached with precision ftolpl
- Line 2567  void powell(double p[], double **xi, int
+ Line 2964  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 2594  void powell(double p[], double **xi, int
+ Line 2992  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 2670  void powell(double p[], double **xi, int
+ Line 3116  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;
+     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);
- Line 2709  Earliest age to start was %d-%d=%d, ncvl
+ Line 3167  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,k, k1;
    int first=0;
    double *min, *max, *meandiff, maxmax,sumnew=0.;
    /* double **matprod2(); */ /* test */
- Line 2739  Earliest age to start was %d-%d=%d, ncvl
+ Line 3197  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 2840  Earliest age to start was %d-%d=%d, ncvl
+ Line 3311  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 2853  Earliest age to start was %d-%d=%d, ncvl
+ Line 3324  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 2900  double **pmij(double **ps, double *cov,
+ Line 3371  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 2909  double **pmij(double **ps, double *cov,
+ Line 3380  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 2938  double **pmij(double **ps, double *cov,
+ Line 3410  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 2959  double **pmij(double **ps, double *cov,
+ Line 3431  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;
- Line 2967  double **pmij(double **ps, double *cov,
+ Line 3439  double **pmij(double **ps, double *cov,
    double **out, **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 2982  double **pmij(double **ps, double *cov,
+ Line 3456  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 3013  double **pmij(double **ps, double *cov,
+ Line 3487  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 3034  double **pmij(double **ps, double *cov,
+ Line 3508  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 3106  double **bpmij(double **ps, double *cov,
+ Line 3580  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 3162  double **matprod2(double **out, double *
+ Line 3636  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 3174  double ***hpxij(double ***po, int nhstep
+ Line 3649  double ***hpxij(double ***po, int nhstep
       */
-   int i, j, d, h, k;
+   int i, j, d, h, k, k1;
    double **out, cov[NCOVMAX+1];
    double **newm;
    double agexact;
- Line 3194  double ***hpxij(double ***po, int nhstep
+ Line 3669  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 3228  double ***hpxij(double ***po, int nhstep
+ Line 3782  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 3263  double ***hpxij(double ***po, int nhstep
+ Line 3817  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 3275  double ***hbxij(double ***po, int nhstep
+ Line 3830  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, k, k1;
    double **out, cov[NCOVMAX+1], **bmij();
    double **newm, ***newmm;
    double agexact;
- Line 3298  double ***hbxij(double ***po, int nhstep
+ Line 3853  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 3385  double ***hbxij(double ***po, int nhstep
+ Line 3968  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 3417  double func( double *x)
+ Line 4004  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 3532  double func( double *x)
+ Line 4163  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 3560  double func( double *x)
+ Line 4191  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 3607  double func( double *x)
+ Line 4243  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 3663  double func( double *x)
+ Line 4302  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 3682  double func( double *x)
+ Line 4321  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 3711  double func( double *x)
+ Line 4353  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, kk, 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 3734  double funcone( double *x)
+ Line 4379  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 3751  double funcone( double *x)
+ Line 4404  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 3760  double funcone( double *x)
+ Line 4424  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
+         * 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 */
+           cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][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 *\/ */
+           cotvarv=covar[itv][i];  /* Good: In V6*V3, 3 is fixed at position of the data */
+         }
+         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 */
+       }
+       /* 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 3793  double funcone( double *x)
+ Line 4598  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 3808  double funcone( double *x)
+ Line 4631  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 3840  double funcone( double *x)
+ Line 4675  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 */
- /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+           fprintf(ficresilk," %g",covar[Tvar[TvarFind[kf]]][i]);
- 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 */
+         for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying  covariates (single and product but no age) including individual from products */
-         gipmx=ipmx;
+           ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
-         gsw=sw;
+           if(ipos!=iposold){ /* Not a product or first of a product */
- }
+             fprintf(ficresilk," %g",cov[ioffset+ipos]);
- return -l;
+             /* 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 */
+   if(globpr==0){ /* First time we count the contributions and weights */
+     gipmx=ipmx;
+     gsw=sw;
+   }
+   return -l;
+ }
  /*************** function likelione ***********/
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+ 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 3882  void likelione(FILE *ficres,double p[],
+ Line 4778  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 3900  void likelione(FILE *ficres,double p[],
+ Line 4826  void likelione(FILE *ficres,double p[],
      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): <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)  */
+             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 3918  void likelione(FILE *ficres,double p[],
+ Line 4896  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,k, jk, jkk=0, iter=0;
    double **xi;
    double fret;
    double fretone; /* Only one call to likelihood */
- Line 3952  void mlikeli(FILE *ficres,double p[], in
+ Line 4930  void mlikeli(FILE *ficres,double p[], in
        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
    fprintf(ficrespow,"\n");
  #ifdef POWELL
+ #ifdef LINMINORIGINAL
+ #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);
- #endif
+ #endif  /* FLATSUP */
+ #ifdef LINMINORIGINAL
+ #else
+       free_ivector(flatdir,1,npar);
+ #endif  /* LINMINORIGINAL*/
+ #endif /* POWELL */
  #ifdef NLOPT
  #ifdef NEWUOA
- Line 3981  void mlikeli(FILE *ficres,double p[], in
+ Line 5016  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 4365  void pstamp(FILE *fichier)
+ Line 5408  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 4372  void  freqsummary(char fileres[], double
+ Line 5429  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 4418  void  freqsummary(char fileres[], double
+ Line 5475  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 4428  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5485  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 4440  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5497  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 4448  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5506  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 4485  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5543  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 4527  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5585  Title=%s <br>Datafile=%s Firstpass=%d La
                  /*       /\* 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 */
- Line 4548  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5609  Title=%s <br>Datafile=%s Firstpass=%d La
                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 4580  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5647  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 */
+                   for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
-                     idq[z1]=idq[z1]+weight[iind];
+                     if(!isnan(covar[ncovcol+z1][iind])){
-                     meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */
+                       idq[z1]=idq[z1]+weight[iind];
-                     stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
+                       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); */
- Line 4607  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5677  Title=%s <br>Datafile=%s Firstpass=%d La
            /* } */
          } /* 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 4623  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5693  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 4646  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5716  Title=%s <br>Datafile=%s Firstpass=%d La
          Printing means of quantitative variables if any
        */
        for (z1=1; z1<= nqfveff; z1++) {
-         fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
+         fprintf(ficlog,"Mean 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");
          }
-         printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
+         /* mu = \frac{w x}{\sum w}
-         fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
+            var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2
-         fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
+         */
+         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++){ */
- Line 4666  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5739  Title=%s <br>Datafile=%s Firstpass=%d La
        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 4746  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5822  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 4823  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 5899  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 4939  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 6015  Title=%s <br>Datafile=%s Firstpass=%d La
      }
    } /* end mle=-2 */
    dateintmean=dateintsum/k2cpt;
+   date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
    fclose(ficresp);
    fclose(ficresphtm);
- Line 5052  void prevalence(double ***probs, double
+ Line 6129  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 5070  void prevalence(double ***probs, double
+ Line 6147  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 5110  void prevalence(double ***probs, double
+ Line 6187  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 5133  void prevalence(double ***probs, double
+ Line 6209  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 5158  void  concatwav(int wav[], int **dh, int
+ Line 6234  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 5209  void  concatwav(int wav[], int **dh, int
+ Line 6293  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 5250  void  concatwav(int wav[], int **dh, int
+ Line 6335  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 5366  void  concatwav(int wav[], int **dh, int
+ Line 6454  void  concatwav(int wav[], int **dh, int
         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 5384  void  concatwav(int wav[], int **dh, int
+ Line 6475  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 5430  void  concatwav(int wav[], int **dh, int
+ Line 6527  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 5451  void  concatwav(int wav[], int **dh, int
+ Line 6554  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 5478  void  concatwav(int wav[], int **dh, int
+ Line 6581  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 5500  void  concatwav(int wav[], int **dh, int
+ Line 6612  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 5521  void  concatwav(int wav[], int **dh, int
+ Line 6633  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 5589  void  concatwav(int wav[], int **dh, int
+ Line 6703  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 5631  void  concatwav(int wav[], int **dh, int
+ Line 6745  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 5778  void  concatwav(int wav[], int **dh, int
+ Line 6893  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 5849  void  concatwav(int wav[], int **dh, int
+ Line 6966  void  concatwav(int wav[], int **dh, int
     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 */
- Line 5896  void  concatwav(int wav[], int **dh, int
+ Line 7014  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 5973  void  concatwav(int wav[], int **dh, int
+ Line 7097  void  concatwav(int wav[], int **dh, int
         }
         /**< 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 */
- Line 5986  void  concatwav(int wav[], int **dh, int
+ Line 7110  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.
+        /**< 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=0 to nhstepm */
-        /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability
+        /**< And for each alive state j, sums over i \f$ 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++){
- Line 6011  void  concatwav(int wav[], int **dh, int
+ Line 7135  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);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
         if (popbased==1) {
- Line 6197  void  concatwav(int wav[], int **dh, int
+ Line 7321  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 6226  void  concatwav(int wav[], int **dh, int
+ Line 7350  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 6288  void  concatwav(int wav[], int **dh, int
+ Line 7412  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 6437  void varprob(char optionfilefiname[], do
+ Line 7564  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 6506  void varprob(char optionfilefiname[], do
+ Line 7634  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 6524  To be simple, these graphs help to under
+ Line 7652  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 6555  To be simple, these graphs help to under
+ Line 7731  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 6759  To be simple, these graphs help to under
+ Line 7977  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 6776  To be simple, these graphs help to under
+ Line 7995  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 dateproj1, double dateback1, \
+                   double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
-                   double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){
+                   double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
    int jj1, k1, i1, cpt, k4, 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 6799  void printinghtml(char fileresu[], char
+ Line 8018  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 6818  void printinghtml(char fileresu[], char
+ Line 8037  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 6853  void printinghtml(char fileresu[], char
+ Line 8082  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 6908  divided by h: <sub>h</sub>P<sub>ij</sub>
+ Line 8135  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. <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.       \
-  <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 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), from year %.1f up to year %.1f tending 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, dateproj1, dateproj2, 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), \
   from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
   account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
- with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
+ 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);
-  <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+          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 6985  See page 'Matrix of variance-covariance
+ Line 8221  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 6999  See page 'Matrix of variance-covariance
+ Line 8235  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 gplotcondition[132], gplotlabel[132];
-   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
+   int 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 7079  void printinggnuplot(char fileresu[], ch
+ Line 8356  void printinggnuplot(char fileresu[], ch
    fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
    fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
-   fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0)  ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+   fprintf(ficgp,"\n#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);
- Line 7116  void printinggnuplot(char fileresu[], ch
+ Line 8393  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 */
+     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 7157  void printinggnuplot(char fileresu[], ch
+ Line 8522  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 title \"Alive state %d %s\" 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 7165  void printinggnuplot(char fileresu[], ch
+ Line 8530  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*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
          for (i=1; i<= nlstate ; i ++) {
            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
            else fprintf(ficgp," %%*lf (%%*lf)");
- Line 7183  void printinggnuplot(char fileresu[], ch
+ Line 8548  void printinggnuplot(char fileresu[], ch
          }else{
            kl=0;
            for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
-             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+             /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
+             lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
- Line 7203  void printinggnuplot(char fileresu[], ch
+ Line 8569  void printinggnuplot(char fileresu[], ch
            } /* end covariate */
          } /* end if no covariate */
-         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+         if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
            /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%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 7211  void printinggnuplot(char fileresu[], ch
+ Line 8577  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 7225  void printinggnuplot(char fileresu[], ch
+ Line 8593  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 7249  void printinggnuplot(char fileresu[], ch
+ Line 8617  void printinggnuplot(char fileresu[], ch
              }
              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 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 7319  void printinggnuplot(char fileresu[], ch
+ Line 8694  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 7374  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 8756  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 7425  set ter svg size 640, 480\nunset log y\n
+ Line 8814  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 7483  set ter svg size 640, 480\nunset log y\n
+ Line 8879  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 7537  set ter svg size 640, 480\nunset log y\n
+ Line 8940  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 7578  set ter svg size 640, 480\nunset log y\n
+ Line 8988  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 7589  set ter svg size 640, 480\nunset log y\n
+ Line 8999  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 7669  set ter svg size 640, 480\nunset log y\n
+ Line 9086  set ter svg size 640, 480\nunset log y\n
              kl=0;
              strcpy(gplotcondition,"(");
              for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
-               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
+               /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
+               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]; /* 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]);
                kl++;
- Line 7705  set ter svg size 640, 480\nunset log y\n
+ Line 9124  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 7781  set ter svg size 640, 480\nunset log y\n
+ Line 9207  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 7818  set ter svg size 640, 480\nunset log y\n
+ Line 9252  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 7856  set ter svg size 640, 480\nunset log y\n
+ Line 9290  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 */
-     for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */
+     /* 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);*/
-       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);
- Line 7928  set ter svg size 640, 480\nunset log y\n
+ Line 9376  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 */
+                       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*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][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*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*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[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 7970  set ter svg size 640, 480\nunset log y\n
+ Line 9451  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 7988  set ter svg size 640, 480\nunset log y\n
+ Line 9474  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[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*x",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*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[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[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*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][Tvard[ijp][1]],Tqinvresult[nres][Tvard[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,")");
              }
- Line 8007  set ter svg size 640, 480\nunset log y\n
+ Line 9583  set ter svg size 640, 480\nunset log y\n
                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," 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," 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);
            }
- Line 8020  set ter svg size 640, 480\nunset log y\n
+ Line 9596  set ter svg size 640, 480\nunset log y\n
        } /* end k2 */
        /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
        fprintf(ficgp,"\n set out; unset title;set key default;\n");
-     } /* end k1 */
+     } /* end resultline */
    } /* end ng */
    /* avoid: */
    fflush(ficgp);
- Line 8035  set ter svg size 640, 480\nunset log y\n
+ Line 9611  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 8132  set ter svg size 640, 480\nunset log y\n
+ Line 9709  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 8164  set ter svg size 640, 480\nunset log y\n
+ Line 9742  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 8256  set ter svg size 640, 480\nunset log y\n
+ Line 9842  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).
    */
+   /* double anprojd, mprojd, jprojd; */
+   /* double anprojf, mprojf, jprojf; */
    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
    double agec; /* generic age */
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double agelim, ppij, yp,yp1,yp2;
    double *popeffectif,*popcount;
    double ***p3mat;
    /* double ***mobaverage; */
- Line 8302  set ter svg size 640, 480\nunset log y\n
+ Line 9893  set ter svg size 640, 480\nunset log y\n
    if(estepm > stepm){ /* Yes every two year */
      stepsize=2;
    }
+   hstepm=hstepm/stepm;
+   /* 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; */
-   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;
+   /* 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",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
    fprintf(ficresf,"#****** Routine prevforecast **\n");
  /*            if (h==(int)(YEARM*yearp)){ */
    for(nres=1; nres <= nresult; nres++) /* For each resultline */
-   for(k=1; k<=i1;k++){
+     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(i1 != 1 && TKresult[nres]!= k)
        continue;
      if(invalidvarcomb[k]){
- Line 8332  set ter svg size 640, 480\nunset log y\n
+ Line 9928  set ter svg size 640, 480\nunset log y\n
      }
      fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
      for(j=1;j<=cptcoveff;j++) {
-       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       /* fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); */
+       fprintf(ficresf," 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]);
- Line 8343  set ter svg size 640, 480\nunset log y\n
+ Line 9940  set ter svg size 640, 480\nunset log y\n
          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 8362  set ter svg size 640, 480\nunset log y\n
+ Line 9959  set ter svg size 640, 480\nunset log y\n
          }
          fprintf(ficresf,"\n");
          for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           /* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Tvaraff not correct *\/ */
-         fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+           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.;
- Line 8391  set ter svg size 640, 480\nunset log y\n
+ Line 9989  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).
- Line 8400  set ter svg size 640, 480\nunset log y\n
+ Line 9999  set ter svg size 640, 480\nunset log y\n
    */
    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
    double agec; /* generic age */
-   double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
    double *popeffectif,*popcount;
    double ***p3mat;
    /* double ***mobaverage; */
- Line 8443  set ter svg size 640, 480\nunset log y\n
+ Line 10042  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);
    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");
- Line 8471  set ter svg size 640, 480\nunset log y\n
+ Line 10070  set ter svg size 640, 480\nunset log y\n
      }
      fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
      for(j=1;j<=cptcoveff;j++) {
-       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficresfb," 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]);
- Line 8482  set ter svg size 640, 480\nunset log y\n
+ Line 10081  set ter svg size 640, 480\nunset log y\n
          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); */
        /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */
        for (agec=bage; agec<=fage; agec++){  /* testing */
- Line 8507  set ter svg size 640, 480\nunset log y\n
+ Line 10106  set ter svg size 640, 480\nunset log y\n
          }
          fprintf(ficresfb,"\n");
          for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-         fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
+         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 8543  set ter svg size 640, 480\nunset log y\n
+ Line 10142  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 8554  set ter svg size 640, 480\nunset log y\n
+ Line 10153  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 8566  set ter svg size 640, 480\nunset log y\n
+ Line 10165  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 8595  set ter svg size 640, 480\nunset log y\n
+ Line 10198  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 8623  set ter svg size 640, 480\nunset log y\n
+ Line 10226  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 8956  void prwizard(int ncovmodel, int nlstate
+ Line 10565  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 8964  double gompertz(double x[])
+ Line 10573  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 8994  double gompertz(double x[])
+ Line 10609  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 9087  int readdata(char datafile[], int firsto
+ Line 10702  int readdata(char datafile[], int firsto
    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 9147  int readdata(char datafile[], int firsto
+ Line 10789  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 9167  int readdata(char datafile[], int firsto
+ Line 10809  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 9188  int readdata(char datafile[], int firsto
+ Line 10830  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 9219  int readdata(char datafile[], int firsto
+ Line 10861  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 9242  int readdata(char datafile[], int firsto
+ Line 10888  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 9281  int readdata(char datafile[], int firsto
+ Line 10931  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 9301  int readdata(char datafile[], int firsto
+ Line 10958  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 9394  void removefirstspace(char **stri){/*, c
+ Line 11053  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 = */
      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);
+     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, %s.\n",j, cptcovs, model);
-     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);
+     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, %s.\n",j, cptcovs, model);
+     /* 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 */
+       /* Tvar[k1]; */ /* Age variable */
+       /* Wrong we want the value of variable name Tvar[k1] */
+       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 */
+       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 9525  int decodemodel( char model[], int lasto
+ Line 11296  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  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 9573  int decodemodel( char model[], int lasto
+ Line 11353  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=j+1-j1; /**<  Number of simple covariates V1 +V1*age +V3 +V3*V4 +age*age => V1 + V3 =4+1-3=2  */
        cptcovt= j+1; /* Number of total covariates in the model, not including
                       * cst, age and age*age
                       * V1+V1*age+ V3 + V3*V4+age*age=> 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 9593  int decodemodel( char model[], int lasto
+ Line 11375  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 9639  int decodemodel( char model[], int lasto
+ Line 11421  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 */
+       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(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
-                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+                                          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 */
+         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 */
-             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) */
+               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 9706  int decodemodel( char model[], int lasto
+ Line 11632  int decodemodel( char model[], int lasto
        } /* 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 9722  int decodemodel( char model[], int lasto
+ Line 11649  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 9731  int decodemodel( char model[], int lasto
+ Line 11658  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;}
+   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 9750  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 11678  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 9771  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 11691  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 9787  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 11714  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 9795  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 11723  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 9802  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 11737  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++){
- Line 9993  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 12150  Dummy[k] 0=dummy (0 1), 1 quantitative (
        if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
          if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
            if(Tvar[k1]==Tvar[k2]){
-             printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
+             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[k1],Dummy[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 10013  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 12170  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 10166  BOOL IsWow64()
+ Line 12325  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 10202  void syscompilerinfo(int logged)
+ Line 12363  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 10218  void syscompilerinfo(int logged)
+ Line 12381  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 10326  void syscompilerinfo(int logged)
+ Line 12487  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 10335  int prevalence_limit(double *p, double *
+ Line 12497  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 10355  int prevalence_limit(double *p, double *
+ Line 12517  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 10390  int prevalence_limit(double *p, double *
+ Line 12557  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 10410  int prevalence_limit(double *p, double *
+ Line 12583  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 10431  int back_prevalence_limit(double *p, dou
+ Line 12604  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 10453  int back_prevalence_limit(double *p, dou
+ Line 12626  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 10481  int back_prevalence_limit(double *p, dou
+ Line 12661  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 10505  int back_prevalence_limit(double *p, dou
+ Line 12685  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 10516  int back_prevalence_limit(double *p, dou
+ Line 12696  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 10526  int back_prevalence_limit(double *p, dou
+ Line 12706  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;
- Line 10536  int hPijx(double *p, int bage, int fage)
+ Line 12716  int hPijx(double *p, int bage, int fage)
    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 10626  int hPijx(double *p, int bage, int fage)
+ Line 12809  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 10638  int hPijx(double *p, int bage, int fage)
+ Line 12821  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? */
-       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+       fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
-       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
+       continue;
-         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
+     }
-         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
+     /* 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=nhstepm*YEARM; aff par mois*/
+       /* 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 */
-         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
+       nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
-         /* and memory limitations if stepm is small */
+       /*          nhstepm=nhstepm*YEARM; aff par mois*/
-         /* oldm=oldms;savm=savms; */
-         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
+       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, k, nres);
+       /* and memory limitations if stepm is small */
-         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
-         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
+       /* oldm=oldms;savm=savms; */
+       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
+       hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */
+       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
+       fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
+       for(i=1; i<=nlstate;i++)
+         for(j=1; j<=nlstate+ndeath;j++)
+           fprintf(ficrespijb," %1d-%1d",i,j);
+       fprintf(ficrespijb,"\n");
+       for (h=0; h<=nhstepm; h++){
+         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+         fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
+         /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
          for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate+ndeath;j++)
-             fprintf(ficrespijb," %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 10705  int main(int argc, char *argv[])
+ Line 12892  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 10731  int main(int argc, char *argv[])
+ Line 12919  int main(int argc, char *argv[])
    double dum=0.; /* Dummy variable */
    double ***p3mat;
    /* double ***mobaverage; */
+   double wald;
    char line[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 jl=0;
    int i1, j1, jk, stepsize=0;
- Line 10748  int main(int argc, char *argv[])
+ Line 12937  int main(int argc, char *argv[])
    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 10760  int main(int argc, char *argv[])
+ Line 12956  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 10773  int main(int argc, char *argv[])
+ Line 12970  int main(int argc, char *argv[])
    double *epj, vepp;
    double dateprev1, dateprev2;
-   double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;
+   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;
+   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 10969  int main(int argc, char *argv[])
+ Line 13167  int main(int argc, char *argv[])
        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)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");
- Line 11057  int main(int argc, char *argv[])
+ Line 13256  int main(int argc, char *argv[])
    }
    if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
      if (num_filled != 1){
-       printf("ERROR %d: Model should be at minimum 'model=1+age' %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' %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 11069  int main(int argc, char *argv[])
+ Line 13268  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);
- Line 11097  int main(int argc, char *argv[])
+ Line 13296  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 11107  int main(int argc, char *argv[])
+ Line 13308  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 11173  int main(int argc, char *argv[])
+ Line 13375  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 11313  Please run with mle=-1 to get a correct
+ Line 13524  Please run with mle=-1 to get a correct
    /*  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 11332  Please run with mle=-1 to get a correct
+ Line 13552  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 11353  Please run with mle=-1 to get a correct
+ Line 13574  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 11370  Please run with mle=-1 to get a correct
+ Line 13593  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 11395  Please run with mle=-1 to get a correct
+ Line 13627  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(-1,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 11412  Please run with mle=-1 to get a correct
+ Line 13647  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 11436  Please run with mle=-1 to get a correct
+ Line 13701  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 11463  Please run with mle=-1 to get a correct
+ Line 13728  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 11472  Please run with mle=-1 to get a correct
+ Line 13737  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 11502  Please run with mle=-1 to get a correct
+ Line 13767  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 11611  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 13876  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 11624  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 13896  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 11654  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 13926  Title=%s <br>Datafile=%s Firstpass=%d La
    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) covariates: ntv=%d ", ntv);
+   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 quantitative time varying covariates: nqtv=%d ", nqtv);
+   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", \
- Line 11667  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 13939  Title=%s <br>Datafile=%s Firstpass=%d La
  <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
-   fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
+   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);
- Line 11689  Interval (in months) between two waves:
+ Line 13961  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 11726  Interval (in months) between two waves:
+ Line 13998  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
- Line 11853  Interval (in months) between two waves:
+ Line 14125  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 11902  Please run with mle=-1 to get a correct
+ Line 14174  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 11937  Please run with mle=-1 to get a correct
+ Line 14210  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");
- Line 11946  Please run with mle=-1 to get a correct
+ Line 14220  Please run with mle=-1 to get a correct
      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 12013  Please run with mle=-1 to get a correct
+ Line 14376  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 12104  Please run with mle=-1 to get a correct
+ Line 14467  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 12149  Please run with mle=-1 to get a correct
+ Line 14513  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 12174  Please run with mle=-1 to get a correct
+ Line 14539  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 12196  Please run with mle=-1 to get a correct
+ Line 14562  Please run with mle=-1 to get a correct
      }
      /* Results */
+     /* Value of covariate in each resultine will be compututed (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.*/
-           }
-           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);
-           fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-           fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-           fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-           /* day and month of proj2 are not used but only year anproj2.*/
            dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
            dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
+           prvbackcast = 1;
+         }
+         else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
+           printf("prevbackcast=%d yearsbproj=%.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 12301  This is probably because your parameter
+ Line 14699  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);
      }
      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, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);
+                  jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
- Line 12314  Please run with mle=-1 to get a correct
+ Line 14745  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 12328  Please run with mle=-1 to get a correct
+ Line 14759  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 12378  Please run with mle=-1 to get a correct
+ Line 14812  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 12399  Please run with mle=-1 to get a correct
+ Line 14843  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 12408  Please run with mle=-1 to get a correct
+ Line 14858  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 12442  Please run with mle=-1 to get a correct
+ Line 14892  Please run with mle=-1 to get a correct
        fprintf(ficreseij,"\n#****** ");
        printf("\n#****** ");
        for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-         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]])]);
        }
        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 12464  Please run with mle=-1 to get a correct
+ Line 14915  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 12503  Please run with mle=-1 to get a correct
+ Line 14954  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 %s \n#****** Result for:", model);
-       fprintf(ficrest,"\n#****** Result for:");
+       fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
-       fprintf(ficlog,"\n#****** Result for:");
+       fprintf(ficlog,"\n# model %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 12540  Please run with mle=-1 to get a correct
+ Line 15045  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 12572  Please run with mle=-1 to get a correct
+ Line 15079  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 12620  Please run with mle=-1 to get a correct
+ Line 15127  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,-1,NCOVMAX,1,2);
      free_imatrix(Tvard,1,NCOVMAX,1,2);
-     free_imatrix(s,1,maxwav+1,1,n);
+     free_imatrix(s,1,maxwav+1,firstobs,lastobs);
-     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(anint,1,maxwav,firstobs,lastobs);
-     free_matrix(mint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,firstobs,lastobs);
-     free_ivector(cod,1,n);
+     free_ivector(cod,firstobs,lastobs);
      free_ivector(tab,1,NCOVMAX);
      fclose(ficresstdeij);
      fclose(ficrescveij);
- Line 12654  Please run with mle=-1 to get a correct
+ Line 15162  Please run with mle=-1 to get a correct
    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 12670  Please run with mle=-1 to get a correct
+ Line 15179  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 12692  Please run with mle=-1 to get a correct
+ Line 15202  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 12777  Please run with mle=-1 to get a correct
+ Line 15296  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') {

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