[pkgsrc/trunk]: pkgsrc/math/R-car Update to 2.1.6

[wen <wen%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/b079e6a40f19
branches:  trunk
changeset: 374389:b079e6a40f19
user:      wen <wen%pkgsrc.org@localhost>
date:      Mon Jan 22 07:41:38 2018 +0000

description:
Update to 2.1.6
Add missing DEPENDS

Upstream changes:
Changes to Version 2.1-6

  o Made several functions compatible with vcov() in R-devel (3.5.0).

Changes to Version 2.1-5

  o Fixed bug in boot.hist, and made Boot.default more general.  Added a vcov method for boot objects

  o Fixed bug in gamLine with non-dentity links.

  o Removed the skewPower transformation functions, and added bcnPower transformation family. Same transformation, new name, new computational algorithms, improved documentation.

  o Fixed bug (reported by Bruno Hebling Vieira) in print.summary.Anova.mlm() that could cause adjusted p-values to be incorrectly ordered.

Changes to Version 2.1-4

  o The smoother functions loessLine, gamLine and quantregLine used in many car functions now evaluate the smoother at an equally spaced grid of points rather than at the observed values on the 
horizontal axis of a plot.

  o spreadLevelPlot.lm now accepts point marking as in most other graphical functions in car.

  o Bug fixed in one of the skewPower support functions; thans to Balazs Banfai

  o Added support for lmer objects in power transformations

  o Added support for skewPower family power transformations for lm and lmer objects

  o Added list, data.frame, and matrix methods for Boxplot(), suggestion of Michael Friendly

  o Added adaptiveKernel() density estimator, with option to use it in densityPlot().

Changes to Version 2.1-3

  o Corrected documentation for mcPlots

  o added id.location argument to showLabels to vary location of labels

  o added fix for compatiblity with Rcmdr with missing data in several plotting functions.

  o deltaMethod() now reports confidence intervals.

  o print.summary.Anova.mlm() has new SSP and SSPE arguments to determine whether the corresponding matrices are printed (suggestion of Michael Friendly).

  o summary() and print() methods for Anova.mlm() can now report univariate ANOVAs (suggestion and some code by Michael Friendly).

  o added "value" and "vcov" attributes to objects returned by linearHypothesis() (after suggestions by Liviu Andronic and Steven Yen).

  o compareCoefs() now checks classes of models.

  o small fixes/changes.

Changes to Version 2.1-2

  o Modified scatter3d() so that plots can be embedded in HTML.

Changes to Version 2.1-1

  o influencePlot now returns Cook's distance, not its square root.

  o Anova() now supports "coxme" objects (produced by coxme() in coxme package) (request of Philipp Sprenger).

  o Anova() now works via its default method with "vglm" objects produced by functions in the VGAM package; and the default method of linearHypothesis() again works with these objects (problem 
reported by Michael Friendly).

  o Fixed Anova.coxph() so that it takes account of method (ties) argument (bug reported by Karl Ove Hufthammer).

  o Improvements to Anova.default() so that a wider variety of model classes are accommodated (following request of Liviu Andronic.)

  o dataEllipse() now throws an error if there are too few colors for the number of groups (fixing bug reported by Ottorino Pantani).

  o spreadLevelPlot.lm() now includes an optional smoother in addition to the fitted straight line (suggestion of Michael Friendly).

  o No longer import methods (as opposed to generics) directly from pbkrtest.

  o Added axis.ticks argument to scatter3d() (code contributed by David Winsemius).

Changes to Version 2.1-0

  o New power family called skewPower has been added that can be used with the Box Cox method with a few negative responses (joint work with Doug Hawkins).  Several functions modified to accomodate 
two-parameter power families.

  o Fixed bug in Anova() for coxph models with clusters (reported by Jesus Humberto Gomez ), due apparently to a change in coxph().

Changes to Version 2.0-26

  o Anova() F-tests for binomial and Poisson GLMs now changes error.estimate="dispersion" to "pearson" as advertized (bug reported by Will Petry).

  o Improved behavior of above-plot legends in scatterplot().

  o Fixed sp() (bug reported by Cesar Rabak).

  o Conforms to new CRAN requirements for package imports.

Changes to Version 2.0-25

  o Fixed df check in linearHypothesis.default() (bug report by Pierre Chausse).

  o Fixed bug when vcov. argument to Anova() is a function (reported by Liviu Andronic).

  o Now export .carEnv to avoid problem with update() in Boot() (reported by Alan T. Arnholt).

Changes to Version 2.0-24

  o Fixed broken URLs.

  o Changed handling of .carEnv environment.

  o Moved pbkrtest, quantreg, and mgcv from Suggests: to Imports:.

Changes to Version 2.0-23

  o Modified ScatterplotSmoothers to add an 'offset' to the vertical axis of spread smooths.  This is required in the marginal model plot functions.

  o Fixed labels on mcPlot with overlay=FALSE

  o Check for 0 residual df and 0 residual deviance (within rounding) in Anova() and linearHypothesis() (problem reported by Jonathan Love).

  o Fixed model.matrix.lme and model.matrix.gls utility functions, and hence Anova and vif, respectively, to work with models specified with formulas supplied as objects (after problem noted by Gang 
Chen).

  o Added Wong data set, used in mixed-models appendix.

Changes to Version 2.0-22

  o corrected bug in 'terms' argument in residualPlots, and other graphic functions with a 'terms' argument

  o added residual curvature tests for glm.nb

  o mcPlot and mcPlots draw 'marginal/conditional' plots for lm objects.  The marginal plot is of the centered response versus a centered regressor; the conditional plot is the corresponding 
added-variable plot.  The plots can be overlaid or viewed side-by-side.

  o added argument marginal.scale to avPlots to scale the added-variable plot for Y on X|Z using the scale from the marginal plot of Y vs X ignoring X.  The default is FALSE, corresponding to using 
scaling to maximize resolution or use xlim and ylim to set user scaling.

  o Fixed bugs in Anova.survreg() that could affect types II, II tests, both Wald and LR, and one similar bug in linearHypothesis.survreg().

  o Replaced calls to require() with requireNamespace() where possible (suggestion of Brian Ripley).

  o The following functions now produce warnings rather than errors when there are empty groups: scatterplot(), scatterplotMatrix(), scatter3d(), densityPlot().

  o Corrected name of "Blackmoor" dataset to "Blackmore".

  o Added KosteckiDillon migraines dataset (contributed by Georges Monette).

  o introduced linearHypothesis.rlm() for rlm models (suggestion of Matthieu Stigler).

  o Small bug fixes/improvements.

Changes to Version 2.0-21

  o residualPlot error when using 'type="rstudent" has been fixed.

  o Minor change to "recode" documentation; improved error checking in recode().

  o Fixed a bug in gamLine with non-canonical links. (Thanks to Hani Christoph)

  o Added has.intercept.multinom() to make Anova() work with multinom objects fit to a dichotomous response (after bug report by Kristian Hovde Liland).

  o Replaced vif.lm() with vif.default() to cover wider variety of models (after question by Laura Rigg about gls models).

  o Diagonal panels in scatterplotMatrix() (except for histograms) show groups separately when plotted by groups (suggestion by Erich Neuwirth).

  o Added vcov. argument to Anova.lm().

Changes to Version 2.0-20

  o Added new id.method="r" to showLabels for labeling plots of residuals; default id.method changed in residualPlots.

  o Fixed handling of labels argument to outlierTest() (bug report by Stephane Laurent).

  o Accommodate numeric variables consisting entirely of NAs in recode() (suggestion of Karl Ove Hufthammer).

  o Prevent dataEllipse() from opening a graphics device when draw=FALSE (fixing bug reported by Rafael Laboissiere).

  o The functions makeHypothesis() and printHypothesis(), intended for internal use, are exported so that they can be used in other packages (request of Arne Henningsen).

  o Small fixes.

Changes to Version 2.0-19

  o allow a grouping variable for color, symbol and fits in residualPlots

  o fixed axis labelling probelm in influenceIndexPlot

  o fixed scoping problems in Boot, bootCase, and ncvTest

  o added an argument to deltaMethod for passing arguments to get scoping right when calling linearHypothesis in another function; other deltaMethod bugs fixed

  o slight modification to documentation of Boot

  o summary() method for "Anova.mlm" objects now returns an object, printed by a corresponding print() method (adapting code contributed by Gabriel Baud-Bovy).

  o added .merMod methods to Anova(), deltaMethod(), linearHypothesis(), matchCoefs(), and unexported utilities df.residual() and has.intercept(); insured compatibility with nlme and CRAN and 
developments versions of lme4.

  o added use argument to scatterplotMatrix() (suggestion of Antoine Lizee).

  o export linearHypothesis.default() for use in other packages (suggestion of Achim Zeileis).

  o small changes and fixes.

diffstat:

 math/R-car/Makefile |   7 +++++--
 math/R-car/distinfo |  10 +++++-----
 2 files changed, 10 insertions(+), 7 deletions(-)

diffs (39 lines):

diff -r f22a7a2fc973 -r b079e6a40f19 math/R-car/Makefile
--- a/math/R-car/Makefile       Mon Jan 22 07:36:31 2018 +0000
+++ b/math/R-car/Makefile       Mon Jan 22 07:41:38 2018 +0000
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.3 2013/08/15 01:56:37 wen Exp $
+# $NetBSD: Makefile,v 1.4 2018/01/22 07:41:38 wen Exp $
 #
 
 CATEGORIES=    math
@@ -10,10 +10,13 @@
 LICENSE=       gnu-gpl-v2
 
 R_PKGNAME=     car
-R_PKGVER=      2.0-18
+R_PKGVER=      2.1-6
 
 WRKSRC=                ${WRKDIR}/car
 USE_LANGUAGES= # none
 
+DEPENDS+=      R-quantreg>=0:../../math/R-quantreg \
+               R-pbkrtest>=0.4.4:../../math/R-pbkrtest
+
 .include "../../math/R/Makefile.extension"
 .include "../../mk/bsd.pkg.mk"
diff -r f22a7a2fc973 -r b079e6a40f19 math/R-car/distinfo
--- a/math/R-car/distinfo       Mon Jan 22 07:36:31 2018 +0000
+++ b/math/R-car/distinfo       Mon Jan 22 07:41:38 2018 +0000
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.4 2015/11/03 23:33:27 agc Exp $
+$NetBSD: distinfo,v 1.5 2018/01/22 07:41:38 wen Exp $
 
-SHA1 (R/car_2.0-18.tar.gz) = f0fb53cedfe698acfe9fbbd5577fe72be11024ba
-RMD160 (R/car_2.0-18.tar.gz) = c2342b641dc8f5d1f4ce54c8577f8f8fe937d775
-SHA512 (R/car_2.0-18.tar.gz) = 36802e5fa300c178050c6c210d9c7d380a58c7561c0fee676f47f231685e569bf1463681cb8b611167d59789c9f2a74c6623b8161d4ef79a4872a5cca9d919f9
-Size (R/car_2.0-18.tar.gz) = 334622 bytes
+SHA1 (R/car_2.1-6.tar.gz) = ddb7968fa138804ff331d5ad0c8068ed0264fb95
+RMD160 (R/car_2.1-6.tar.gz) = 817d08becd22cc674def8336d0769ec411527316
+SHA512 (R/car_2.1-6.tar.gz) = dac8063e76293accab6daf1db7e9e71bcc0df30a7148828744e46f3164d52ee218eba9bdd8af1037af929832fa283cd12f12b92c3ede79a7356d8298d84c7668
+Size (R/car_2.1-6.tar.gz) = 627349 bytes