Subject: CVS commit: pkgsrc/math/R-car
From: Wen Heping
Date: 2018-01-22 08:41:38
Message id: 20180122074138.43E37FBDE@cvs.NetBSD.org

Log Message:
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.

Files:
RevisionActionfile
1.4modifypkgsrc/math/R-car/Makefile
1.5modifypkgsrc/math/R-car/distinfo