./math/R-car, Companion to Applied Regression

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Branch: CURRENT, Version: 3.0.3, Package name: R-car-3.0.3, Maintainer: pkgsrc-users

Functions to Accompany J. Fox and S. Weisberg, An R Companion to
Applied Regression, Third Edition, Sage, in press.

Required to run:
[math/R-abind] [math/R] [math/R-quantreg] [math/R-lme4] [math/R-pbkrtest] [math/R-carData] [geography/R-maptools] [devel/R-rio]

Required to build:

Master sites: (Expand)

Version history: (Expand)

CVS history: (Expand)

   2019-08-08 21:53:58 by Brook Milligan | Files touched by this commit (189) | Package updated
Log message:
Update all R packages to canonical form.

The canonical form [1] of an R package Makefile includes the

- The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as
  needed), and CATEGORIES.

- HOMEPAGE is not present but defined in math/R/Makefile.extension to
  refer to the CRAN web page describing the package.  Other relevant
  web pages are often linked from there via the URL field.

This updates all current R packages to this form, which will make
regular updates _much_ easier, especially using pkgtools/R2pkg.

[1] http://mail-index.netbsd.org/tech-pkg/2 … 21711.html
   2018-07-28 16:40:53 by Brook Milligan | Files touched by this commit (126)
Log message:
Remove MASTER_SITES= from individual R package Makefiles.

Each R package should include ../../math/R/Makefile.extension, which also
defines MASTER_SITES.  Consequently, it is redundant for the individual
packages to do the same.  Package-specific definitions also prevent
redefining MASTER_SITES in a single common place.
   2018-01-22 08:41:38 by Wen Heping | Files touched by this commit (2) | Package updated
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 \ 

  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 \ 

  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 \ 

  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(), \ 

  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 \ 

  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 \ 

  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 \ 

  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 \ 

  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 \ 

  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.
   2015-11-04 00:33:46 by Alistair G. Crooks | Files touched by this commit (262)
Log message:
Add SHA512 digests for distfiles for math category

Problems found locating distfiles:
	Package dfftpack: missing distfile dfftpack-20001209.tar.gz
	Package eispack: missing distfile eispack-20001130.tar.gz
	Package fftpack: missing distfile fftpack-20001130.tar.gz
	Package linpack: missing distfile linpack-20010510.tar.gz
	Package minpack: missing distfile minpack-20001130.tar.gz
	Package odepack: missing distfile odepack-20001130.tar.gz
	Package py-networkx: missing distfile networkx-1.10.tar.gz
	Package py-sympy: missing distfile sympy-
	Package quadpack: missing distfile quadpack-20001130.tar.gz

Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden).  All existing
SHA1 digests retained for now as an audit trail.
   2013-08-15 03:56:37 by Wen Heping | Files touched by this commit (2) | Package updated
Log message:
Update to 2.0.18

Upstream changes:
Changes to Version 2.0-18

    o Bug fix to boot with type="residual"

    o Added densityPlot() function.

Changes to Version 2.0-17

    o Add a variable to AMSsurvey.

    o Fix to residualPlots to compute lack of fit tests with missing values and glms.

    o Fix to residualPlots with a 0/1 variable not declared a factor.

    o Boxplot() now works properly with at argument passed to boxplot() via ... \ 
(contribution of Steve Ellison).

    o qqPlot.lm() now works with "aov" objects (fixing problem \ 
reported by Thomas Burk).

    o Small fixes to code and docs.

Changes to Version 2.0-16

    o Fixed bug in printing of hypotheses by linearHypothesis(), where numeric
constants of the form 1.* or -1.* were printed incorrectly (reported by Johannes \ 

    o Fixed a bug in showLabels() with multiple groups in the scatterplot() and \ 
scatterplotMatrix() function.

    o linearHypothesisTest() now tolerates newlines and tabs in hypotheses \ 
(suggestion of David Hugh-Jones).

    o two bugs fixed in Boot() (found by David Pain) changed argument f to f. in \ 

    o summary.Boot(), confint.Boot() and hist.Boot() handle aliases correctly.

    o Boxplot.formula() now accepts more than one conditioning variable \ 
(suggestion of Christina Yassouridis).

    O Boxplot() now properly handles at argument passed through via ... to \ 
boxplot() (contribution of Steve Ellison).

    o Small fixes.

Changes to Version 2.0-15

    o Added an argument coef. to linearHypothesis so tests of the linear \ 
hypohtesis form can be computed without reference to a fitted model

    o Added a linearHypothesis.nlsList method

    o Added an nls method for Boot

    o Recode() introduced as alias for recode() to avoid name clash with Hmisc.

    o residualPlots for glms now ignore starting values for the computing \ 
algorithm when computing lack of fit tests; starting values previously caused an \ 

    o Marginal Model Plots now allow conditioning on a categorical variable.

Changes to Version 2.0-14

    o Smoothers now given as arguments to scatterplot(), scatterplotMatrix(), \ 
residualPlots() and other functions; gamLine(), loessLine() (default), and \ 
quantregLine() smoothers provided.

    o linearHypothesis.mer() and Anova.mer() now consistent with pbkrtest \ 
version 0.3-2.

    o Small changes and fixes.

Changes to Version 2.0-13

    o Added point marking (id.n, etc.) to dataEllipse

    o Changed the default for id.method with the invTranPlot to "x".

    o The ncvTest has been rewritten for stability, and unneeded 'data', \ 
'subset' and 'na.action' argument have been removed

    o Added new function 'Boot' that is a simple front-end to boot::boot that \ 
will be useful when bootstrapping regression models.  Implemented for lm and \ 
glm, but this is likely to work for many other S3 regression models with and \ 
'update' method, 'subset' argument.

    o Fixed bug in 'compareCoefs' with non-full rank models

    o Modified 'bootCase' to return a matrix of class c("bootCase", \ 
"matrix") so generic functions can be written to summarize these \ 

    o Minor changes to the returned value of showLabels to give both the label \ 
and the corresponding row number.  showLabels documentation tweaked.

    o Improved handling of center.pch argument to ellipse() (suggestion of Rob \ 

    o New test argument for linearHypothesis.mer()  and test.statistic argument \ 
for Anova.mer() for F-tests with Kenward/Roger df, provided by pbkrtest package.

    o Anova.mlm() now will do univariate repeated-measures ANOVA even if the \ 
error SSP matrix is singular.

    o hccm() will now accept a weighted linear models (suggestion of Stefan \ 
Holst Bache).

    o deltaMethod.default() now applies coef() and vcov() to a model for which \ 
these are supported (generalizing a suggestion by Scott Kostyshak).

    o Fixed handling of labels argument in scatterplot.formula() and \ 

    o Fixed qqPlot.default() so that it honors line="none" (bug \ 
reported by Rob Kushler).

    o Added new default method for confidenceEllipse(), which now can construct \ 
confidence ellipses for linear functions of coefficients.

    o globalVariables() called for R 2.15.1 or later.

    o Fixed bug in logit() when percents=TRUE and largest percent is 1 (reported \ 
by Eric Goodwin).

    o Added radius argument to scatter3d() (suggestion of Antonino Messina).

    o Fixed spurious errors message in scatter3d() when groups present but \ 
surface=FALSE (reported by David L. Carlson).
   2012-04-15 17:15:48 by Brook Milligan | Files touched by this commit (2) | Package updated
Log message:
Update to car v2.0-12 and add LICENSE.
   2011-09-26 21:33:02 by Ryo ONODERA | Files touched by this commit (3) | Imported package
Log message:
Import R-car-2.0.11 as math/R-car

This package accompanies J. Fox and S. Weisberg, An R Companion to
Applied Regression, Second Edition, Sage, 2011.

Used by math/R-Rcmdr.
OKed by wiz@.