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CVS Commit History:

   2022-12-18 11:19:13 by Makoto Fujiwara | Files touched by this commit (2)
Log message:
(math/R-car) Updated 3.0.13 to 3.1.1

Changes to Version 3.1-1

  o Fixed bug in hccm(): when some cases are fit exactly all versions
    of the hccm estimate are singular and inconsistent.  A error message
    is now returned.

  o Fixed bug in Anova.survreg() for Wald tests (reported by Megan
    Taylor Jones), which failed with a spurious "missing residual df"

  o Made Anova.lm() more robust when there are aliased coefficients
    (following report of cryptic output by Taiwo Fagbohungbe).

  o Added reg.function, reg.function.col, and mouseMode arguments to
    scatter3d(), and mouseMode to crPlot3d().

  o Added fill and associated arguments to influencePlot() (initial
    implementation of Michael Friendly).

  o Added confidenceEllipses() function to create matrix of all
    pairwise confidence ellipses for a regression model (suggestion of
    Michael Friendly).

  o Moved the pointLabel() function from the maptools package in
    anticipation of the retirement of that package, and with the
    permission of the function author, Tom Short.

Changes to Version 3.1-0

  o New 3D added-variable and component+residual plots, avPlot3d() and

  o More flexible recode()/Recode().

  o Added Anova.svycoxph() to prevent selection of test.statistic="LR".

  o New take on vif.lm().
   2022-05-22 01:09:12 by Makoto Fujiwara | Files touched by this commit (2)
Log message:
(math/R-car) Updated 3.0.11 to 3.0.13

Changes to Version 3.0-13

  o Handle singularities better in Anova.mlm() (suggestion of Marius Barth).

  o Fixed error reporting in logit() (bug reported by Collin Erickson).

  o Added pt.cex and cex sub-arguments to legend argument of
  scatterplotMatrix() (implicit suggestion of Duncan Mackay).

  o New vif.lm() method with options for handling linear models with interactions.

  o Fixed bug in cooks.distance.influence.lme() (in effect, incorrect
  division by the error variance twice rather than once), and a sign
  error in dfbeta.influence.lme() and dfbetas.influence.lme()
  (following report by Ben Bolker).

  o Added an error.df argument to the default methods of
  linearHypothesis() and Anova() for computing F-tests; if the
  argument is unspecified, then df.residual() is applied to the model,
  and if df.residual() returns NULL or NA, then an asymptotic
  chi-square test is substituted for the F-test (in response to a
  report by Adrian Olszewski that Anova() fails for gls models when an
  F-test is requested).

Changes to Version 3.0-12

  o The 'rio` package is now suggested, not required.  To use the
  Import() and Export() functions users may need to install rio using

  o hccm() now reports an interpretable error, except for type = "hc0"
  or "hc1", when there are cases with hatvalues = 1 (following problem
  reported by Peng Ding).

  o Fix bug in rownames in dfbetasPlots.lm() (reported by Shu Fai

  o Package 'rio' was moved from Imports to Suggests. Both Import()
  and Export() now check for the availability of 'rio' first and
  report an error otherwise.
   2021-10-26 12:56:13 by Nia Alarie | Files touched by this commit (458)
Log message:
math: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 16:28:36 by Nia Alarie | Files touched by this commit (458)
Log message:
math: Remove SHA1 hashes for distfiles
   2021-09-11 14:31:42 by Makoto Fujiwara | Files touched by this commit (2)
Log message:
(math/R-car) Updated 3.0.10 to 3.0.11

Changes to Version 3.0-11

  o boxCox() function now allows the use of any of the usual graphics
    parameters in the plot() function.  If particuar boxCox(model,
    main="my title") will add a title to the plot, and boxCox(model,
    main="") will suppress it.

  o car::Boot(object, method="residual") will work for
    method="residual" only if the car package has been previously
    attached via either library(car) or require(car).

  o Added error checking with vcov. argument.  Changed vcov.boot to
    print a warning of bootstrap replicates that returned NA

  o Introduced brief.tbl(), which simply calls print(), to cope with
    changes to tibbles.

  o qqPlot() fills (shades) confidence envelopes by default, and
    smoothers for scatterplots fill variance (spread) envelopes by
    default (suggestions of Michael Friendly).

  o Fixed problem in infIndexPlot.influence.lme() (reported by Francis
    L. Huang).

  o New "polr" and "svyolr" methods for vif() (following \ 
report by
    Abra Jeffers).

  o Make linearHypothesis() and Anova() work with "svyolr" objects via
    their default methods.

  o Regularize handling of vcov. argument in Anova() and

  o vcov. argument now works with Anova() for models produced by
    lme4::lmer() and glmer(), (fixing a bug reported by Amy MacDougall).

  o New linearHypothesis.lmList() method.

  o New "lm" method for symbox().

  o New cex and pt.wts arguments for avPlot() "lm" and "glm" \ 
    and for mcPlot.lm().

  o Fix handling of imatrix argument to Anova.mlm() (suggestion of
    Benedikt Langenberg).

  o Remove influence.merMod() and related methods in favor of versions
    of these methods in the lme4 package.

  o Rewrite "embedding" vignette.

  o Small fixes and improvements.
   2020-10-02 12:31:59 by Wen Heping | Files touched by this commit (2)
Log message:
Update to 3.0.10

Upstream changes:
Changes to Version 3.0-10

  o Fixed as error when using parameter name "(Intercept)" with \ 

  o Several changes to Boot() to correct bugs, support the plinear algorithm, to \ 
correct use of weights for lm, and allow use of weights for nls.

  o Fix quantregLine() to work with development version 5.69 of quantreg package \ 
(following heads-up from Roger Koenker).
   2020-09-21 01:46:00 by Makoto Fujiwara | Files touched by this commit (2)
Log message:
(math/R-car) Updated 3.0.3 to 3.0.9. make test fails

Changes to Version 3.0-9

  o Declare linearHypothesis.survreg() method, previously omitted from
    NAMESPACE (following question by Robert Dinterman); tweaks to survreg
    methods for linearHypothesis(), Anova(), and deltaMethod() to make them
    more robust.

  o Fix bug in hccm() when model matrix includes just one column (reported by
    Justin Yap).

  o Fix buglet in scatterplotMatrix.formula() when groups specified.

  o Several functions are now generic: avPlots(), ceresPlots(), crPlots(),

  o Enable spread smoothers for crPlot(), ceresPlot(), and residualPlot()
    (suggestion of Dave Armstrong).

  o Small changes to docs.

Changes to Version 3.0-8

  o Import() now defaults to stringsAsFactors=FALSE to match the default
    behavior of read.table() as of R 4.0.0.

  o New strings2factors() function to convert character variables in a data
    frame to factors.

  o Added data.frame method for S().

  o Fixed a bug in estimateTransform.lm() that returned the correct answer
    with an unneeded warning.

  o Fixed Anova.coxph() to handle weights properly (problem reported by
    Daniel Morillo Cuadrado).

Changes to Version 3.0-7

  o Fixed boxCox(), powerTransform() to work when 'car' package is not attached

  o Fixed Anova() to work with "lme" models without an intercept (to \ 
fix bug
    reported by Benjamin Tyner).

Changes to Version 3.0-6

  o Explicitly import utils::globalVariables() (suggestion of Vince Carey).

Changes to Version 3.0-5

  o Change class(x) == "y" to inherits(x, "y") throughout \ 
code (thanks to Martin Maechler).

Changes to Version 3.0-4

  o Scoping improvements to deltaMethod(), which now also takes an optional
    hypothesized value; contribution and suggestion by Pavel Krivitsky.

  o Make Anova() work for coxph() models with strata (following problem
    reported by Susan Galloway Hilsenbeck).

  o Modify carPalette() to provide a colorblind-friendly palette as an option
    (suggestion of Sercan Kahveci).

  o Small improvements.
   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.

   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.

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