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"
error.
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
crPlot3d().
o More flexible recode()/Recode().
o Added Anova.svycoxph() to prevent selection of test.statistic="LR".
o New take on vif.lm().
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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
install.packages("rio")
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
Cheun).
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.
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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
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2021-10-07 16:28:36 by Nia Alarie | Files touched by this commit (458) |
Log message:
math: Remove SHA1 hashes for distfiles
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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
linearHypothesis().
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" \
methods,
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.
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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 \
deltaMethod().
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).
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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(),
mcPlots().
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.
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2019-08-08 21:53:58 by Brook Milligan | Files touched by this commit (189) |  |
Log message:
Update all R packages to canonical form.
The canonical form [1] of an R package Makefile includes the
following:
- 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/2019/08/02/msg021711.html
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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) |  |
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.
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