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.
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.
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).
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.
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
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.
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.
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 Kutsam).
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 bootCase().
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 error.
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 objects.
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 Kushler).
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 scatterplotMatrix.formula().
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).
