NEWS

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heplots 1.7.1 (2024-11-24)

This is a modest update, adding two new datasets for simple examples and a PDF vignette

• Extended the "datasets" vignette with further description of how this was done.
• Added dogfood and oral datasets, both simple MANOVA examples.
• Added HE Plots for Repeated Measures Designs vignette
• Fixed nits from URLs vanished or moved

heplots 1.7.0 (2024-05-02)

This is a semi-major release, primarily documenting all datasets in the package with @concept tags. It also adds new datasets and fixes bugs and documentation errors since the last CRAN release (v 1.6.2)

• Added a new example (AddHealth data) to the HE_manova vignette
• Added Overdose data, a simple MMRA example.
• All datasets now classified by @concept tags in documentation, giving the primary methods ("MANOVA", "MMRA", "repeated", ...) that they illustrate. These supplement @keyword tags and appear in the index of the package documentation.
• A new vignette (datasets) lists the datasets in the package, classified by these @concept tags.

heplots 1.6.3

• Correct documentation error in cqplot()
• cqplot() now returns DSQ values for identified points
• Fixed small buglet re: labeling of hypothesis ellipses in heplot()

heplots 1.6.2 (2024-02-15)

• Add peng dataset, a version of palmerpenguins::penguins
• Correct documentation problems from Roxygen 7.3.1 (@docType)

heplots 1.6.1

• add warning to label.ellipse() if length(label.pos) > 1
• fixed label.pos in coefplot.mlm()
• add ellipse.axes() to draw axes of a covariance ellipse
• add ellipse.box() to draw conjugate axes of a covariance ellipse

heplots 1.6.0 (2023-09-05)

• converted pkg to roxygen documentation
• now Suggests: car rather than Depends:
• fix CITATION authors

heplots 1.5.0

• covEllipses() gains a formula method
• Internal function ellipsoid() used in heplot3d() becomes an (experimental) exported function, Ellipsoid()

heplots 1.4-3

• replace rgl.pop() with pop3D (PR #7); thx: D. Murdoch

heplots 1.4-2 (2022-10-19)

• Fix CITATION

heplots 1.4-1 (2022-10-01)

• (Ugh) broom becomes a Depend: so as not to override broom::glance()

heplots 1.4-0

• Added Iwasaki_Big_Five data [Thx: James Grice]
• Added cex.label arg to heplot3d()
• Convert old Rnw vignettes to Rmd
• Fix documentation infelicities
• Added TIPI data
• Added glance.mlm() as an extension of broom::glance.lm()

heplots 1.3-9 (2021-10-06)

• Fix potential problem with URL links to JSS articles, now converted to DOIs

heplots 1.3-8 (2021-01-21)

• fix CRAN nit re rgl in examples

heplots 1.3-7 (2020-10-28)

• Fix rendering of 3D heplots [Thx: Duncan Murdoch]
• Fix URLs

heplots 1.3-6

• add mathscore data
• fix bug in etasq.lm() per #1 [thx: Phil Chalmers]
• bump pkg version
• remove Suggests: FRB

heplots 1.3-5 (2018-04-03)

• fix references to car datasets -> carData
• fix error resulting from car 3.0 changes
• bump pkg version

heplots 1.3-4 (2017-09-15)

• Added Diabetes data, a nice example of heterogeneity of covariances

heplots 1.3-3 (2016-10-21)

• Added Parenting data, a simple one-way MANOVA design (used in TQMP paper)
• Prepare for CRAN release

heplots 1.3-1 (2016-06-14)

• added plot.robmlm(), a plot method for "robmlm" objects. Currently, it plots the weights given to observations in the last iteration as an index plot.
• Re-built vignettes

heplots 1.3-0 (2016-06-04)

• In cqplot, pch, col, and cex can now be vectors
• Bump version, prepare for release

heplots 1.2-1

• in coefplot.mlm(), now pass label.pos to label.ellipse()
• added Mahalanobis() for classical and robust squared distances; handles missing data gracefully and provides a confidence envelope
• added SocialCog data [Thx: Leah Hartman]
• added cqplot() of Mahalanobis distances as a plot method for an mlm and for multivariate data

heplots 1.2-0 (2016-05-19)

• covEllipses() extended to more than two variables, giving a scatterplot matrix plot
• plot.boxM() now can plot other measures of the eigenvalues of the covariance matrices, useful for understanding the properties of the test.
• added bartlettTests() for a collection of univariate Bartlett tests
• added leveneTests() for a collection of univariate Levene tests
• added NeuroCog data, a simple one-way MANOVA [Thx: Leah Hartman]
• label.ellipse() now uses a much more flexible label.pos argument for positioning the text labels used in heplot() and friends.

heplots 1.1-0 (2016-03-26)

• Added boXM from biotools
• Fleshed out boxM() with formula, lm, plot and summary methods
• added plot.boxM() method
• Added covEllipses() methods for plotting (possibly robust) covariance ellipses
• Added colDevs() as a utility and for use in other multivariate tests.
• Added data(AddHealth), a simple example of a one-way MANOVA with nice views [thx: Russell Warne]
• summary.boxM() now returns the calculated statistics and can be used to construct other kinds of plots.
• plot.boxM() gets a gplabel argument to provide a label for the group factor
• pairs.mlm() gets a var.cex argument to control size of variable labels
• Added logdetCI() for confidence intervals on log determinants of covariance matrices (experimental)
• Now use logdetCI() in plot.boxM()

heplots 1.0-16 (2015-07-13)

• use importsFrom for base packages

heplots 1.0-15 (2015-04-18)

• Fix require -> requireNamespace

heplots 1.0-14

• Updated broken urls in documentation
• Removed vcov.mlm from exports to conform to CRAN policies
• Now use rgl:: for rgl functions in *3d.R
• Removed robmlm.default, robmlm.formula from exports
• Imports: rgl

heplots 1.0-12 (2014-07-02)

• Removed Authors: to satisfy CRAN nits
• Fixed doc for Hernior.Rd
• Now importsFrom(MASS) rather than Depends:

heplots 1.0-11 (2013-08-21)

• Cosmetic changes to pass CRAN checks
• For R 3.1.0, revised vcov.mlm() to avoid calling summary.mlm() directly
• fixed long lines in .Rd files for R 3.0.1 checks
• removed require() calls for MASS & car (Depends:)
• removed ::: calls to car and stats

heplots 1.0-10

• Added demo/HE-other.R, exploring other representations of HE plots

heplots 1.0-9

• Added Pottery2 data, extending car::Pottery
• Fixed heplot3d to minimize striated rendering of ellipsoids, and also modified default colors and fill.alpha

heplots 1.0-8 (2013-04-11)

• In heplot.mlm(), added ... to label.ellipse to be able to pass cex=
• Added NLSY data with examples of testing linearHypotheses
• In heplot3d(), rgl.* functions replaced with *3d() equivalents
• Extended gsorth description and examples

heplots 1.0-7 (2013-02-08)

• Made some heplot3d() examples \dontrun{} to reduce example execution time to satisfy CRAN nits

heplots 1.0-6

• Added label.ellipse() as a more general exported function.
• heplot() gets a label.pos= argument allowing more flexible labeling, with the label position to be specified (bottom, left, top, right or center)
• Added coefplot S3 generic and a coefplot.mlm method to plot ellipses for mlm coefficients. This generalizes car::confidenceEllipse to the mlm setting.

heplots 1.0-4

• Added interpPlot for plotting interpolations between two data sets, with data ellipses, etc. Main use for this is in animated demos of multivariate statistical concepts.
• interpPlot gains add=, points= and col= arguments for greater control of graphical parameters.

heplots 1.0-2 (2012-12-17)

• Added Schooldata and further example of comparison of mlm with robmlm()

heplots 1.0-1

• Added simple robmlm methods for robust MLMss with print and summary methods and a vcov.mlm method. This allows heplot() and related methods to show robust HE plots.

heplots 1.0-0 (2012-08-08)

• Added Olso data
• Corrected error in demo/OBK.R

heplots 0.9-13

• Extended HE-examples vignette with example based on SocGrades data

heplots 0.9-12 (2012-05-17)

• Added Skulls data
• Extended HE-examples vignette with example based on Skulls data
• Changed the default colors for heplot() and heplot1d() to allow global setting of options("heplot.colors"); similarly, heplot3d() now allows a global option for colors, options("heplot3d.colors"), differing only in using pink for error ellipsoid.
• Extended Hernior.Rd examples to show 1D plots in canonical space; added a discussion of this example to HE-examples vignette.
• Extended SocGrades.Rd examples to show plots in canonical space.

heplots 0.9-11 (2012-02-12)

• Added Probe1, Probe2 data sets-- repeated measures design
• Added Sake data

heplots 0.9-10 (2011-10-17)

• Fixed Authors@R in DESCRIPTION for R 2.14.x
• Added var.labels argument to pairs.mlm
• gsorth.R: Made sd() a local function to avoid deprecated warnings

heplots 0.9-9

• Added data(Hernior), another MMRA, cancorr example data set
• Added data(SocGrades), another MANOVA, MMRA, cancorr example data set
• Corrected buglet with fill.alpha in heplot

heplots 0.9-8 (2011-05-21)

• Added an MMRA example to HE-examples vignette
• Added err.label argument to heplot and heplot3d to allow changing the label for the error ellipsoid

heplots 0.9-7

o Added trans.colors() to make colors transparent o Modifications to heplot() for filled ellipses: added fill= and fill.alpha= arguments; replaced lines() with polygon() for H and E ellipses; calculate H.rank to distinguish degenerate ellipses o added last() to utility.R o Modified some examples to show fill=TRUE and use wire=FALSE in heplot3d() o Modified pairs.mlm() to pass fill= and fill.alpha= to heplot() o Updated reference URLs to point to datavis.ca o Fixed buglet in gsorth when matrix has no row/col names [Thx: [email protected]] o Fixed buglet in etasq.lm with partial=FALSE [Thx: [email protected]]

Version 0.9-6 (2010-11-2) o added CITATION to JSS article and references to .Rd files o modified repeated vignette to [nojss]

Version 0.9-5 (2010-10-01) o Added repeated vignette

Version 0.9-4 (2010-07-29) o Minor documentation changes o Added etasq.lm() method o Added data/MockJury - 1-way and 2-way MANOVA, step-down tests, ANCOVA o Generalized termMeans() and exported it o Added HE-examples vignette

Version 0.9-3 (2010-07-27) o Added gsorth() for Gram-Schmidt orthogonalization of a matrix or data frame, preserving column means and standard deviations o Avoid Deprecated warnings (linear.hypothesis) with car2 o Fixed documentation warnings with car2 (linear.hypothesis, data.ellipse)

Version 0.9-2 (2010-02-12) o Added demo/Big5.R - Analysis of scores on the 'Big 5' personality traits for three groups o fixed buglet with text3d causing rgl to crash (thx: Duncan Murdoch) o switched inst/CHANGES to NEWS o Added data/RatWeight and examples - repeated measures on Weight Gain in Rats o Added data/Headache and examples - repeated measures on treatment for headaches o Fixed buglets in heplot, heplot1d, heplot3d regarding number of variables o Added etasq.mlm methods for multivariate measures of association (\eta^2) o Return ellipse radius from heplot, heplot3d

heplots 0.9-1

o heplot.mlm, pairs.mlm, heplot3d.mlm now work for repeated measure designs with only covariates on the rhs. o Implemented heplot1d() for repeated measures designs (untested) o Revised documentation for repeated measures o Added center.cex to heplot.mlm() o Revised mark.H0() to handle 3D plots also o Added Adoption data -- MMreg with repeated measures o Added ReactTime data -- 2 within-S, no between-S factors o Fixed bug with icontrasts o Added markH0 argument to heplot o Added label argument to mark.H0() o Added arrow3d() o Fixed buglet in pairs.mlm (type)

heplots 0.9-0

o Implemented 2D HE plots in heplot.mlm for repeated measures designs by adding idata=, idesign=, icontrasts= arguments.
o imatrix= argument for doubly-multivariate designs implemented, but depends on car 2.0+ o Updated example(OBK) o Updated example(WeightLoss) o Implemented 3D HE plots in heplot3d.mlm for repeated measures designs (OK) o Implemented pairs() for repeated measures designs (OK)

heplots 0.8-11 (2009-12-23)

o Minor fixes to heplot1d o Added contrasts example to RootStock.Rd o Added WeightLoss data -- doubly multivariate o Added mark.H0

heplots 0.8-10 (2009-10-13)

o Fixes to cross-references in .Rd files.

heplots 0.8-9 (2009-07-23)

o Added data(RootStock) o heplot.mlm, heplot3d.mlm now include center in the returned object

heplots 0.8-8

o Added data(FootHead) o Extended example(FootHead)

Version 0.8-7 (2009-04-17) o Initial version of heplot1d o Added data(Bees), demo(bees.contrasts) o Now suggest: effects package

heplots 0.8-6 (2009-04-19)

o Added VocabGrowth data, with an example of heplot() for a repeated measures design o Fixed label.ellipse in heplot.mlm.R to center the label horizontally o Added demo(OBK) o Added axes= to heplot.mlm to fix warnings arising from axes=FALSE in pairs.mlm

heplots 0.8-5 (2009-04-03)

o Minor documentation changes for Rdoc 2 o Michael Friendly as maintainer

heplots 0.8-4 (2008-11-18)

o Documentation additions o added CITATION file

heplots 0.8-3

• Changes to heplot3d.mlm: o added xlim, ylim, zlim arguments

heplots 0.8-2

• Package changes o added suggests: candisc o added utility.R, cross3d.R

• Changes to heplot.mlm: o moved lambda.crit to utility.R o added he.rep to handle common task of repeating HE argument values

• Changes to heplot3d.mlm: o added shade=, shade.alpha=, wire= parameters o fixed: grand.mean=FALSE not respected o replaced sphere at grand.mean with cross3d() o color means according to the color of the term o return bounding boxes of the ellipsoids o replaced rgl.texts with texts3d

• Changes to utility.R: o Generalized lambda.crit to provide Roy.crit and HLT.crit; only Roy.crit is used

heplots 0.8-1 (2008-11-03)

o heplot now passes ... not only to plot() but to calls to text() and points().

heplots 0.8-0 (2007-01-31)

• Initial version released to CRAN.