NEWS

heplots 1.7.4

added plotting all X vs all Y to Rohwer doc
added schoolsites dataset
cqplot() now prints a warning if there are missing cases and also returns the upper tail p-values corresponding to Mahalanobis $D^2$.
Default method.id in cqplot() changed to "r", to identify points with the largest $D^2$.

heplots 1.7.3 (2024-12-22)

This is a moderate update, adding new functionality

leveneTests() gains formula and lm methods
bartlettTests() gains formula and lm methods
colDevs() gains a group.var argument; examples extended
Added uniStats() for an anova version of glance.mlm()
Corrected documentation of covEllipses() to more accurately describe recycling of arguments.
size="significance" now allowed as a synonym for size="evidence" in heplot functions.

heplots 1.7.2

Fixed bug in ellipse.axes() re center/centre
ellipse.axes() gains a type argument to draw lines or arrows
ellipse.axes() gains a extend argument to extend/shrink the axes

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.