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New datasets, traceCI(), standardized coefficients, and 3D heplots

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@friendly friendly released this 13 Sep 16:40
· 41 commits to master since this release

Version 1.8.5

  • Added the LearnDis dataset (Tabachnick & Fidell, 2013, Table 7.1): a small
    3 (Disability: Mild/Moderate/Severe) x 2 (Treatment/Control) factorial giving
    reading (WRAT_R) and arithmetic (WRAT_A) achievement scores and IQ, for
    worked MANOVA/MANCOVA examples and, in particular, a citable, hand-checkable
    example for the Roy-Bargmann stepdown analysis under development. Its
    Disability factor is ordered (Mild < Moderate < Severe).

  • Added the ReadingDisability dataset: 571 children classified into four
    reading-achievement groups (Severe/Mild/Average/Superior, an ordered
    factor) on six cognitive/achievement measures (PPVT, RD, EF, VF,
    VMI, SIM). Reconstructed by simulation from the group means, SDs, and
    pooled within-cells correlations in Bray & Maxwell (1985, Multivariate
    Analysis of Variance
    , Table 2.3).

  • Added traceCI(): analytic (Bai & Silverstein, 2004) confidence intervals
    for the trace (sum of eigenvalues) of one or more covariance matrices,
    complementing logdetCI() and eigstatCI().

  • Added stdmodel() and stdcoef() for standardized ("beta") coefficients on
    lm/mlm objects: responses and numeric predictors are standardized, factor
    predictors are left raw. coefplot.mlm() gains a std = TRUE argument using
    this to plot standardized-coefficient confidence ellipses.

  • Added a live heplot3d() example to the HE_manova vignette's MockJury
    section (ratings on phyattr, independent, and sophisticated), shown as
    a rotatable, zoomable 3D widget.

Maintenance

  • Clarified the coefplot.mlm() documentation to explain how it differs from
    car::confidenceEllipse()'s mlm method: coefplot() fixes a pair of
    responses as plot axes and overlays one ellipse per predictor, while
    confidenceEllipse() fixes a pair of coefficients and shows their joint
    confidence region.

  • Added an explicit rgl::rglwidget() call to heplot3d()'s example, so its
    pkgdown reference page shows an interactive 3D plot instead of nothing.
    rgl's automatic pkgdown widget support only fires for a visibly-returned
    object of class rglId/rglOpen3d; heplot3d() returns a different class
    invisibly, so nothing triggered it without this explicit call.

  • Calling rgl::rglwidget() directly in a bookdown-based, as_is vignette
    (like HE_manova's new example above) renders fine in a standalone vignette
    build but shows as a blank box on the pkgdown site: pkgdown replaces the
    <head> of the article page when assembling it, silently dropping the
    <script> tags the widget needs. The fix -- pre-rendering the widget to a
    self-contained file and embedding it with an <iframe> instead -- is
    documented in heplot3d()'s @details for reuse in other vignettes.

  • Fixed math rendering on the pkgdown site for all four as_is vignettes
    (HE_manova, HE_mmra, Robust, datasets): _pkgdown.yml never
    configured a math renderer, so $...$ expressions showed as literal text
    instead of typeset equations. Configured KaTeX (matching the working setup
    already used in the matlib package) after finding that MathJax's CDN
    bundle doesn't support \boldsymbol, needed for bold Greek letters like
    \boldsymbol{\beta} (\mathbf{} only covers Roman symbols, not Greek).

  • Bare/dollar-math H/E references to the hypothesis and error matrices (in
    heplot(), heplot1d(), heplot3d(), pairs.mlm(), etasq(), and the
    package overview) are now \eqn{\mathbf{H}}{H}/\eqn{\mathbf{E}}{E} -- the
    earlier $\mathbf{H}$ form isn't valid Rd and rendered as mangled literal
    text in plain ?fun help.

  • Modernized roxygen documentation across R/: legacy Rd macros (\code{},
    \link{}/\link[pkg]{}, \pkg{}, \emph{}) converted to markdown syntax
    in 44 files, fixing two pre-existing broken links (missing-backslash typos)
    and two stale rgl link targets found along the way.

  • Reorganized vignette assets: images and figures moved from vignettes/fig/
    to vignettes/images/, and four orphaned, unreferenced 2017-era images
    removed.

  • Dropped the hard Depends: broom for glance.mlm(); now Imports: generics
    (the lightweight package defining the glance generic, which broom itself
    depends on) instead, with broom moved to Suggests. glance() still works
    the same as before with just library(heplots).