heplot1d: One-Dimensional HE Plots
In heplots: Visualizing Hypothesis Tests in Multivariate Linear Models

heplot1d

R Documentation

One-Dimensional HE Plots

Description

This function plots a 1-dimensional representation of the hypothesis (H) and error (E) sums-of-squares-and-products matrices for terms and linear hypotheses in a multivariate linear model.

Usage

heplot1d(mod, ...)

## S3 method for class 'mlm'
heplot1d(
  mod,
  terms,
  hypotheses,
  term.labels = TRUE,
  hyp.labels = TRUE,
  variables = 1,
  error.ellipse = !add,
  factor.means = !add,
  grand.mean = !add,
  remove.intercept = TRUE,
  type = c("II", "III", "2", "3"),
  idata = NULL,
  idesign = NULL,
  icontrasts = c("contr.sum", "contr.poly"),
  imatrix = NULL,
  iterm = NULL,
  manova,
  size = c("evidence", "effect.size"),
  level = 0.68,
  alpha = 0.05,
  center.pch = "|",
  col = getOption("heplot.colors", c("red", "blue", "black", "darkgreen", "darkcyan",
    "magenta", "brown", "darkgray")),
  lty = 2:1,
  lwd = 1:2,
  xlab,
  main = "",
  xlim,
  axes = TRUE,
  offset.axes = 0.1,
  add = FALSE,
  verbose = FALSE,
  ...
)

Arguments

`mod`	a model object of class `"mlm"`.
`...`	arguments to pass down to `plot`, `text`, and `points`.
`terms`	a logical value or character vector of terms in the model for which to plot hypothesis matrices; if missing or `TRUE`, defaults to all terms; if `FALSE`, no terms are plotted.
`hypotheses`	optional list of linear hypotheses for which to plot hypothesis matrices; hypotheses are specified as for the `linearHypothesis` function in the `car` package; the list elements can be named, in which case the names are used.
`term.labels`	logical value or character vector of names for the terms to be plotted. If `TRUE` (the default) the names of the terms are used; if `FALSE`, term labels are not plotted.
`hyp.labels`	logical value or character vector of names for the hypotheses to be plotted. If `TRUE` (the default) the names of components of the list of hypotheses are used; if `FALSE`, hypothesis labels are not plotted.
`variables`	indices or names of the two response variables to be plotted; defaults to `1:2`.
`error.ellipse`	if `TRUE`, plot the error ellipse; defaults to `TRUE`, if the argument `add` is `FALSE` (see below).
`factor.means`	logical value or character vector of names of factors for which the means are to be plotted, or `TRUE` or `FALSE`; defaults to `TRUE`, if the argument `add` is `FALSE` (see below).
`grand.mean`	if `TRUE`, plot the centroid for all of the data; defaults to `TRUE`, if the argument `add` is `FALSE` (see below).
`remove.intercept`	if `TRUE` (the default), do not plot the ellipse for the intercept even if it is in the MANOVA table.
`type`	“type” of sum-of-squares-and-products matrices to compute; one of `"II"`, `"III"`, `"2"`, or `"3"`, where `"II"` is the default (and `"2"` is a synonym).
`idata`	an optional data frame giving a factor or factors defining the intra-subject model for multivariate repeated-measures data. See Details of `Anova` for an explanation of the intra-subject design and for further explanation of the other arguments relating to intra-subject factors.
`idesign`	a one-sided model formula using the “data” in idata and specifying the intra-subject design for repeated measure models.
`icontrasts`	names of contrast-generating functions to be applied by default to factors and ordered factors, respectively, in the within-subject “data”; the contrasts must produce an intra-subject model matrix in which different terms are orthogonal. The default is c("contr.sum", "contr.poly").
`imatrix`	In lieu of `idata` and `idesign`, you can specify the intra-subject design matrix directly via `imatrix`, in the form of list of named elements. Each element gives the columns of the within-subject model matrix for an intra-subject term to be tested, and must have as many rows as there are responses; the columns of the within-subject model matrix for different terms must be mutually orthogonal.
`iterm`	For repeated measures designs, you must specify one intra-subject term (a character string) to select the SSPE (E) matrix used in the HE plot. Hypothesis terms plotted include the `iterm` effect as well as all interactions of `iterm` with `terms`.
`manova`	optional `Anova.mlm` object for the model; if absent a MANOVA is computed. Specifying the argument can therefore save computation in repeated calls.
`size`	how to scale the hypothesis ellipse relative to the error ellipse; if `"evidence"`, the default, the scaling is done so that a “significant” hypothesis ellipse extends outside of the error ellipse; if `"effect.size"`, the hypothesis ellipse is on the same scale as the error ellipse.
`level`	equivalent coverage of ellipse for normally-distributed errors, defaults to `0.68`.
`alpha`	significance level for Roy's greatest-root test statistic; if `size="evidence"`, then the hypothesis ellipse is scaled so that it just touches the error ellipse at the specified alpha level; a larger hypothesis ellipse therefore indicates statistical significance; defaults to `0.05`.
`center.pch`	character to use in plotting the centroid of the data; defaults to `"\|"`.
`col`	a color or vector of colors to use in plotting ellipses; the first color is used for the error ellipse; the remaining colors — recycled as necessary — are used for the hypothesis ellipses. A single color can be given, in which case it is used for all ellipses. For convenience, the default colors for all heplots produced in a given session can be changed by assigning a color vector via `options(heplot.colors =c(...)`. Otherwise, the default colors are `c("red", "blue", "black", "darkgreen", "darkcyan", "magenta", "brown", "darkgray")`.
`lty`	vector of line types to use for plotting the ellipses; the first is used for the error ellipse, the rest — possibly recycled — for the hypothesis ellipses; a single line type can be given. Defaults to `2:1`.
`lwd`	vector of line widths to use for plotting the ellipses; the first is used for the error ellipse, the rest — possibly recycled — for the hypothesis ellipses; a single line width can be given. Defaults to `1:2`.
`xlab`	x-axis label; defaults to name of the x variable.
`main`	main plot label; defaults to `""`.
`xlim`	x-axis limits; if absent, will be computed from the data.
`axes`	Whether to draw the x, y axes; defaults to `TRUE`
`offset.axes`	proportion to extend the axes in each direction if computed from the data; optional.
`add`	if `TRUE`, add to the current plot; the default is `FALSE`. If `TRUE`, the error ellipse is not plotted.
`verbose`	if `TRUE`, print the MANOVA table and details of hypothesis tests; the default is `FALSE`.

Details

In particular, for a given response, the 1-D representations of H and E matrices correspond to line segments. The E “ellipse” is shown as a filled rectangle whose width equals the mean squared error for that response. The H “ellipse” for each model term is shown as a line segment whose length represents either the size of the effect or the evidence for that effect.

This version is an initial sketch. Details of the implementation are subject to change.

Value

The function invisibly returns an object of class "heplot1d", with coordinates for the various hypothesis ellipses and the error ellipse, and the limits of the horizontal and vertical axes. (No methods for manipulating these objects are currently available.)

The components are:

`H`	ranges for the hypothesis terms
`E`	range for E
`xlim`	x-axis limits

Author(s)

Michael Friendly

Examples


## Plastics data
plastic.mod <- lm(cbind(tear, gloss, opacity) ~ rate*additive, data=Plastic)
heplot1d(plastic.mod, col=c("pink","blue"))
heplot1d(plastic.mod, col=c("pink","blue"),variables=2)
heplot1d(plastic.mod, col=c("pink","blue"),variables=3)

## Bees data
bees.mod <- lm(cbind(Iz,Iy) ~ caste*treat*time, data=Bees)
heplot1d(bees.mod)
heplot1d(bees.mod, variables=2)

heplots documentation built on May 29, 2024, 9:24 a.m.