Description Usage Arguments Details Value References See Also Examples
This function plots ellipsoids in 3D representing the hypothesis and error sums-of-squares-and-products matrices for terms and linear hypotheses in a multivariate linear model.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | heplot3d(mod, ...)
## S3 method for class 'mlm'
heplot3d(mod, terms, hypotheses, term.labels = TRUE,
hyp.labels = TRUE, err.label="Error", variables = 1:3, error.ellipsoid = !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, segments = 40,
col=getOption("heplot3d.colors",
c("red", "blue", "black", "darkgreen",
"darkcyan","magenta", "brown","darkgray")),
lwd=c(1, 4),
shade=TRUE, shade.alpha=0.2, wire=c(TRUE,FALSE),
bg.col = c("white", "black"),
fogtype = c("none", "exp2", "linear", "exp"),
fov = 30, offset = 0.01,
xlab, ylab, zlab, xlim, ylim, zlim,
add = FALSE, verbose = FALSE,
warn.rank = FALSE, ...)
|
mod |
a model object of class |
terms |
a logical value or character vector of terms in the model
for which to plot
hypothesis matrices; if missing or |
hypotheses |
optional list of linear hypotheses for which to plot hypothesis
matrices; hypotheses are specified as for the
|
term.labels |
logical value or character vector of names for the terms to be
plotted. If |
hyp.labels |
logical value or character vector of names for the hypotheses to
be plotted. If |
err.label |
Label for the error ellipse |
variables |
indices or names of the three response variables to be plotted;
defaults to |
error.ellipsoid |
if |
factor.means |
logical value or character vector of names of
factors for which the means
are to be plotted, or |
grand.mean |
if |
remove.intercept |
if |
type |
“type” of sum-of-squares-and-products matrices to compute; one of
|
idata |
an optional data frame giving a factor or factors defining the
intra-subject model for multivariate repeated-measures data.
See Details of |
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 |
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 |
manova |
optional |
size |
how to scale the hypothesis ellipsoid relative to the error
ellipsoid; if |
level |
equivalent coverage of ellipsoid for normally-distributed
errors, defaults to |
alpha |
signficance level for Roy's greatest-root test statistic; if
|
segments |
number of segments composing each elliposid; defaults to
|
col |
a color or vector of colors to use in plotting ellipsoids; the first
color is used for the error ellipsoid; the remaining colors — recycled
as necessary — are used for the hypothesis ellipsoid.
A single color can be given, in which case it is used for all ellipsoid.
For convenience, the default colors for all heplots produced in a given session can be changed
by assigning a color vector via |
lwd |
a two-element vector giving the line width for drawing ellipsoids
(including those that degenerate to an ellipse) and
for drawing ellipsoids that degenerate to a line segment. The default
is |
shade |
a logical scalar or vector, indicating whether the ellipsoids should be
rendered with |
shade.alpha |
a numeric value in the range [0,1], or a vector of such values, giving
the alpha transparency for ellipsoids rendered with |
wire |
a logical scalar or vector, indicating whether the ellipsoids should be
rendered with |
bg.col |
background colour, |
fogtype |
type of “fog” to use for depth-cueing; the default is
|
fov |
field of view angle; controls perspective.
See |
offset |
proportion of axes to off set labels; defaults to
|
xlab |
x-axis label; defaults to name of the x variable. |
ylab |
y-axis label; defaults to name of the y variable. |
zlab |
z-axis label; defaults to name of the z variable. |
xlim |
x-axis limits; if absent, will be computed from the data. |
ylim |
y-axis limits; if absent, will be computed from the data. |
zlim |
z-axis limits; if absent, will be computed from the data. |
add |
if |
verbose |
if |
warn.rank |
if |
... |
arguments passed from generic. |
When the H matrix for a term has rank < 3, the ellipsoid collapses to an ellipse (rank(H)=2) or a line (rank(H)=1).
Rotating the plot can be particularly revealing, showing views in which H variation
is particularly large or small in relation to E variation. See play3d
and movie3d
for details on creating animations.
The arguments xlim
, ylim
, and zlim
can be used to expand the bounding
box of the axes, but cannot decrease it.
heplot3d
invisibly returns a list containing the bounding boxes of the error (E)
ellipsoid and for each term or linear hypothesis specified in the call.
Each of these is a 2 x 3 matrix with rownames "min" and "max" and colnames
corresponding to the variables plotted. An additional component, center
,
contains the coordinates of the centroid in the plot.
The function also leaves an object named
.frame
in the global environment, containing the rgl object IDs for
the axes, axis labels, and bounding box; these are deleted and the axes, etc.
redrawn if the plot is added to.
Friendly, M. (2006). Data Ellipses, HE Plots and Reduced-Rank Displays for Multivariate Linear Models: SAS Software and Examples Journal of Statistical Software, 17(6), 1-42. http://www.jstatsoft.org/v17/i06/
Friendly, M. (2007). HE plots for Multivariate General Linear Models. Journal of Computational and Graphical Statistics, 16(2) 421-444. http://datavis.ca/papers/jcgs-heplots.pdf
Anova
, linearHypothesis
, for details on MANOVA tests and
linear hypotheses
heplot
, pairs.mlm
, for other plotting methods for mlm
objects
rgl-package
, for details about 3D plots with rgl
heplot3d.candisc
for 3D HE plots in canonical space.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # Soils data, from car package
soils.mod <- lm(cbind(pH,N,Dens,P,Ca,Mg,K,Na,Conduc) ~ Block + Contour*Depth, data=Soils)
Anova(soils.mod)
heplot(soils.mod, variables=c("Ca", "Mg"))
pairs(soils.mod, terms="Depth", variables=c("pH", "N", "P", "Ca", "Mg"))
heplot3d(soils.mod, variables=c("Mg", "Ca", "Na"), wire=FALSE)
# Plastic data
plastic.mod <- lm(cbind(tear, gloss, opacity) ~ rate*additive, data=Plastic)
## Not run:
heplot3d(plastic.mod, col=c("red", "blue", "brown", "green3"), wire=FALSE)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.