Package ‘candisc’

October 12, 2022

Type Package
Title Visualizing Generalized Canonical Discriminant and Canonical
Correlation Analysis
Version 0.8-6
Date 2021-10-06
Depends R (>= 3.5.0), car, heplots (>= 0.8-6), graphics, stats
Suggests rgl, corrplot, knitr, rmarkdown, MASS, rpart, rpart.plot
LazyLoad yes
LazyData yes
Author Michael Friendly [aut, cre],
John Fox [aut]
Maintainer Michael Friendly <[email protected]>
Language en-US
Description Functions for computing and visualizing
generalized canonical discriminant analyses and canonical correlation analysis
for a multivariate linear model.
Traditional canonical discriminant analysis is restricted to a one-way 'MANOVA'
design and is equivalent to canonical correlation analysis between a set of quantitative
response variables and a set of dummy variables coded from the factor variable.
The 'candisc' package generalizes this to higher-way 'MANOVA' designs
for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The graphic functions provide low-
rank (1D, 2D, 3D)
visualizations of terms in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Re-
lated plots are
now provided for canonical correlation analysis when all predictors are quantitative.
License GPL (>= 2)
VignetteBuilder knitr
BugReports https://github.com/friendly/candisc/issues
NeedsCompilation no
Repository CRAN
Date/Publication 2021-10-07 17:10:02 UTC

1
2 candisc-package

R topics documented:
candisc-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
cancor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
candisc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
candiscList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
can_lm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
dataIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Grass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
heplot.cancor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
heplot.candisc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
heplot.candiscList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
HSB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
plot.cancor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
redundancy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
varOrder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
vecscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Wilks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Wine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Wolves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Index 38

candisc-package Visualizing Generalized Canonical Discriminant and Canonical Cor-

relation Analysis

Description
This package includes functions for computing and visualizing generalized canonical discriminant
analyses and canonical correlation analysis for a multivariate linear model. The goal is to provide
ways of visualizing such models in a low-dimensional space corresponding to dimensions (linear
combinations of the response variables) of maximal relationship to the predictor variables.
Traditional canonical discriminant analysis is restricted to a one-way MANOVA design and is
equivalent to canonical correlation analysis between a set of quantitative response variables and
a set of dummy variables coded from the factor variable. The candisc package generalizes this
to multi-way MANOVA designs for all terms in a multivariate linear model (i.e., an mlm object),
computing canonical scores and vectors for each term (giving a candiscList object).
The graphic functions are designed to provide low-rank (1D, 2D, 3D) visualizations of terms in
a mlm via the plot.candisc method, and the HE plot heplot.candisc and heplot3d.candisc
methods. For mlms with more than a few response variables, these methods often provide a much
simpler interpretation of the nature of effects in canonical space than heplots for pairs of responses
or an HE plot matrix of all responses in variable space.
Analogously, a multivariate linear (regression) model with quantitative predictors can also be rep-
resented in a reduced-rank space by means of a canonical correlation transformation of the Y and X
candisc-package 3

variables to uncorrelated canonical variates, Ycan and Xcan. Computation for this analysis is pro-
vided by cancor and related methods. Visualization of these results in canonical space are provided
by the plot.cancor, heplot.cancor and heplot3d.cancor methods.
These relations among response variables in linear models can also be useful for “effect ordering”
(Friendly & Kwan (2003) for variables in other multivariate data displays to make the displayed
relationships more coherent. The function varOrder implements a collection of these methods.
A new vignette, vignette("diabetes", package="candisc"), illustrates some of these methods.
A more comprehensive collection of examples is contained in the vignette for the heplots package,
vignette("HE-examples", package="heplots").

Details

Package: candisc
Type: Package
Version: 0.8-6
Date: 2021-10-06
License: GPL (>= 2)

The organization of functions in this package and the heplots package may change in a later version.

Author(s)
Michael Friendly and John Fox
Maintainer: Michael Friendly <[email protected]>

References
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
Friendly, M. & Kwan, E. (2003). Effect Ordering for Data Displays, Computational Statistics and
Data Analysis, 43, 509-539. doi: 10.1016/S01679473(02)002906
Friendly, M. & Sigal, M. (2014). Recent Advances in Visualizing Multivariate Linear Models.
Revista Colombiana de Estadistica , 37(2), 261-283. doi: 10.15446/rce.v37n2spe.47934.
Friendly, M. & Sigal, M. (2017). Graphical Methods for Multivariate Linear Models in Psy-
chological Research: An R Tutorial, The Quantitative Methods for Psychology, 13 (1), 20-45.
doi: 10.20982/tqmp.13.1.p020.
Gittins, R. (1985). Canonical Analysis: A Review with Applications in Ecology, Berlin: Springer.

See Also
heplot for details about HE plots.
candisc, cancor for details about canonical discriminant analysis and canonical correlation analy-
sis.
4 cancor

cancor Canonical Correlation Analysis

Description
The function cancor generalizes and regularizes computation for canonical correlation analysis in
a way conducive to visualization using methods in the heplots package.

Usage

cancor(x, ...)

## S3 method for class 'formula'

cancor(formula, data, subset, weights, na.rm=TRUE, method = "gensvd", ...)

## Default S3 method:
cancor(x, y, weights,
X.names = colnames(x), Y.names = colnames(y),
row.names = rownames(x),
xcenter = TRUE, ycenter = TRUE, xscale = FALSE, yscale = FALSE,
ndim = min(p, q),
set.names = c("X", "Y"),
prefix = c("Xcan", "Ycan"),
na.rm = TRUE, use = if (na.rm) "complete" else "pairwise",
method = "gensvd",
...
)

## S3 method for class 'cancor'

print(x, digits = max(getOption("digits") - 2, 3), ...)

## S3 method for class 'cancor'

summary(object, digits = max(getOption("digits") - 2, 3), ...)

## S3 method for class 'cancor'

coef(object, type = c("x", "y", "both", "list"), standardize=FALSE, ...)

scores(x, ...)

## S3 method for class 'cancor'

scores(x, type = c("x", "y", "both", "list", "data.frame"), ...)

Arguments
formula A two-sided formula of the form cbind(y1, y2, y3, ...) ~ x1 + x2 + x3 + ...
cancor 5

data The data.frame within which the formula is evaluated

subset an optional vector specifying a subset of observations to be used in the calcula-
tions.
weights Observation weights. If supplied, this must be a vector of length equal to the
number of observations in X and Y, typically within [0,1]. In that case, the
variance-covariance matrices are computed using cov.wt, and the number of
observations is taken as the number of non-zero weights.
na.rm logical, determining whether observations with missing cases are excluded in the
computation of the variance matrix of (X,Y). See Notes for details on missing
data.
method the method to be used for calculation; currently only method = "gensvd" is sup-
ported;
x Varies depending on method. For the cancor.default method, this should be
a matrix or data.frame whose columns contain the X variables
y For the cancor.default method, a matrix or data.frame whose columns contain
the Y variables
X.names, Y.names
Character vectors of names for the X and Y variables.
row.names Observation names in x, y
xcenter, ycenter
logical. Center the X, Y variables? [not yet implemented]
xscale, yscale logical. Scale the X, Y variables to unit variance? [not yet implemented]
ndim Number of canonical dimensions to retain in the result, for scores, coefficients,
etc.
set.names A vector of two character strings, giving names for the collections of the X, Y
variables.
prefix A vector of two character strings, giving prefixes used to name the X and Y
canonical variables, respectively.
use argument passed to var determining how missing data are handled. Only the
default, use="complete" is allowed when observation weights are supplied.
object A cancor object for related methods.
digits Number of digits passed to print and summary methods
... Other arguments, passed to methods
type For the coef method, the type of coefficients returned, one of "x", "y", "both".
For the scores method, the same list, or "data.frame", which returns a data.frame
containing the X and Y canonical scores.
standardize For the coef method, whether coefficients should be standardized by dividing
by the standard deviations of the X and Y variables.

Details
Canonical correlation analysis (CCA), as traditionally presented is used to identify and measure
the associations between two sets of quantitative variables, X and Y. It is often used in the same
6 cancor

situations for which a multivariate multiple regression analysis (MMRA) would be used. However,
CCA is is “symmetric” in that the sets X and Y have equivalent status, and the goal is to find
orthogonal linear combinations of each having maximal (canonical) correlations. On the other hand,
MMRA is “asymmetric”, in that the Y set is considered as responses, each one to be explained by
separate linear combinations of the Xs.
This implementation of cancor provides the basic computations for CCA, together with some ex-
tractor functions and methods for working with the results in a convenient fashion.
However, for visualization using HE plots, it is most natural to consider plots representing the re-
lations among the canonical variables for the Y variables in terms of a multivariate linear model
predicting the Y canonical scores, using either the X variables or the X canonical scores as pre-
dictors. Such plots, using heplot.cancor provide a low-rank (1D, 2D, 3D) visualization of the
relations between the two sets, and so are useful in cases when there are more than 2 or 3 variables
in each of X and Y.
The connection between CCA and HE plots for MMRA models can be developed as follows. CCA
can also be viewed as a principal component transformation of the predicted values of one set of
variables from a regression on the other set of variables, in the metric of the error covariance matrix.
For example, regress the Y variables on the X variables, giving predicted values Ŷ = X(X 0 X)−1 X 0 Y
and residuals R = Y − Ŷ . The error covariance matrix is E = R0 R/(n − 1). Choose a trans-
formation Q that orthogonalizes the error covariance matrix to an identity, that is, (RQ)0 (RQ) =
Q0 R0 RQ = (n − 1)I, and apply the same transformation to the predicted values to yield, say,
Z = Ŷ Q. Then, a principal component analysis on the covariance matrix of Z gives eigenvalues of
E −1 H, and so is equivalent to the MMRA analysis of lm(Y ~ X) statistically, but visualized here in
canonical space.

Value
An object of class cancorr, a list with the following components:
cancor Canonical correlations, i.e., the correlations between each canonical variate for
the Y variables with the corresponding canonical variate for the X variables.
names Names for various items, a list of 4 components: X, Y, row.names, set.names
ndim Number of canonical dimensions extracted, <= min(p,q)
dim Problem dimensions, a list of 3 components: p (number of X variables), q (num-
ber of Y variables), n (sample size)
coef Canonical coefficients, a list of 2 components: X, Y

scores Canonical variate scores, a list of 2 components:

X Canonical variate scores for the X variables
Y Canonical variate scores for the Y variables
X The matrix X
Y The matrix Y
weights Observation weights, if supplied, else NULL

structure Structure correlations ("loadings"), a list of 4 components:

X.xscores Structure correlations of the X variables with the Xcan canonical
scores
cancor 7

Y.xscores Structure correlations of the Y variables with the Xcan canonical

scores
X.yscores Structure correlations of the X variables with the Ycan canonical
scores
Y.yscores Structure correlations of the Y variables with the Ycan canonical
scores
The formula method also returns components call and terms

Note
Not all features of CCA are presently implemented: standardized vs. raw scores, more flexible
handling of missing data, other plot methods, ...

Author(s)
Michael Friendly

References
Gittins, R. (1985). Canonical Analysis: A Review with Applications in Ecology, Berlin: Springer.
Mardia, K. V., Kent, J. T. and Bibby, J. M. (1979). Multivariate Analysis. London: Academic Press.

See Also
Other implementations of CCA: cancor (very basic), cca in the yacca (fairly complete, but very
messy return structure), cc in CCA (fairly complete, very messy return structure, no longer main-
tained).
redundancy, for redundancy analysis; plot.cancor, for enhanced scatterplots of the canonical
variates.
heplot.cancor for CCA HE plots and heplots for generic heplot methods.
candisc for related methods focused on multivariate linear models with one or more factors among
the X variables.

Examples
data(Rohwer, package="heplots")
X <- as.matrix(Rohwer[,6:10]) # the PA tests
Y <- as.matrix(Rohwer[,3:5]) # the aptitude/ability variables

# visualize the correlation matrix using corrplot()

if (require(corrplot)) {
M <- cor(cbind(X,Y))
corrplot(M, method="ellipse", order="hclust", addrect=2, addCoef.col="black")
}

(cc <- cancor(X, Y, set.names=c("PA", "Ability")))

## Canonical correlation analysis of:

8 cancor

## 5 PA variables: n, s, ns, na, ss

## with 3 Ability variables: SAT, PPVT, Raven
##
## CanR CanRSQ Eigen percent cum scree
## 1 0.6703 0.44934 0.81599 77.30 77.30 ******************************
## 2 0.3837 0.14719 0.17260 16.35 93.65 ******
## 3 0.2506 0.06282 0.06704 6.35 100.00 **
##
## Test of H0: The canonical correlations in the
## current row and all that follow are zero
##
## CanR WilksL F df1 df2 p.value
## 1 0.67033 0.44011 3.8961 15 168.8 0.000006
## 2 0.38366 0.79923 1.8379 8 124.0 0.076076
## 3 0.25065 0.93718 1.4078 3 63.0 0.248814

# formula method
cc <- cancor(cbind(SAT, PPVT, Raven) ~ n + s + ns + na + ss, data=Rohwer,
set.names=c("PA", "Ability"))

# using observation weights

set.seed(12345)
wts <- sample(0:1, size=nrow(Rohwer), replace=TRUE, prob=c(.05, .95))
(ccw <- cancor(X, Y, set.names=c("PA", "Ability"), weights=wts) )

# show correlations of the canonical scores

zapsmall(cor(scores(cc, type="x"), scores(cc, type="y")))

# standardized coefficients
coef(cc, type="both", standardize=TRUE)

plot(cc, smooth=TRUE)

##################
data(schooldata)
##################

#fit the MMreg model

school.mod <- lm(cbind(reading, mathematics, selfesteem) ~
education + occupation + visit + counseling + teacher, data=schooldata)
Anova(school.mod)
pairs(school.mod)

# canonical correlation analysis

school.cc <- cancor(cbind(reading, mathematics, selfesteem) ~
education + occupation + visit + counseling + teacher, data=schooldata)
school.cc
heplot(school.cc, xpd=TRUE, scale=0.3)
candisc 9

candisc Canonical discriminant analysis

Description
candisc performs a generalized canonical discriminant analysis for one term in a multivariate linear
model (i.e., an mlm object), computing canonical scores and vectors. It represents a transformation
of the original variables into a canonical space of maximal differences for the term, controlling for
other model terms.
In typical usage, the term should be a factor or interaction corresponding to a multivariate test with
2 or more degrees of freedom for the null hypothesis.

Usage
candisc(mod, ...)

## S3 method for class 'mlm'

candisc(mod, term, type = "2", manova, ndim = rank, ...)

## S3 method for class 'candisc'

coef(object, type = c("std", "raw", "structure"), ...)

## S3 method for class 'candisc'

plot(x, which = 1:2, conf = 0.95, col, pch, scale, asp = 1,
var.col = "blue", var.lwd = par("lwd"), var.labels, var.cex = 1, var.pos,
rev.axes=c(FALSE, FALSE),
ellipse=FALSE, ellipse.prob = 0.68, fill.alpha=0.1,
prefix = "Can", suffix=TRUE,
titles.1d = c("Canonical scores", "Structure"),
points.1d = FALSE, ...)

## S3 method for class 'candisc'

print(x, digits=max(getOption("digits") - 2, 3), LRtests=TRUE, ...)

## S3 method for class 'candisc'

summary(object, means = TRUE, scores = FALSE, coef = c("std"),
ndim, digits = max(getOption("digits") - 2, 4), ...)

Arguments
mod An mlm object, such as computed by lm() with a multivariate response
term the name of one term from mod for which the canonical analysis is performed.
type type of test for the model term, one of: "II", "III", "2", or "3"
manova the Anova.mlm object corresponding to mod. Normally, this is computed inter-
nally by Anova(mod)
10 candisc

ndim Number of dimensions to store in (or retrieve from, for the summary method) the
means, structure, scores and coeffs.* components. The default is the rank
of the H matrix for the hypothesis term.
object, x A candisc object
which A vector of one or two integers, selecting the canonical dimension(s) to plot. If
the canonical structure for a term has ndim==1, or length(which)==1, a 1D
representation of canonical scores and structure coefficients is produced by the
plot method. Otherwise, a 2D plot is produced.
conf Confidence coefficient for the confidence circles around canonical means plotted
in the plot method
col A vector of the unique colors to be used for the levels of the term in the plot
method, one for each level of the term. In this version, you should assign col-
ors and point symbols explicitly, rather than relying on the somewhat arbitrary
defaults, based on palette
pch A vector of the unique point symbols to be used for the levels of the term in the
plot method.
scale Scale factor for the variable vectors in canonical space. If not specified, a scale
factor is calculated to make the variable vectors approximately fill the plot space.
asp Aspect ratio for the plot method. The asp=1 (the default) assures that the units
on the horizontal and vertical axes are the same, so that lengths and angles of
the variable vectors are interpretable.
var.col Color used to plot variable vectors
var.lwd Line width used to plot variable vectors
var.labels Optional vector of variable labels to replace variable names in the plots
var.cex Character expansion size for variable labels in the plots
var.pos Position(s) of variable vector labels wrt. the end point. If not specified, the
labels are out-justified left and right with respect to the end points.
rev.axes Logical, a vector of length(which). TRUE causes the orientation of the canoni-
cal scores and structure coefficients to be reversed along a given axis.
ellipse Draw data ellipses for canonical scores?
ellipse.prob Coverage probability for the data ellipses
fill.alpha Transparency value for the color used to fill the ellipses. Use fill.alpha to
draw the ellipses unfilled.
prefix Prefix used to label the canonical dimensions plotted
suffix Suffix for labels of canonical dimensions. If suffix=TRUE the percent of hy-
pothesis (H) variance accounted for by each canonical dimension is added to the
axis label.
titles.1d A character vector of length 2, containing titles for the panels used to plot the
canonical scores and structure vectors, for the case in which there is only one
canonical dimension.
points.1d Logical value for plot.candisc when only one canonical dimension.
means Logical value used to determine if canonical means are printed
candisc 11

scores Logical value used to determine if canonical scores are printed

coef Type of coefficients printed by the summary method. Any one or more of "std",
"raw", or "structure"
digits significant digits to print.
LRtests logical; should likelihood ratio tests for the canonical dimensions be printed?
... arguments to be passed down. In particular, type="n" can be used with the plot
method to suppress the display of canonical scores.

Details
Canonical discriminant analysis is typically carried out in conjunction with a one-way MANOVA
design. It represents a linear transformation of the response variables into a canonical space in
which (a) each successive canonical variate produces maximal separation among the groups (e.g.,
maximum univariate F statistics), and (b) all canonical variates are mutually uncorrelated. For a
one-way MANOVA with g groups and p responses, there are dfh = min( g-1, p) such canonical
dimensions, and tests, initially stated by Bartlett (1938) allow one to determine the number of
significant canonical dimensions.
Computational details for the one-way case are described in Cooley & Lohnes (1971), and in the
SAS/STAT User’s Guide, "The CANDISC procedure: Computational Details," http://support.
sas.com/documentation/cdl/en/statug/63962/HTML/default/viewer.htm#statug_candisc_
sect012.htm.
A generalized canonical discriminant analysis extends this idea to a general multivariate linear
model. Analysis of each term in the mlm produces a rank dfh H matrix sum of squares and crossprod-
ucts matrix that is tested against the rank dfe E matrix by the standard multivariate tests (Wilks’
Lambda, Hotelling-Lawley trace, Pillai trace, Roy’s maximum root test). For any given term in the
mlm, the generalized canonical discriminant analysis amounts to a standard discriminant analysis
based on the H matrix for that term in relation to the full-model E matrix.
The plot method for candisc objects is typically a 2D plot, similar to a biplot. It shows the canonical
scores for the groups defined by the term as points and the canonical structure coefficients as vectors
from the origin.
If the canonical structure for a term has ndim==1, or length(which)==1, the 1D representation
consists of a boxplot of canonical scores and a vector diagram showing the magnitudes of the
structure coefficients.

Value
An object of class candisc with the following components:

dfh hypothesis degrees of freedom for term

dfe error degrees of freedom for the mlm
rank number of non-zero eigenvalues of HE −1
eigenvalues eigenvalues of HE −1
canrsq squared canonical correlations
pct A vector containing the percentages of the canrsq of their total.
12 candisc

ndim Number of canonical dimensions stored in the means, structure and coeffs.*
components
means A data.frame containing the class means for the levels of the factor(s) in the term
factors A data frame containing the levels of the factor(s) in the term
term name of the term
terms A character vector containing the names of the terms in the mlm object
coeffs.raw A matrix containing the raw canonical coefficients
coeffs.std A matrix containing the standardized canonical coefficients
structure A matrix containing the canonical structure coefficients on ndim dimensions,
i.e., the correlations between the original variates and the canonical scores.
These are sometimes referred to as Total Structure Coefficients.
scores A data frame containing the predictors in the mlm model and the canonical scores
on ndim dimensions. These are calculated as Y %*% coeffs.raw, where Y con-
tains the standardized response variables.

Author(s)
Michael Friendly and John Fox

References
Bartlett, M. S. (1938). Further aspects of the theory of multiple regression. Proc. Cambridge
Philosophical Society 34, 33-34.
Cooley, W.W. & Lohnes, P.R. (1971). Multivariate Data Analysis, New York: Wiley.
Gittins, R. (1985). Canonical Analysis: A Review with Applications in Ecology, Berlin: Springer.

See Also
candiscList, heplot, heplot3d

Examples
grass.mod <- lm(cbind(N1,N9,N27,N81,N243) ~ Block + Species, data=Grass)
Anova(grass.mod, test="Wilks")

grass.can1 <-candisc(grass.mod, term="Species")

plot(grass.can1)

# library(heplots)
heplot(grass.can1, scale=6, fill=TRUE)

# iris data
iris.mod <- lm(cbind(Petal.Length, Sepal.Length, Petal.Width, Sepal.Width) ~ Species, data=iris)
iris.can <- candisc(iris.mod, data=iris)
#-- assign colors and symbols corresponding to species
col <- c("red", "brown", "green3")
pch <- 1:3
plot(iris.can, col=col, pch=pch)
candiscList 13

heplot(iris.can)

# 1-dim plot
iris.can1 <- candisc(iris.mod, data=iris, ndim=1)
plot(iris.can1)

candiscList Canonical discriminant analyses

Description
candiscList performs a generalized canonical discriminant analysis for all terms in a multivariate
linear model (i.e., an mlm object), computing canonical scores and vectors.

Usage
candiscList(mod, ...)

## S3 method for class 'mlm'

candiscList(mod, type = "2", manova, ndim, ...)

## S3 method for class 'candiscList'

plot(x, term, ask = interactive(), graphics = TRUE, ...)

## S3 method for class 'candiscList'

print(x, ...)

## S3 method for class 'candiscList'

summary(object, ...)

Arguments
mod An mlm object, such as computed by lm() with a multivariate response
type type of test for the model term, one of: "II", "III", "2", or "3"
manova the Anova.mlm object corresponding to mod. Normally, this is computed inter-
nally by Anova(mod)
ndim Number of dimensions to store in the means, structure, scores and coeffs.*
components. The default is the rank of the H matrix for the hypothesis term.
object, x A candiscList object
term The name of one term to be plotted for the plot method. If not specified, one
candisc plot is produced for each term in the mlm object.
ask If TRUE (the default, when running interactively), a menu of terms is presented;
if ask is FALSE, canonical plots for all terms are produced.
graphics if TRUE (the default, when running interactively), then the menu of terms to plot
is presented in a dialog box rather than as a text menu.
... arguments to be passed down.
14 can_lm

Value
An object of class candiscList which is a list of candisc objects for the terms in the mlm.

Author(s)
Michael Friendly and John Fox

See Also
candisc, heplot, heplot3d

Examples
grass.mod <- lm(cbind(N1,N9,N27,N81,N243) ~ Block + Species, data=Grass)

grass.canL <-candiscList(grass.mod)
names(grass.canL)
names(grass.canL$Species)

## Not run:
print(grass.canL)

## End(Not run)
plot(grass.canL, type="n", ask=FALSE)
heplot(grass.canL$Species, scale=6)
heplot(grass.canL$Block, scale=2)

can_lm Transform a Multivariate Linear model mlm to a Canonical Represen-

tation

Description
This function uses candisc to transform the responses in a multivariate linear model to scores on
canonical variables for a given term and then uses those scores as responses in a linear (lm) or
multivariate linear model (mlm).

Usage
can_lm(mod, term, ...)

Arguments
mod A mlm object
term One term in that model
... Arguments passed to candisc
dataIndex 15

Details
The function constructs a model formula of the form Can ~ terms where Can is the canonical
score(s) and terms are the terms in the original mlm, then runs lm() with that formula.

Value
A lm object if term is a rank 1 hypothesis, otherwise a mlm object

Author(s)
Michael Friendly

See Also
candisc, cancor

Examples
iris.mod <- lm(cbind(Petal.Length, Sepal.Length, Petal.Width, Sepal.Width) ~ Species, data=iris)
iris.can <- can_lm(iris.mod, "Species")
iris.can
Anova(iris.mod)
Anova(iris.can)

dataIndex Indices of observations in a model data frame

Description
Find sequential indices for observations in a data frame corresponding to the unique combinations
of the levels of a given model term from a model object or a data frame

Usage
dataIndex(x, term)

Arguments
x Either a data frame or a model object
term The name of one term in the model, consisting only of factors

Value
A vector of indices.

Author(s)
Michael Friendly
16 Grass

Examples
factors <- expand.grid(A=factor(1:3),B=factor(1:2),C=factor(1:2))
n <- nrow(factors)
responses <-data.frame(Y1=10+round(10*rnorm(n)),Y2=10+round(10*rnorm(n)))

test <- data.frame(factors, responses)

mod <- lm(cbind(Y1,Y2) ~ A*B, data=test)

dataIndex(mod, "A")
dataIndex(mod, "A:B")

Grass Yields from Nitrogen nutrition of grass species

Description
The data frame Grass gives the yield (10 * log10 dry-weight (g)) of eight grass Species in five
replicates (Block) grown in sand culture at five levels of nitrogen.

Usage
data(Grass)

Format
A data frame with 40 observations on the following 7 variables.
Species a factor with levels B.media D.glomerata F.ovina F.rubra H.pubesens K.cristata
L.perenne P.bertolonii
Block a factor with levels 1 2 3 4 5
N1 species yield at 1 ppm Nitrogen
N9 species yield at 9 ppm Nitrogen
N27 species yield at 27 ppm Nitrogen
N81 species yield at 81 ppm Nitrogen
N243 species yield at 243 ppm Nitrogen

Details
Nitrogen (NaNO3) levels were chosen to vary from what was expected to be from critically low to
almost toxic. The amount of Nitrogen can be considered on a log3 scale, with levels 0, 2, 3, 4, 5.
Gittins (1985, Ch. 11) treats these as equally spaced for the purpose of testing polynomial trends in
Nitrogen level.
The data are also not truly multivariate, but rather a split-plot experimental design. For the purpose
of exposition, he regards Species as the experimental unit, so that correlations among the responses
refer to a composite representative of a species rather than to an individual exemplar.
heplot.cancor 17

Source
Gittins, R. (1985), Canonical Analysis: A Review with Applications in Ecology, Berlin: Springer-
Verlag, Table A-5.

Examples
str(Grass)
grass.mod <- lm(cbind(N1,N9,N27,N81,N243) ~ Block + Species, data=Grass)
Anova(grass.mod)

grass.canL <-candiscList(grass.mod)
names(grass.canL)
names(grass.canL$Species)

heplot.cancor Canonical Correlation HE plots

Description
These functions plot ellipses (or ellipsoids in 3D) in canonical space representing the hypothesis and
error sums-of-squares-and-products matrices for terms in a multivariate linear model representing
the result of a canonical correlation analysis. They provide a low-rank 2D (or 3D) view of the
effects in the space of maximum canonical correlations, together with variable vectors representing
the correlations of Y variables with the canonical dimensions.
For consistency with heplot.candisc, the plots show effects in the space of the canonical Y vari-
ables selected by which.

Usage
## S3 method for class 'cancor'
heplot(mod, which = 1:2, scale, asp=1,
var.vectors = "Y", var.col = c("blue", "darkgreen"), var.lwd = par("lwd"),
var.cex = par("cex"), var.xpd = TRUE,
prefix = "Ycan", suffix = TRUE, terms = TRUE, ...)

## S3 method for class 'cancor'

heplot3d(mod, which = 1:3, scale, asp="iso",
var.vectors = "Y", var.col = c("blue", "darkgreen"), var.lwd = par("lwd"),
var.cex = par("cex"), var.xpd = NA,
prefix = "Ycan", suffix = FALSE, terms = TRUE, ...)

Arguments
mod A cancor object
which A numeric vector containing the indices of the Y canonical dimensions to plot.
18 heplot.cancor

scale Scale factor for the variable vectors in canonical space. If not specified, the
function calculates one to make the variable vectors approximately fill the plot
window.
asp aspect ratio setting. Use asp=1 in 2D plots and asp="iso" in 3D plots to ensure
equal units on the axes. Use asp=NA in 2D plots and asp=NULL in 3D plots to
allow separate scaling for the axes. See Details below.
var.vectors Which variable vectors to plot? A character vector containing one or more of
"X" and "Y".
var.col Color(s) for variable vectors and labels, a vector of length 1 or 2. The first color
is used for Y vectors and the second for X vectors, if these are plotted.
var.lwd Line width for variable vectors
var.cex Text size for variable vector labels
var.xpd logical. Allow variable labels outside the plot box? Does not apply to 3D plots.
prefix Prefix for labels of the Y canonical dimensions.
suffix Suffix for labels of canonical dimensions. If suffix=TRUE the percent of hy-
pothesis (H) variance accounted for by each canonical dimension is added to the
axis label.
terms Terms for the X variables to be plotted in canonical space. The default, terms=TRUE
or terms="X" plots H ellipses for all of the X variables. terms="Xcan" plots H
ellipses for all of the X canonical variables, Xcan1, Xcan2, . . . .
... Other arguments passed to link[heplots]{heplot}. In particular, you can
pass linear hypotheses among the term variables via hypotheses.

Details

The interpretation of variable vectors in these plots is different from that of the terms plotted as
H "ellipses," which appear as degenerate lines in the plot (because they correspond to 1 df tests of
rank(H)=1).
In canonical space, the interpretation of the H ellipses for the terms is the same as in ordinary
HE plots: a term is significant iff its H ellipse projects outside the (orthogonalized) E ellipsoid
somewhere in the space of the Y canonical dimensions. The orientation of each H ellipse with
respect to the Y canonical dimensions indicates which dimensions that X variate contributes to.
On the other hand, the variable vectors shown in these plots are intended only to show the corre-
lations of Y variables with the canonical dimensions. Only their relative lengths and angles with
respect to the Y canonical dimensions have meaning. Relative lengths correspond to proportions
of variance accounted for in the Y canonical dimensions plotted; angles between the variable vec-
tors and the canonical axes correspond to the structure correlations. The absolute lengths of these
vectors are typically manipulated by the scale argument to provide better visual resolution and
labeling for the variables.
Setting the aspect ratio of these plots is important for the proper interpretation of angles between
the variable vectors and the coordinate axes. However, this then makes it impossible to change the
aspect ratio of the plot by re-sizing manually.
heplot.cancor 19

Value

Returns invisibly an object of class "heplot", with coordinates for the various hypothesis ellipses
and the error ellipse, and the limits of the horizontal and vertical axes.

Author(s)

Michael Friendly

References

Gittins, R. (1985). Canonical Analysis: A Review with Applications in Ecology, Berlin: Springer.
Mardia, K. V., Kent, J. T. and Bibby, J. M. (1979). Multivariate Analysis. London: Academic Press.

See Also

cancor for details on canonical correlation as implemented here; plot.cancor for scatterplots of
canonical variable scores.
heplot.candisc, heplot, linearHypothesis

Examples
data(Rohwer, package="heplots")
X <- as.matrix(Rohwer[,6:10])
Y <- as.matrix(Rohwer[,3:5])
cc <- cancor(X, Y, set.names=c("PA", "Ability"))

# basic plot
heplot(cc)

# note relationship of joint hypothesis to individual ones

heplot(cc, scale=1.25, hypotheses=list("na+ns"=c("na", "ns")))

# more options
heplot(cc, hypotheses=list("All X"=colnames(X)),
fill=c(TRUE,FALSE), fill.alpha=0.2,
var.cex=1.5, var.col="red", var.lwd=3,
prefix="Y canonical dimension"
)

# 3D version
## Not run:
heplot3d(cc, var.lwd=3, var.col="red")

## End(Not run)
20 heplot.candisc

heplot.candisc Canonical Discriminant HE plots

Description
These functions plot ellipses (or ellipsoids in 3D) in canonical discriminant space representing
the hypothesis and error sums-of-squares-and-products matrices for terms in a multivariate linear
model. They provide a low-rank 2D (or 3D) view of the effects for that term in the space of
maximum discrimination.

Usage
## S3 method for class 'candisc'
heplot(mod, which = 1:2, scale, asp = 1, var.col = "blue",
var.lwd = par("lwd"), var.cex=par("cex"), var.pos,
rev.axes=c(FALSE, FALSE),
prefix = "Can", suffix = TRUE, terms = mod$term, ...)

## S3 method for class 'candisc'

heplot3d(mod, which = 1:3, scale, asp="iso", var.col = "blue",
var.lwd=par("lwd"), var.cex=rgl::par3d("cex"),
prefix = "Can", suffix = FALSE, terms = mod$term,
...)

Arguments
mod A candisc object for one term in a mlm
which A numeric vector containing the indices of the canonical dimensions to plot.
scale Scale factor for the variable vectors in canonical space. If not specified, the
function calculates one to make the variable vectors approximately fill the plot
window.
asp Aspect ratio for the horizontal and vertical dimensions. The defaults, asp=1 for
heplot.candisc and asp="iso" for heplot3d.candisc ensure equal units on
all axes, so that angles and lengths of variable vectors are interpretable. As well,
the standardized canonical scores are uncorrelated, so the Error ellipse (ellip-
soid) should plot as a circle (sphere) in canonical space. For heplot3d.candisc,
use asp=NULL to suppress this transformation to iso-scaled axes.
var.col Color for variable vectors and labels
var.lwd Line width for variable vectors
var.cex Text size for variable vector labels
var.pos Position(s) of variable vector labels wrt. the end point. If not specified, the
labels are out-justified left and right with respect to the end points.
rev.axes Logical, a vector of length(which). TRUE causes the orientation of the canoni-
cal scores and structure coefficients to be reversed along a given axis.
heplot.candisc 21

prefix Prefix for labels of canonical dimensions.

suffix Suffix for labels of canonical dimensions. If suffix=TRUE the percent of hy-
pothesis (H) variance accounted for by each canonical dimension is added to the
axis label.
terms Terms from the original mlm whose H ellipses are to be plotted in canonical
space. The default is the one term for which the canonical scores were com-
puted. If terms=TRUE, all terms are plotted.
... Arguments to be passed down to heplot or heplot3d

Details
The generalized canonical discriminant analysis for one term in a mlm is based on the eigenvalues,
λi , and eigenvectors, V, of the H and E matrices for that term. This produces uncorrelated canonical
scores which give the maximum univariate F statistics. The canonical HE plot is then just the HE
plot of the canonical scores for the given term.
For heplot3d.candisc, the default asp="iso" now gives a geometrically correct plot, but the third
dimension, CAN3, is often small. Passing an expanded range in zlim to heplot3d usually helps.

Value
heplot.candisc returns invisibly an object of class "heplot", with coordinates for the various
hypothesis ellipses and the error ellipse, and the limits of the horizontal and vertical axes.
Similarly, heploted.candisc returns an object of class "heplot3d".

Author(s)
Michael Friendly and John Fox

References
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.
doi: 10.18637/jss.v017.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

See Also
candisc, candiscList, heplot, heplot3d, aspect3d

Examples
## Pottery data, from car package
pottery.mod <- lm(cbind(Al, Fe, Mg, Ca, Na) ~ Site, data=Pottery)
pottery.can <-candisc(pottery.mod)

heplot(pottery.can, var.lwd=3)
if(requireNamespace("rgl")){
22 heplot.candiscList

heplot3d(pottery.can, var.lwd=3, scale=10, zlim=c(-3,3), wire=FALSE)

}

# reduce example for CRAN checks time

grass.mod <- lm(cbind(N1,N9,N27,N81,N243) ~ Block + Species, data=Grass)

grass.can1 <-candisc(grass.mod,term="Species")
grass.canL <-candiscList(grass.mod)

heplot(grass.can1, scale=6)
heplot(grass.can1, scale=6, terms=TRUE)
heplot(grass.canL, terms=TRUE, ask=FALSE)

heplot3d(grass.can1, wire=FALSE)
# compare with non-iso scaling
rgl::aspect3d(x=1,y=1,z=1)
# or,
# heplot3d(grass.can1, asp=NULL)

## Can't run this in example

# rgl::play3d(rgl::spin3d(axis = c(1, 0, 0), rpm = 5), duration=12)

# reduce example for CRAN checks time

## FootHead data, from heplots package

library(heplots)
data(FootHead)

# use Helmert contrasts for group

contrasts(FootHead$group) <- contr.helmert

foot.mod <- lm(cbind(width, circum,front.back,eye.top,ear.top,jaw)~group, data=FootHead)

foot.can <- candisc(foot.mod)
heplot(foot.can, main="Candisc HE plot",
hypotheses=list("group.1"="group1","group.2"="group2"),
col=c("red", "blue", "green3", "green3" ), var.col="red")

heplot.candiscList Canonical Discriminant HE plots

Description
These functions plot ellipses (or ellipsoids in 3D) in canonical discriminant space representing
the hypothesis and error sums-of-squares-and-products matrices for terms in a multivariate linear
model. They provide a low-rank 2D (or 3D) view of the effects for that term in the space of
maximum discrimination.
heplot.candiscList 23

Usage

## S3 method for class 'candiscList'

heplot(mod, term, ask = interactive(), graphics = TRUE, ...)

## S3 method for class 'candiscList'

heplot3d(mod, term, ask = interactive(), graphics = TRUE, ...)

Arguments

mod A candiscList object for terms in a mlm

term The name of one term to be plotted for the heplot and heplot3d methods. If
not specified, one plot is produced for each term in the mlm object.
ask If TRUE (the default), a menu of terms is presented; if ask is FALSE, canonical
HE plots for all terms are produced.
graphics if TRUE (the default, when running interactively), then the menu of terms to plot
is presented in a dialog box rather than as a text menu.
... Arguments to be passed down

Value

No useful value; used for the side-effect of producing canonical HE plots.

Author(s)

Michael Friendly and John Fox

References

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.
doi: 10.18637/jss.v017.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

See Also

candisc, candiscList, heplot, heplot3d

24 HSB

HSB High School and Beyond Data

Description
The High School and Beyond Project was a longitudinal study of students in the U.S. carried out in
1980 by the National Center for Education Statistics. Data were collected from 58,270 high school
students (28,240 seniors and 30,030 sophomores) and 1,015 secondary schools. The HSB data
frame is sample of 600 observations, of unknown characteristics, originally taken from Tatsuoka
(1988).

Usage
data(HSB)

Format
A data frame with 600 observations on the following 15 variables. There is no missing data.

id Observation id: a numeric vector

gender a factor with levels male female
race Race or ethnicity: a factor with levels hispanic asian african-amer white
ses Socioeconomic status: a factor with levels low middle high
sch School type: a factor with levels public private
prog High school program: a factor with levels general academic vocation
locus Locus of control: a numeric vector
concept Self-concept: a numeric vector
mot Motivation: a numeric vector
career Career plan: a factor with levels clerical craftsman farmer homemaker laborer manager
military operative prof1 prof2 proprietor protective sales school service technical
not working
read Standardized reading score: a numeric vector
write Standardized writing score: a numeric vector
math Standardized math score: a numeric vector
sci Standardized science score: a numeric vector
ss Standardized social science (civics) score: a numeric vector

Source
Tatsuoka, M. M. (1988). Multivariate Analysis: Techniques for Educational and Psychological
Research (2nd ed.). New York: Macmillan, Appendix F, 430-442.
plot.cancor 25

References
High School and Beyond data files: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/
7896

Examples
str(HSB)
# main effects model
hsb.mod <- lm( cbind(read, write, math, sci, ss) ~
gender + race + ses + sch + prog, data=HSB)
Anova(hsb.mod)

# Add some interactions

hsb.mod1 <- update(hsb.mod, . ~ . + gender:race + ses:prog)
heplot(hsb.mod1, col=palette()[c(2,1,3:6)], variables=c("read","math"))

hsb.can1 <- candisc(hsb.mod1, term="race")

heplot(hsb.can1, col=c("red", "black"))

# show canonical results for all terms

## Not run:
hsb.can <- candiscList(hsb.mod)
hsb.can

## End(Not run)

plot.cancor Canonical Correlation Plots

Description
This function produces plots to help visualize X, Y data in canonical space.
The present implementation plots the canonical scores for the Y variables against those for the X
variables on given dimensions. We treat this as a view of the data in canonical space, and so offer
additional annotations to a standard scatterplot.

Usage
## S3 method for class 'cancor'
plot(x, which = 1, xlim, ylim, xlab, ylab,
points = TRUE, add = FALSE, col = palette()[1],
ellipse = TRUE, ellipse.args = list(),
smooth = FALSE, smoother.args = list(), col.smooth = palette()[3],
abline = TRUE, col.lines = palette()[2], lwd = 2,
labels = rownames(xy),
id.method = "mahal", id.n = 0, id.cex = 1, id.col = palette()[1],
...)
26 plot.cancor

Arguments
x A "cancor" object
which Which dimension to plot? An integer in 1:x$ndim.
xlim, ylim Limits for x and y axes
xlab, ylab Labels for x and y axes. If not specified, these are constructed from the set.names
component of x.
points logical. Display the points?
add logical. Add to an existing plot?
col Color for points.
ellipse logical. Draw a data ellipse for the canonical scores?
ellipse.args A list of arguments passed to dataEllipse. Internally, the function sets the
default value for levels to 0.68.
smooth logical. Draw a (loess) smoothed curve?
smoother.args Arguments passed to loessLine, which should be consulted for details and de-
faults.
col.smooth Color for the smoothed curve.
abline logical. Draw the linear regression line for Ycan[,which] on Xcan[,which]?
col.lines Color for the linear regression line
lwd Line widths
labels Point labels for point identification via the id.method argument.
id.method Method used to identify individual points. See showLabels for details. The
default, id.method = "mahal" identifies the id.n points furthest from the cen-
troid.
id.n Number of points to identify
id.cex, id.col Character size and color for labeled points
... Other arguments passed down to plot(...) and points(...)

Details
Canonical correlation analysis assumes that the all correlations between the X and Y variables can
be expressed in terms of correlations the canonical variate pairs, (Xcan1, Ycan1), (Xcan2, Ycan2),
. . . , and that the relations between these pairs are indeed linear.
Data ellipses, and smoothed (loess) curves, together with the linear regression line for each canon-
ical dimension help to assess whether there are peculiarities in the data that might threaten the
validity of CCA. Point identification methods can be useful to determine influential cases.

Value
None. Used for its side effect of producing a plot.

Author(s)
Michael Friendly
redundancy 27

References
Mardia, K. V., Kent, J. T. and Bibby, J. M. (1979). Multivariate Analysis. London: Academic Press.

See Also
cancor,
dataEllipse, loessLine, showLabels

Examples
data(Rohwer, package="heplots")
X <- as.matrix(Rohwer[,6:10]) # the PA tests
Y <- as.matrix(Rohwer[,3:5]) # the aptitude/ability variables

cc <- cancor(X, Y, set.names=c("PA", "Ability"))

plot(cc)
# exercise some options
plot(cc, smooth=TRUE, id.n=3, ellipse.args=list(fill=TRUE))
plot(cc, which=2, smooth=TRUE)
plot(cc, which=3, smooth=TRUE)

# plot vectors showing structure correlations of Xcan and Ycan with their own variables
plot(cc)
struc <- cc$structure
Xstruc <- struc$X.xscores[,1]
Ystruc <- struc$Y.yscores[,1]
scale <- 2

# place vectors in the margins of the plot

usr <- matrix(par("usr"), nrow=2, dimnames=list(c("min", "max"), c("x", "y")))
ypos <- usr[2,2] - (1:5)/10
arrows(0, ypos, scale*Xstruc, ypos, angle=10, len=0.1, col="blue")
text(scale*Xstruc, ypos, names(Xstruc), pos=2, col="blue")

xpos <- usr[2,1] - ( 1 + 1:3)/10

arrows(xpos, 0, xpos, scale*Ystruc, angle=10, len=0.1, col="darkgreen")
text(xpos, scale*Ystruc, names(Ystruc), pos=1, col="darkgreen")

redundancy Canonical Redundancy Analysis

Description
Calculates indices of redundancy (Stewart & Love, 1968) from a canonical correlation analysis.
These give the proportion of variances of the variables in each set (X and Y) which are accounted
for by the variables in the other set through the canonical variates.
28 redundancy

Usage

redundancy(object, ...)

## S3 method for class 'cancor.redundancy'

print(x, digits = max(getOption("digits") - 3, 3), ...)

Arguments

object A "cancor" object

x A "cancor.redundancy" for the print method.
digits Number of digits to print
... Other arguments

Details

None yet.

Value

An object of class "cancor.redundancy", a list with the following 5 components:

Xcan.redun Canonical redundancies for the X variables, i.e., the total fraction of X variance
accounted for by the Y variables through each canonical variate.
Ycan.redun Canonical redundancies for the Y variables
X.redun Total canonical redundancy for the X variables, i.e., the sum of Xcan.redun.
Y.redun Total canonical redundancy for the Y variables
set.names names for the X and Y sets of variables

Author(s)

Michael Friendly

References

Stewart, D. and Love, W. (1968). A general canonical correlation index. Psychological Bulletin,
70, 160-163.

See Also

cancor, ~~~
varOrder 29

Examples
data(Rohwer, package="heplots")
X <- as.matrix(Rohwer[,6:10]) # the PA tests
Y <- as.matrix(Rohwer[,3:5]) # the aptitude/ability variables

cc <- cancor(X, Y, set.names=c("PA", "Ability"))

redundancy(cc)
##
## Redundancies for the PA variables & total X canonical redundancy
##
## Xcan1 Xcan2 Xcan3 total X|Y
## 0.17342 0.04211 0.00797 0.22350
##
## Redundancies for the Ability variables & total Y canonical redundancy
##
## Ycan1 Ycan2 Ycan3 total Y|X
## 0.2249 0.0369 0.0156 0.2774

varOrder Order variables according to canonical structure or other criteria

Description
The varOrder function implements some features of “effect ordering” (Friendly & Kwan (2003)
for variables in a multivariate data display to make the displayed relationships more coherent.
This can be used in pairwise HE plots, scatterplot matrices, parallel coordinate plots, plots of mul-
tivariate means, and so forth.
For a numeric data frame, the most useful displays often order variables according to the angles of
variable vectors in a 2D principal component analysis or biplot. For a multivariate linear model, the
analog is to use the angles of the variable vectors in a 2D canonical discriminant biplot.

Usage

varOrder(x, ...)

## S3 method for class 'mlm'

varOrder(x, term, variables,
type = c("can", "pc"),
method = c("angles", "dim1", "dim2", "alphabet", "data", "colmean"),
names = FALSE, descending = FALSE, ...)

## S3 method for class 'data.frame'

varOrder(x, variables,
method = c("angles", "dim1", "dim2", "alphabet", "data", "colmean"),
names = FALSE, descending = FALSE, ...)
30 varOrder

Arguments
x A multivariate linear model or a numeric data frame
term For the mlm method, one term in the model for which the canonical structure
coefficients are found.
variables indices or names of the variables to be ordered; defaults to all response variables
an MLM or all numeric variables in a data frame.
type For an MLM, type="can" uses the canonical structure coefficients for the given
term; type="pc" uses the principal component variable eigenvectors.
method One of c("angles", "dim1", "dim2", "alphabet", "data", "colmean") giv-
ing the effect ordering method.
"angles" Orders variables according to the angles their vectors make with di-
mensions 1 and 2, counter-clockwise starting from the lower-left quadrant
in a 2D biplot or candisc display.
"dim1" Orders variables in increasing order of their coordinates on dimension
1
"dim2" Orders variables in increasing order of their coordinates on dimension
2
"alphabet" Orders variables alphabetically
"data" Uses the order of the variables in the data frame or the list of responses
in the MLM
"colmean" Uses the order of the column means of the variables in the data
frame or the list of responses in the MLM
names logical; if TRUE the effect ordered names of the variables are returned; otherwise,
their indices in variables are returned.
descending If TRUE, the ordered result is reversed to a descending order.
... Arguments passed to methods

Value
A vector of integer indices of the variables or a character vector of their names.

Author(s)
Michael Friendly

References
Friendly, M. & Kwan, E. (2003). Effect Ordering for Data Displays, Computational Statistics and
Data Analysis, 43, 509-539. doi: 10.1016/S01679473(02)002906

Examples
data(Wine, package="candisc")
Wine.mod <- lm(as.matrix(Wine[, -1]) ~ Cultivar, data=Wine)
Wine.can <- candisc(Wine.mod)
plot(Wine.can, ellipse=TRUE)
vecscale 31

# pairs.mlm HE plot, variables in given order

pairs(Wine.mod, fill=TRUE, fill.alpha=.1, var.cex=1.5)

order <- varOrder(Wine.mod)

pairs(Wine.mod, variables=order, fill=TRUE, fill.alpha=.1, var.cex=1.5)

vecscale Scale vectors to fill the current plot

Description

Calculates a scale factor so that a collection of vectors nearly fills the current plot, that is, the longest
vector does not extend beyond the plot region.

Usage

vecscale(vectors, bbox = matrix(par("usr"), 2, 2), origin = c(0, 0), factor = 0.95)

Arguments

vectors a two-column matrix giving the end points of a collection of vectors

bbox the bounding box of the containing plot region within which the vectors are to
be plotted
origin origin of the vectors
factor maximum length of the rescaled vectors relative to the maximum possible

Value

scale factor, the multiplier of the vectors

Author(s)

Michael Friendly

See Also

vectors
32 vectors

Examples
bbox <- matrix(c(-3, 3, -2, 2), 2, 2)
colnames(bbox) <- c("x","y")
rownames(bbox) <- c("min", "max")
bbox

vecs <- matrix( runif(10, -1, 1), 5, 2)

plot(bbox)
arrows(0, 0, vecs[,1], vecs[,2], angle=10, col="red")
(s <- vecscale(vecs))
arrows(0, 0, s*vecs[,1], s*vecs[,2], angle=10)

vectors Draw Labeled Vectors in 2D or 3D

Description
Graphics utility functions to draw vectors from an origin to a collection of points (using arrows in
2D or lines3d in 3D) with labels for each (using text or texts3d).

Usage
vectors(x, origin = c(0, 0), labels = rownames(x),
scale = 1,
col="blue",
lwd=1, cex=1,
length=.1, angle=13, pos=NULL,
...)

vectors3d(x, origin=c(0,0,0), labels=rownames(x),

scale=1,
col="blue",
lwd=1, cex=1,
...)

Arguments
x A two-column matrix or a three-column matrix containing the end points of the
vectors
origin Starting point(s) for the vectors
labels Labels for the vectors
scale A multiplier for the length of each vector
col color(s) for the vectors.
lwd line width(s) for the vectors.
cex color(s) for the vectors.
Wilks 33

length For vectors, length of the edges of the arrow head (in inches).
angle For vectors, angle from the shaft of the arrow to the edge of the arrow head.
pos For vectors, position of the text label relative to the vector head. If pos==NULL,
labels are positioned labels outside, relative to arrow ends.
... other graphical parameters, such as lty, xpd, ...

Details
The graphical parameters col, lty and lwd can be vectors of length greater than one and will be
recycled if necessary

Value
None

Author(s)
Michael Friendly

See Also
arrows, text, segments
lines3d, texts3d

Examples
plot(c(-3, 3), c(-3,3), type="n")
X <- matrix(rnorm(10), ncol=2)
rownames(X) <- LETTERS[1:5]
vectors(X, scale=2, col=palette())

Wilks Wilks Lambda Tests for Canonical Correlations

Description
Tests the sequential hypotheses that the ith canonical correlation and all that follow it are zero,
ρi = ρi+1 = · · · = 0

Usage

Wilks(object, ...)

## S3 method for class 'cancor'

Wilks(object, ...)
## S3 method for class 'candisc'
Wilks(object, ...)
34 Wine

Arguments
object An object of class "cancor""} or \code{"candisc""
... Other arguments passed to methods (not used)

Details
Wilks’ Lambda values are calculated from the eigenvalues and converted to F statistics using Rao’s
approximation.

Value
A data.frame (of class "anova") containing the test statistics

Author(s)
Michael Friendly

References
Mardia, K. V., Kent, J. T. and Bibby, J. M. (1979). Multivariate Analysis. London: Academic Press.

See Also
cancor, ~~~

Examples
data(Rohwer, package="heplots")
X <- as.matrix(Rohwer[,6:10]) # the PA tests
Y <- as.matrix(Rohwer[,3:5]) # the aptitude/ability variables

cc <- cancor(X, Y, set.names=c("PA", "Ability"))

Wilks(cc)

iris.mod <- lm(cbind(Petal.Length, Sepal.Length, Petal.Width, Sepal.Width) ~ Species, data=iris)

iris.can <- candisc(iris.mod, data=iris)
Wilks(iris.can)

Wine Chemical composition of three cultivars of wine

Description
These data are the results of a chemical analysis of wines grown in the same region in Italy but
derived from three different cultivars. The analysis determined the quantities of 13 constituents
found in each of the three types of wines.
This data set is a classic in the machine learning literature as an easy high-D classification problem,
but is also of interest for examples of MANOVA and discriminant analysis.
Wine 35

Usage
data("Wine")

Format
A data frame with 178 observations on the following 14 variables.

Cultivar a factor with levels barolo grignolino barbera

Alcohol a numeric vector
MalicAcid a numeric vector
Ash a numeric vector
AlcAsh a numeric vector, Alkalinity of ash
Mg a numeric vector, Magnesium
Phenols a numeric vector, Total phenols
Flav a numeric vector, Flavanoids
NonFlavPhenols a numeric vector
Proa a numeric vector, Proanthocyanins
Color a numeric vector, color intensity
Hue a numeric vector
OD a numeric vector, OD280/OD315 of diluted wines
Proline a numeric vector

Details
The precise definitions of these variables is unknown: units, how they were measured, etc.

Source
This data set was obtained from the UCI Machine Learning Repository, http://archive.ics.uci.edu/ml/datasets/Wine
This page references a large number of papers that use this data set to compare different methods.

References
In R, a comparable data set is contained in the ggbiplot package.

Examples
data(Wine)
str(Wine)
#summary(Wine)

Wine.mlm <- lm(as.matrix(Wine[, -1]) ~ Cultivar, data=Wine)

Wine.can <- candisc(Wine.mlm)
Wine.can
36 Wolves

plot(Wine.can, ellipse=TRUE)
plot(Wine.can, which=1)

Wolves Wolf skulls

Description
Skull morphometric data on Rocky Mountain and Arctic wolves (Canis Lupus L.) taken from Mor-
rison (1990), originally from Jolicoeur (1959).

Usage
data(Wolves)

Format
A data frame with 25 observations on the following 11 variables.
group a factor with levels ar:f ar:m rm:f rm:m, comprising the combinations of location and
sex
location a factor with levels ar=Arctic, rm=Rocky Mountain
sex a factor with levels f=female, m=male
x1 palatal length, a numeric vector
x2 postpalatal length, a numeric vector
x3 zygomatic width, a numeric vector
x4 palatal width outside first upper molars, a numeric vector
x5 palatal width inside second upper molars, a numeric vector
x6 postglenoid foramina width, a numeric vector
x7 interorbital width, a numeric vector
x8 braincase width, a numeric vector
x9 crown length, a numeric vector

Details
All variables are expressed in millimeters.
The goal was to determine how geographic and sex differences among the wolf populations are
determined by these skull measurements. For MANOVA or (canonical) discriminant analysis, the
factors group or location and sex provide alternative parameterizations.

Source
Morrison, D. F. Multivariate Statistical Methods, (3rd ed.), 1990. New York: McGraw-Hill, p.
288-289.
Wolves 37

References
Jolicoeur, P. “Multivariate geographical variation in the wolf Canis lupis L.”, Evolution, XIII, 283–
299.

Examples
data(Wolves)

# using group
wolf.mod <-lm(cbind(x1,x2,x3,x4,x5,x6,x7,x8,x9) ~ group, data=Wolves)
Anova(wolf.mod)

wolf.can <-candisc(wolf.mod)
plot(wolf.can)
heplot(wolf.can)

# using location, sex

wolf.mod2 <-lm(cbind(x1,x2,x3,x4,x5,x6,x7,x8,x9) ~ location*sex, data=Wolves)
Anova(wolf.mod2)

wolf.can2 <-candiscList(wolf.mod2)
plot(wolf.can2)
Index

∗ aplot candisc, 3, 7, 9, 14, 15, 21, 23

vectors, 32 candisc-package, 2
∗ datasets candiscList, 12, 13, 21, 23
Grass, 16 cc, 7
HSB, 24 cca, 7
Wine, 34 coef.cancor (cancor), 4
Wolves, 36 coef.candisc (candisc), 9
∗ hplot cov.wt, 5
candisc, 9
candiscList, 13 dataEllipse, 26, 27
heplot.cancor, 17 dataIndex, 15
heplot.candisc, 20
Grass, 16
heplot.candiscList, 22
plot.cancor, 25 heplot, 3, 12, 14, 19, 21, 23
∗ htest heplot.cancor, 3, 6, 7, 17
Wilks, 33 heplot.candisc, 2, 17, 19, 20
∗ manip heplot.candiscList, 22
dataIndex, 15 heplot3d, 12, 14, 21, 23
varOrder, 29 heplot3d.cancor, 3
vecscale, 31 heplot3d.cancor (heplot.cancor), 17
∗ multivariate heplot3d.candisc, 2
cancor, 4 heplot3d.candisc (heplot.candisc), 20
candisc, 9 heplot3d.candiscList
candisc-package, 2 (heplot.candiscList), 22
candiscList, 13 heplots, 4, 7
heplot.cancor, 17 HSB, 24
heplot.candisc, 20
heplot.candiscList, 22 linearHypothesis, 19
redundancy, 27 lines3d, 32, 33
varOrder, 29 loessLine, 26, 27
∗ package
candisc-package, 2 palette, 10
∗ utilities plot.cancor, 3, 7, 19, 25
dataIndex, 15 plot.candisc, 2
plot.candisc (candisc), 9
arrows, 32, 33 plot.candiscList (candiscList), 13
aspect3d, 21 print.cancor (cancor), 4
print.cancor.redundancy (redundancy), 27
can_lm, 14 print.candisc (candisc), 9
cancor, 3, 4, 7, 15, 19, 27, 28, 34 print.candiscList (candiscList), 13

38
INDEX 39

redundancy, 7, 27

scores (cancor), 4
segments, 33
showLabels, 26, 27
summary.cancor (cancor), 4
summary.candisc (candisc), 9
summary.candiscList (candiscList), 13

text, 32, 33
texts3d, 32, 33

varOrder, 3, 29
vecscale, 31
vectors, 31, 32
vectors3d (vectors), 32

Wilks, 33
Wine, 34
Wolves, 36