HE plot MMRA Examples
Vignette built using heplots, version 1.7.1 and
candisc, version 0.9.0.
Multivariate Multiple Regression Designs
The ideas behind HE plots extend naturally to multivariate multiple regression (MMRA) and multivariate analysis of covariance (MANCOVA). In MMRA designs, the X matrix contains only quantitative predictors, while in MANCOVA designs, it contains a mixture of factors and quantitative predictors (covariates), but typically there is just one “group” factor.
In the MANCOVA case, there is often a subtle difference in emphasis: true MANCOVA analyses focus on the differences among groups defined by the factors, adjusting for (or controlling for) the quantitative covariates. Analyses concerned with homogeneity of regression focus on quantitative predictors and attempt to test whether the regression relations are the same for all groups defined by the factors.
Rohwer data: Aptitude and achievement
To illustrate the homogeneity of regression flavor, we use data from a study by Rohwer (given in Timm (1975), Ex. 4.3, 4.7, and 4.23) on kindergarten children, designed to determine how well a set of paired-associate (PA) tasks predicted performance on measures of achievement:
- the Peabody Picture Vocabulary test (
PPVT), - a student achievement test (
SAT), and - the Raven Progressive matrices test (
Raven).
The PA tasks were considered measures of learning aptitude and varied
in how the stimuli were presented, and are called named
(n), still (s), named still
(ns), named action (na), and
sentence still (ss).
Two groups were tested: a group of n = 37 children from a low
socioeconomic status (SES) school, and a group of n = 32 high SES children from an
upper-class, white residential school. The data are in the data frame
Rohwer in the heplots package:
data(Rohwer)
Rohwer |> dplyr::sample_n(6)
#> group SES SAT PPVT Raven n s ns na ss
#> 31 1 Lo 9 63 11 2 12 5 25 14
#> 7 1 Lo 6 71 21 0 1 20 23 18
#> 18 1 Lo 45 54 10 0 6 6 14 16
#> 17 1 Lo 19 66 13 7 12 21 35 27
#> 50 2 Hi 4 87 14 1 4 14 25 19
#> 59 2 Hi 36 89 15 1 6 15 23 28Preliminary plots
Before fitting models, it is usually useful to do some data exploration and graphing. With multivariate multiple regression data, among the most helpful plots are scatterplots of each response variable, Y, against each predictor, X, and we can get a better sense of the relationships by adding linear regression lines, loess smooths or other enhancements.
A scatterplot matrix, using graphics::pairs() or
GGally::ggpairs() is easy to do. However, with 3 response
variables, 4 predictors and a group factor (SES), this can
be overwhelming. An alternative is to compose a rectangular matrix of
plots for only the Y variables against the Xs.
This turned out to be not as easy as it might seem, because none of
the pairs() methods allow for this possibility. The trick
is to reshape the data from wide to long format and use facets in
ggplot2 to compose the pairwise scatterplots into the
desired rectangular matrix format.1
library(tidyr)
library(dplyr)
library(ggplot2)
yvars <- c("SAT", "PPVT", "Raven" ) # outcome variables
xvars <- c("n", "s", "ns", "na", "ss") # predictors
xvars <- c("n", "s", "ns") # make a smaller example
Rohwer_long <- Rohwer %>%
dplyr::select(-group, -na, -ss) |>
tidyr::pivot_longer(cols = all_of(xvars),
names_to = "xvar", values_to = "x") |>
tidyr::pivot_longer(cols = all_of(yvars),
names_to = "yvar", values_to = "y") |>
dplyr::mutate(xvar = factor(xvar, levels = xvars),
yvar = factor(yvar, levels = yvars))
Rohwer_long
#> # A tibble: 621 × 5
#> SES xvar x yvar y
#> <fct> <fct> <int> <fct> <int>
#> 1 Lo n 1 SAT 49
#> 2 Lo n 1 PPVT 48
#> 3 Lo n 1 Raven 8
#> 4 Lo s 2 SAT 49
#> 5 Lo s 2 PPVT 48
#> 6 Lo s 2 Raven 8
#> 7 Lo ns 6 SAT 49
#> 8 Lo ns 6 PPVT 48
#> 9 Lo ns 6 Raven 8
#> 10 Lo n 5 SAT 47
#> # ℹ 611 more rowsThen, we can use ggplot2 to make produce the pairwise
plots for each combination of x and y
variables. Using color=SES in the aesthetic results in a
separate regression line for the two SES groups produced by
geom_smooth().
ggplot(Rohwer_long, aes(x, y, color = SES, shape = SES)) +
geom_jitter(size=1.5) +
geom_smooth(method = "lm",
se = FALSE,
formula = y ~ x,
size=1.5) +
facet_grid(yvar ~ xvar, # plot matrix of Y by X
scales = "free") +
theme_bw(base_size = 16) +
theme(legend.position = "bottom")
Plot matrix of the response variables (SAT,
PPVT and Raven) against each of three
predictors (n, s, ns). The lines
show separate linear regressions for each SES group.
Such plots form a framework for understanding model fits and statistical tests we turn to now.
Separate models
As one approach, we might be tempted to fit separate regression models for each of the High and Low SES groups. This approach is not generally recommended because it lacks power (smaller sample sizes in each group than a combined analysis) and does not allow hypotheses about equality of slopes and intercepts to be tested directly.
rohwer.ses1 <- lm(cbind(SAT, PPVT, Raven) ~ n + s + ns + na + ss, data=Rohwer,
subset=SES=="Hi")
Anova(rohwer.ses1)
#>
#> Type II MANOVA Tests: Pillai test statistic
#> Df test stat approx F num Df den Df Pr(>F)
#> n 1 0.202 2.02 3 24 0.1376
#> s 1 0.310 3.59 3 24 0.0284 *
#> ns 1 0.358 4.46 3 24 0.0126 *
#> na 1 0.465 6.96 3 24 0.0016 **
#> ss 1 0.089 0.78 3 24 0.5173
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
rohwer.ses2 <- lm(cbind(SAT, PPVT, Raven) ~ n + s + ns + na + ss, data=Rohwer,
subset=SES=="Lo")
Anova(rohwer.ses2)
#>
#> Type II MANOVA Tests: Pillai test statistic
#> Df test stat approx F num Df den Df Pr(>F)
#> n 1 0.0384 0.39 3 29 0.764
#> s 1 0.1118 1.22 3 29 0.321
#> ns 1 0.2252 2.81 3 29 0.057 .
#> na 1 0.2675 3.53 3 29 0.027 *
#> ss 1 0.1390 1.56 3 29 0.220
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1This fits separate slopes and intercepts for each of the two groups, but it is difficult to compare the coefficients numerically.
coef(rohwer.ses1)
#> SAT PPVT Raven
#> (Intercept) -28.4675 39.69709 13.24384
#> n 3.2571 0.06728 0.05935
#> s 2.9966 0.36998 0.49244
#> ns -5.8591 -0.37438 -0.16402
#> na 5.6662 1.52301 0.11898
#> ss -0.6227 0.41016 -0.12116
coef(rohwer.ses2)
#> SAT PPVT Raven
#> (Intercept) 4.15106 33.00577 11.17338
#> n -0.60887 -0.08057 0.21100
#> s -0.05016 -0.72105 0.06457
#> ns -1.73240 -0.29830 0.21358
#> na 0.49456 1.47042 -0.03732
#> ss 2.24772 0.32396 -0.05214The function heplots::coefplot() makes this a bit
easier, by plotting bivariate confidence ellipses for the coefficients
in a multivariate linear model. In this problem, with three response
variables, the 95% confidence regions are 3D ellipsoids, but we only
plot them in 2D. The 3D versions have the property that a given
predictor is significant by a multivariate test if the ellipsoid
excludes the point (0, 0, 0).
coefplot(rohwer.ses1, fill=TRUE, cex.label=1.5, cex.lab=1.5)
text(-10, 3, "High SES group", pos=4, cex=1.4)
coefplot(rohwer.ses2, fill=TRUE, cex.label=1.5, cex.lab=1.5)
text(-4.7, 2.5, "Low SES group", pos=4, cex=1.4)
Coefficient plots for the separate models for the High and Low SES groups in the Rohwer data. The ellipses are 95% confidence regions for the pairs of regression coefficients of (SAT, PPVT) for each predictor in the model.
Alternatively, we can visualize the results of the multivariate tests
for the predictors with HE plots. Here we make use of the fact that
several HE plots can be overlaid using the option add=TRUE
as shown in Figure @ref(fig:rohwer-HE1).
heplot(rohwer.ses1,
ylim=c(40,110), # allow more room for 2nd plot
col=c("red", "black"),
fill = TRUE, fill.alpha = 0.1,
lwd=2, cex=1.2)
heplot(rohwer.ses2,
add=TRUE,
col=c("brown", "black"),
grand.mean=TRUE, error.ellipse=TRUE, # not shown by default when add=TRUE
fill = TRUE, fill.alpha = 0.1,
lwd=2, cex=1.2)
# label the groups at their centroid
means <- aggregate(cbind(SAT,PPVT)~SES, data=Rohwer, mean)
text(means[,2], means[,3], labels=means[,1], pos=3, cex=2, col="black")
HE plot for SAT and PPVT, showing the effects
for the PA predictors for the High and Low SES groups separately
We can readily see the difference in means for the two SES groups
(Hi has greater scores on both variables) and it also
appears that the slopes of the predictor ellipses are shallower for the
High than the Low group, indicating greater relation with the
SAT score.
MANCOVA model
Alternatively (and optimistically), we can fit a MANCOVA model that allows different means for the two SES groups on the responses, but constrains the slopes for the PA covariates to be equal.
# MANCOVA, assuming equal slopes
rohwer.mod <- lm(cbind(SAT, PPVT, Raven) ~ SES + n + s + ns + na + ss,
data=Rohwer)
Anova(rohwer.mod)
#>
#> Type II MANOVA Tests: Pillai test statistic
#> Df test stat approx F num Df den Df Pr(>F)
#> SES 1 0.379 12.18 3 60 2.5e-06 ***
#> n 1 0.040 0.84 3 60 0.4773
#> s 1 0.093 2.04 3 60 0.1173
#> ns 1 0.193 4.78 3 60 0.0047 **
#> na 1 0.231 6.02 3 60 0.0012 **
#> ss 1 0.050 1.05 3 60 0.3770
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Note that, although the multivariate tests for two of the covariates
(ns and na) are highly significant, univariate
multiple regression tests for the separate responses [from
summary(rohwer.mod)] are relatively weak.
We can also test the global 5 df hypothesis, B = 0, that
all covariates have null effects for all responses as a linear
hypothesis. First, extract the names of the PA tests predictors from the
model. car::linearHypothesis() takes a vector of the names
coefficients to be tested simultaneously.
Regr <- linearHypothesis(rohwer.mod, covariates)
print(Regr, digits=4, SSP=FALSE)
#>
#> Multivariate Tests:
#> Df test stat approx F num Df den Df Pr(>F)
#> Pillai 5 0.6658 3.537 15 186 2.31e-05 ***
#> Wilks 5 0.4418 3.812 15 166 8.28e-06 ***
#> Hotelling-Lawley 5 1.0309 4.032 15 176 2.79e-06 ***
#> Roy 5 0.7574 9.392 5 62 1.06e-06 ***
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Then 2D views of the additive MANCOVA model rohwer.mod
and the overall test for all covariates are produced as follows, giving
the plots in Figure @ref(fig:rohwer-HE2).
colors <- c("red", "blue", rep("black",5), "#969696")
heplot(rohwer.mod,
col=colors, variables=c(1,2),
hypotheses=list("Regr" = covariates),
fill = TRUE, fill.alpha = 0.1,
cex=1.5, lwd=c(2, rep(3,5), 4),
main="(SAT, PPVT) in Rohwer MANCOVA model")
heplot(rohwer.mod,
col=colors, variables=c(1,3),
hypotheses=list("Regr" = covariates),
fill = TRUE, fill.alpha = 0.1,
cex=1.5, lwd=c(2, rep(3,5), 4),
main="(SAT, Raven) in Rohwer MANCOVA model")
HE plot for SAT and PPVT (left) and for
SAT and Raven (right) using the MANCOVA model.
The ellipses labeled ‘Regr’ show the test of the overall model,
including all predictors.
The positive orientation of the Regr ellipses shows that
the predicted values for all three responses are positively correlated
(more so for SAT and PPVT). As well, the High
SES group is higher on all responses than the Low SES group.
Alternatively, all pairwise plots among these responses could be
drawn using the pairs.mlm() function,
pairs(rohwer.mod, col=colors,
hypotheses=list("Regr" = c("n", "s", "ns", "na", "ss")),
cex=1.3, lwd=c(2, rep(3,5), 4))
or as a 3D plot, using heplot3d() as shown in Figure
@ref(fig:rohwer-HE3D).
colors <- c("pink", "blue", rep("black",5), "#969696")
heplot3d(rohwer.mod, col=colors,
hypotheses=list("Regr" = c("n", "s", "ns", "na", "ss")))
3D HE plot for the MANCOVA model fit to the Rohwer data.
Testing homogeneity of regression
The MANCOVA model, rohwer.mod, has relatively simple
interpretations (large effect of SES, with ns
and na as the major predictors) but the test of relies on
the assumption of homogeneity of slopes for the predictors. We can test
this assumption as follows, by adding interactions of SES
with each of the covariates:
rohwer.mod2 <- lm(cbind(SAT, PPVT, Raven) ~ SES * (n + s + ns + na + ss),
data=Rohwer)
Anova(rohwer.mod2)
#>
#> Type II MANOVA Tests: Pillai test statistic
#> Df test stat approx F num Df den Df Pr(>F)
#> SES 1 0.391 11.78 3 55 4.5e-06 ***
#> n 1 0.079 1.57 3 55 0.20638
#> s 1 0.125 2.62 3 55 0.05952 .
#> ns 1 0.254 6.25 3 55 0.00100 ***
#> na 1 0.307 8.11 3 55 0.00015 ***
#> ss 1 0.060 1.17 3 55 0.32813
#> SES:n 1 0.072 1.43 3 55 0.24417
#> SES:s 1 0.099 2.02 3 55 0.12117
#> SES:ns 1 0.118 2.44 3 55 0.07383 .
#> SES:na 1 0.148 3.18 3 55 0.03081 *
#> SES:ss 1 0.057 1.12 3 55 0.35094
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1It appears from the above that there is only weak evidence of unequal
slopes from the separate SES: terms. The evidence for
heterogeneity is stronger, however, when these terms are tested
collectively using the linearHypothesis() function:
(coefs <- rownames(coef(rohwer.mod2)))
#> [1] "(Intercept)" "SESLo" "n" "s" "ns"
#> [6] "na" "ss" "SESLo:n" "SESLo:s" "SESLo:ns"
#> [11] "SESLo:na" "SESLo:ss"
print(linearHypothesis(rohwer.mod2, coefs[grep(":", coefs)]), SSP=FALSE)
#>
#> Multivariate Tests:
#> Df test stat approx F num Df den Df Pr(>F)
#> Pillai 5 0.4179 1.845 15 171.0 0.03209 *
#> Wilks 5 0.6236 1.894 15 152.2 0.02769 *
#> Hotelling-Lawley 5 0.5387 1.927 15 161.0 0.02396 *
#> Roy 5 0.3846 4.385 5 57.0 0.00191 **
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1This model (rohwer.mod2) is similar in spirit to the two
models (rohwer.ses1 and rohwer.ses2) fit for
the two SES groups separately and show in Figure @ref(fig:rohwer-HE1),
except that model rohwer.mod2 assumes a common
within-groups error covariance matrix and allows overall tests.
To illustrate model rohwer.mod2, we construct an HE plot
for SAT and PPVT shown in Figure
@ref(fig:rohwer-HE4). To simplify this display, we show the hypothesis
ellipses for the overall effects of the PA tests in the baseline
high-SES group, and a single combined ellipse for all the
SESLo: interaction terms that we tested previously,
representing differences in slopes between the low and high-SES
groups.
Because SES is “treatment-coded” in this model, the ellipse for each
covariate represents the hypothesis that the slopes for that covariate
are zero in the high-SES baseline category. With this parameterization,
the ellipse for Slopes represents the joint hypothesis that
slopes for the covariates do not differ in the low-SES group.
colors <- c("red", "blue", rep("black",5), "#969696")
heplot(rohwer.mod2, col=c(colors, "brown"),
terms=c("SES", "n", "s", "ns", "na", "ss"),
hypotheses=list("Regr" = c("n", "s", "ns", "na", "ss"),
"Slopes" = coefs[grep(":", coefs)]))
HE plot for SAT and PPVT, fitting the model
rohwer.mod2 that allows unequal slopes for the covariates.
Comparing Figure @ref(fig:rohwer-HE4) for the heterogeneous slopes
model with Figure @ref(fig:rohwer-HE2) (left) for the homogeneous slopes
model, it can be seen that most of the covariates have ellipses of
similar size and orientation, reflecting similar evidence against the
respective null hypotheses, as does the effect of SES,
showing the greater performance of the high-SES group on all response
measures. Somewhat more subtle, the error ellipse is noticeably smaller
in Figure @ref(fig:rohwer-HE4), reflecting the additional variation
accounted for by differences in slopes.
Recovery from hernia repair
This example uses the Hernior data (from Mosteller & Tukey (1977), Data Exhibit 8,
p. 567-568), comprising data on measures of post-operative recovery of
32 patients undergoing an elective herniorrhaphy operation, in relation
to pre-operative measures.
The outcome measures are:
leave, the patient’s condition upon leaving the recovery room (a 1-4 scale, 1=best),nurse, level of nursing required one week after operation (a 1-5 scale, 1=worst) andlos, length of stay in hospital after operation (in days)
The predictor variables are:
- patient
age,sex, - `pstat, physical status ( a 1-5 scale, with 1=perfect health, …, 5=very poor health),
build, body build (a 1-5 scale, with 1=emaciated, …, 5=obese), and- preoperative complications with (
cardiac) heart and respiration (resp), 1-4 scales, 1=none, …, 4=severe.
data(Hernior)
str(Hernior)
#> 'data.frame': 32 obs. of 9 variables:
#> $ age : int 78 60 68 62 76 76 64 74 68 79 ...
#> $ sex : Factor w/ 2 levels "f","m": 2 2 2 2 2 2 2 1 2 1 ...
#> $ pstat : int 2 2 2 3 3 1 1 2 3 2 ...
#> $ build : int 3 3 3 5 4 3 2 3 4 2 ...
#> $ cardiac: int 1 2 1 3 3 1 1 2 2 1 ...
#> $ resp : int 1 2 1 1 2 1 2 2 1 1 ...
#> $ leave : int 2 2 1 1 2 1 1 1 1 2 ...
#> $ los : int 9 4 7 35 9 7 5 16 7 11 ...
#> $ nurse : num 3 5 4 3 4 5 5 3 5 3 ...All predictors model
We begin with a model fitting all predictors. Note that the ordinal
predictors, pstat, build, cardiac
and resp could arguably be treated as factors, rather than
linear, regression terms. Doing so would give tests for nonlinear
effects of their relations with the responses. We ignore this
possibility in this example.
Hern.mod <- lm(cbind(leave, nurse, los) ~ age + sex + pstat + build + cardiac + resp,
data=Hernior)
Anova(Hern.mod)
#>
#> Type II MANOVA Tests: Pillai test statistic
#> Df test stat approx F num Df den Df Pr(>F)
#> age 1 0.143 1.27 3 23 0.307
#> sex 1 0.026 0.21 3 23 0.892
#> pstat 1 0.333 3.84 3 23 0.023 *
#> build 1 0.257 2.65 3 23 0.073 .
#> cardiac 1 0.228 2.26 3 23 0.108
#> resp 1 0.248 2.53 3 23 0.082 .
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1The results of the multivariate tests above are somewhat
disappointing. Only the physical status predictor (pstat)
appears to be significant at conventional levels.
The univariate models for each response are implicit in the MLM
Hern.mod. These can be printed using
summary(), or we can use summary() to extract
certain statistics for each univariate response model, as we do
here.
Hern.summary <- summary(Hern.mod)
unlist(lapply(Hern.summary, function(x) x$r.squared))
#> Response leave Response nurse Response los
#> 0.5918 0.2474 0.3653More conveniently, the function heplots::glance.mlm()
extends broom::glance.lm() to give a one-line summary of
statistics for each response variable in a MLM. The R2 and F statistics are those for each
overall model assessing the impact of all predictors.
glance.mlm(Hern.mod)
#> # A tibble: 3 × 9
#> response r.squared adj.r.squared sigma fstatistic numdf dendf p.value nobs
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <int>
#> 1 leave 0.592 0.494 0.388 6.04 6 25 0.000519 32
#> 2 nurse 0.247 0.0668 0.841 1.37 6 25 0.265 32
#> 3 los 0.365 0.213 5.62 2.40 6 25 0.0573 32Univariate tests for predictors in each of these models (not shown
here) are hard to interpret, and largely show only significant effects
for the leave variable. Yet, the R2 values for the other
responses are slightly promising. We proceed to a multivariate overall
test of B = 0 for all
predictors, whose term names can be easily extracted from the rownames
of the coefficients.
# test overall regression
(predictors <- rownames(coef(Hern.mod))[-1])
#> [1] "age" "sexm" "pstat" "build" "cardiac" "resp"
Regr <- linearHypothesis(Hern.mod, predictors)
print(Regr, digits=5, SSP=FALSE)
#>
#> Multivariate Tests:
#> Df test stat approx F num Df den Df Pr(>F)
#> Pillai 6 1.10198 2.4192 18 75.000 0.0041356 **
#> Wilks 6 0.21734 2.6046 18 65.539 0.0025239 **
#> Hotelling-Lawley 6 2.26797 2.7300 18 65.000 0.0016285 **
#> Roy 6 1.55434 6.4764 6 25.000 0.0003232 ***
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1clr <- c("red", "darkgray", "blue", "darkgreen", "magenta", "brown", "black")
vlab <- c("LeaveCondition\n(leave)",
"NursingCare\n(nurse)",
"LengthOfStay\n(los)")
hyp <- list("Regr" = predictors)
pairs(Hern.mod,
hypotheses=hyp,
col=clr, var.labels=vlab,
fill=c(TRUE,FALSE), fill.alpha = 0.1,
cex=1.25)
HE pairs plot for Hernior data
A pairs() plot for the MLM gives the set of plots shown
in Figure @ref(fig:hern-pairs) helps to interpret the relations among
the predictors which lead to the highly significant overall test. Among
the predictors, age and sex have small and insignificant effects on the
outcome measures jointly. The other predictors all contribute to the
overall test of B = 0,
though in different ways for the various responses. For example, in the
panel for (leave, los) in Figure
@ref(fig:hern-pairs), it can be seen that while only pstat
individually is outside the E ellipse,
build and resp contribute to the overall test
in an opposite direction.
Canonical analysis
In this multivariate regression example, all of the terms in the
model Hern.mod have 1 df, and so plot as lines in HE plots.
An alternative view of these effects can be seen in canonical
discriminant space, which, for each predictor shows the scores on the
linear combination of the responses that contributes most to the
multivariate test of that effect, together with the weights for the
responses.
We use candiscList() to calculate the canonical analyses
for all predictor terms in Hern.mod.
1D canonical discriminant plots for all terms can be obtained
interactively with a menu, simply by plotting the Hern.canL
object.
Plots for separate terms are produced by the lines below, and shown in Figure @ref(fig:hern-can1) and Figure @ref(fig:hern-can2).
For pstat and build:
1D Canonical discriminant plots for physical status (pstat)
and build. The canonical scores are such that better
outcomes are associated with smaller scores. Arrows show the
correlations of the responses with the 1D canonical scores.
For age and cardiac:
1D Canonical discriminant plots for age and
cardiac. The canonical scores are such that better outcomes
are associated with smaller scores.
In these plots, the canonical scores panel shows the linear combinations of the response variables which have the largest possible R2. Better outcomes correspond to numerically smaller canonical scores. The arrows in the structure panel are proportional to the canonical weights.
These plots provide simple interpretations of the results for the canonical combinations of the responses. Better physical status, smaller body build, lower age and absence of cardiac complications are all positively related to better outcomes.
Grades in a Sociology Course
The data set SocGrades contains four outcome measures on
student performance in an introductory sociology course together with
six potential predictors. These data were used by Marascuilo & Levin (1983) for an example of
canonical correlation analysis, but are also suitable as examples of
multivariate multiple regression, MANOVA, MANCOVA and step-down analysis
in multivariate linear models.
The outcome measures used here are three test scores during the
course, midterm1, midterm2,
final, and a course evaluation (eval).2
Predictor variables are:
class, the student’s social class (an ordered factor with levels1>2>3)sex,gpa, grade point average,boards, College Board test scores,hssoc, previous high school unit in sociology? (with valuesno,yes), andpretest, score on a course pretest.
str(SocGrades)
#> 'data.frame': 40 obs. of 10 variables:
#> $ class : Ord.factor w/ 3 levels "3"<"2"<"1": 2 2 2 1 2 1 3 2 1 2 ...
#> $ sex : Factor w/ 2 levels "F","M": 2 2 2 2 2 2 1 2 2 1 ...
#> $ gpa : num 3.55 2.7 3.5 2.91 3.1 3.49 3.17 3.57 3.76 3.81 ...
#> $ boards : int 410 390 510 430 600 610 610 560 700 460 ...
#> $ hssoc : Factor w/ 2 levels "no","yes": 1 1 1 1 1 1 1 1 2 2 ...
#> $ pretest : int 17 20 22 13 16 28 14 10 28 30 ...
#> $ midterm1: int 43 50 47 24 47 57 42 42 69 48 ...
#> $ midterm2: int 61 47 79 40 60 59 61 79 83 67 ...
#> $ final : int 129 60 119 100 79 99 92 107 156 110 ...
#> $ eval : int 3 1 1 1 2 1 3 2 1 1 ...Models
The basic MLM is fit below as grades.mod with all
predictor variables.
data(SocGrades)
grades.mod <- lm(cbind(midterm1, midterm2, final, eval) ~
class + sex + gpa + boards + hssoc + pretest,
data=SocGrades)
Anova(grades.mod, test="Roy")
#>
#> Type II MANOVA Tests: Roy test statistic
#> Df test stat approx F num Df den Df Pr(>F)
#> class 2 1.567 11.75 4 30 7.3e-06 ***
#> sex 1 0.553 4.01 4 29 0.0104 *
#> gpa 1 1.208 8.76 4 29 9.2e-05 ***
#> boards 1 0.731 5.30 4 29 0.0025 **
#> hssoc 1 0.035 0.25 4 29 0.9052
#> pretest 1 0.313 2.27 4 29 0.0859 .
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Screening for interactions
In both univariate and multivariate response models, it is often
useful to screen for higher-order terms (interactions, non-linear
predictors). This can most easily be done using update(),
as we do below. First, try the extended model with all pairwise
interactions of the predictors. In the model formula, ~.^2,
the . represents all terms in the model, and the
^2 generates all products of terms, such as
class:sex, class:gpa, and so forth.
grades.mod2 <- update(grades.mod, . ~ .^2)
Anova(grades.mod2, test="Roy")
#>
#> Type II MANOVA Tests: Roy test statistic
#> Df test stat approx F num Df den Df Pr(>F)
#> class 2 2.817 7.04 4 10 0.0058 **
#> sex 1 0.487 1.09 4 9 0.4152
#> gpa 1 1.998 4.49 4 9 0.0286 *
#> boards 1 2.338 5.26 4 9 0.0183 *
#> hssoc 1 0.281 0.63 4 9 0.6522
#> pretest 1 0.510 1.15 4 9 0.3946
#> class:sex 2 2.039 5.10 4 10 0.0168 *
#> class:gpa 2 0.982 2.45 4 10 0.1137
#> class:boards 2 0.522 1.31 4 10 0.3321
#> class:hssoc 2 0.356 0.89 4 10 0.5041
#> class:pretest 2 1.005 2.51 4 10 0.1082
#> sex:gpa 1 0.269 0.60 4 9 0.6694
#> sex:boards 1 0.184 0.41 4 9 0.7944
#> sex:hssoc 1 0.909 2.04 4 9 0.1714
#> sex:pretest 1 0.885 1.99 4 9 0.1795
#> gpa:boards 1 0.447 1.00 4 9 0.4537
#> gpa:hssoc 1 0.596 1.34 4 9 0.3269
#> gpa:pretest 1 0.472 1.06 4 9 0.4291
#> boards:hssoc 1 0.353 0.80 4 9 0.5573
#> boards:pretest 1 0.705 1.59 4 9 0.2593
#> hssoc:pretest 1 1.464 3.29 4 9 0.0635 .
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1In the results above, only the interaction of class:sex
is significant, and the main effects of hssoc and
pretest remain insignificant. A revised model to explore is
grades.mod3,
grades.mod3 <- update(grades.mod, . ~ . + class:sex - hssoc - pretest)
Anova(grades.mod3, test="Roy")
#>
#> Type II MANOVA Tests: Roy test statistic
#> Df test stat approx F num Df den Df Pr(>F)
#> class 2 1.588 11.91 4 30 6.5e-06 ***
#> sex 1 0.575 4.17 4 29 0.00864 **
#> gpa 1 1.434 10.40 4 29 2.4e-05 ***
#> boards 1 0.895 6.49 4 29 0.00074 ***
#> class:sex 2 0.450 3.38 4 30 0.02143 *
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1A pairwise HE plot for all responses (Figure @ref(fig:grades-pairs)
shows that nearly all effects are in the expected directions: higher
gpa, boards, class leads to
better performance on most outcomes. The interaction of
class:sex seems to be confined largely to
midterm1.
HE pairs plot for SocGrade, model grades.mod3.
These effects are easier to appreciate for the three exam grades jointly in a 3D HE plot when you can rotate it interactively. A snapshot is shown in Figure @ref(fig:grades-HE3D).
3D HE plot for SocGrades, model grades.mod3
Interactive rotation of this plot shows that the effect of
class is only two dimensional, and of these, one dimension
is very small. The major axis of the class ellipsoid is
aligned with increasing performance on all three grades, with the
expected ordering of the three social classes.
Canonical analysis
The representation of these effects in canonical space is
particularly useful here. Again, use candiscList() to
compute the canonical decompositions for all terms in the model, and
extract the canonical R2 from the terms in the
result.
# calculate canonical results for all terms
grades.can <- candiscList(grades.mod3)
# extract canonical R^2s
unlist(lapply(grades.can, function(x) x$canrsq))
#> class1 class2 sex gpa boards class:sex1 class:sex2
#> 0.61362 0.02419 0.36527 0.58915 0.47227 0.31046 0.13293We use heplot() on the "candiscList" object
to show the effects of class in canonical space, giving
Figure @ref(fig:grades-can-class).
# plot class effect in canonical space
heplot(grades.can, term="class",
scale=4, fill=TRUE, var.col="black", var.lwd=2)
Canonical HE plot for class effect in
grades.mod3
It can be seen in Figure @ref(fig:grades-can-class) that nearly all variation in exam performance due to class is aligned with the first canonical dimension. The three tests and course evaluation all have similar weights on this dimension, but the course evaluation differs from the rest along a second, very small dimension.
1D plots of the canonical scores for other effects in the model are also of interest, and provide simple interpretations of these effects on the response variables. The statements below produce the plots shown in Figure @ref(fig:grades-can-all).
1D Canonical discriminant plots for sex and
gpa. Higher canonical scores reflect better course
performance.
It is readily seen that males perform better overall, but the effect
of sex is strongest for the midterm2. As well,
increasing course performance on tests is strongly associated with
gpa.
References
This solution was suggested in an answer to a Stackoverflow question, https://stackoverflow.com/questions/73859139/how-to-make-a-scatterplot-rectangular-matrix-y1-y2-x1-x2-in-r↩︎
It is arguable that the students’ course evaluation should not be considered a response variable here. It could be used as a predictor in a follow-up, step-down analysis, which would address the separate question of whether the effects on exam grades remain, when
evalis controlled for.↩︎