Chapter 8: Analysis of Variance (ANOVA) and

Covariance (ANCOVA)
Table of contents

1 Introduction to Analysis of Variance (ANOVA) 3

2 One Way ANOVA 5

3 Assumptions and Transformations 13

4 Two-Way ANOVA 16

5 Two Way ANOVA with Interaction 21

6 Indicator Variables 31
6.1 Another example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

7 Analysis of Covariance (ANCOVA) 38

8 Summary 42

“To consult a statistician after an experiment is finished is often merely to ask him
to conduct a post mortem examination. He can perhaps say what the experiment
died of.” – Sir RA Fisher

2
1 Introduction to Analysis of Variance
(ANOVA)

We consider ANOVA models for data which have, in many cases, been collected using
experimental designs. The model provides a quantitative assessment of the treatment effects.
The first model we shall consider is the One-Way ANOVA model. The data for these models
are used when only one set of treatments is to be compared. Here the set of treatments is
called a factor and the various treatments are referred to as the factor levels.
A One-Way ANOVA model is expressed in terms of an overall effect (the overall response
mean) and a treatment effect (the average effect for a particular treatment or level on the
response variable). The model has the form
fit = overall effect + treatment effect.
The second model we shall consider later is a Two-Way Model. The experiments used to
produce these data may be from two sets of treatments (that is, two factors). Again we refer
to the treatments for each factor as the levels for each factor. We shall assume that the data
are fully balanced in that the same number of observations is obtained for each combination
of factor levels. For instance, if factor 1 has 3 levels and factor 2 has 2 levels then the total
number of observations must be a multiple of 6.
The computer output for an ANOVA often includes the mean response for each combination
of factor levels. These means are often represented as a table with the rows corresponding to
the levels of the first factor and the columns corresponding to the levels of the second factor.
For convenience we shall refer to the levels of factor 1 as the rows and we shall refer to the
levels of factor 2 as the columns. There are two possible Two-Way ANOVA models. The first
model assumes that the effects of factors 1 and 2 are independent. The appropriate model is
expressed in terms of the overall effect (overall mean), the row effect and the column effect.
That is
fit = overall effect + row effect + column effect.
The second Two-Way ANOVA allows for an interaction between the row and column effects.
That is
fit = overall effect + row effect + column effect + interaction effect.
Finally we shall consider an Analysis of Covariance (ANCOVA) model. In these experiments
paired (𝑋, 𝑌 ) measurements are obtained for each observation. 𝑋 is the explanatory variable

3
and 𝑌 is the response variable. When there is only one experimental factor the following model
is applied,
fit = overall effect + treatment effect + 𝑋-effect.
ANCOVA models are, in essence, a mixture of regression and ANOVA models. For all the
above models
observed = fitted + residual.
The residuals are used to test the adequacy of the model fitted as in regression.

4
2 One Way ANOVA

As part of a multi-lab study, four fabrics were tested for flammability at the National Bureau
of Standards. The burn times in seconds were recorded after a paper tab was ignited on the
hem of each fabric. The experimental data are presented below (Table 2.1; taken from p.496
of Bhattacharyya and Johnson [1].

library(tidyverse)
theme_set(theme_minimal())

download.file(
url = "http://www.massey.ac.nz/~anhsmith/data/fabric.RData",
destfile = "fabric.RData")

load("fabric.RData")

dtf <- fabric |> unstack(burntime ~ Fabric)

dtf

Note that the response variable 𝑌 is quantitative in that they are measurements of burn times
in seconds. The five measurements for each fabric are assumed to be a random sample for all
possible burn times for that fabric so that the five readings are true replications.
In this example, each of the four fabrics is replicated the same number of times, namely five, so
the experiment is said to be “balanced”. The approaches explained in this section on One-Way

Table 2.1: Fabric Burntime data

Fabric.1 Fabric.2 Fabric.3 Fabric.4

17.8 11.2 11.8 14.9
16.2 11.4 11.0 10.8
17.5 15.8 10.0 12.8
17.4 10.0 9.2 10.7
15.0 10.4 9.2 10.7

5
ANOVA can easily be extended to unbalanced experiments. This is not the case for Two-Way
ANOVA.
Using the same approach as in Chapter 4, we could compare any two fabrics by a 𝑡-test or
by considering the confidence interval for the difference in means. With 4 fabrics, there are 6
comparisons which could be made (Fabric 1 vs. Fabric 2 etc.).
How should we proceed? Should we test each of these 6 differences in means? Unfortunately,
there is a problem in this procedure. One tends to find too many significant differences between
means. There are two reasons for this:

1. The comparisons are not independent. If one fabric mean happened to be unduly large
by chance, every comparison involving that mean would tend to yield a significant (say,
at the 5% level) difference with each of the other means.
2. For one comparison, the 95% confidence level (5% level of the 𝑡-test) would yield a
significant difference between the means in about 5% of samples of these two fabrics even
if the fabrics responded equally to the flammability test. The more comparisons
that are made on pairs of fabrics, the more likely it is that sooner or later some of the
difference will appear significant at the 5% level, even when there is no difference between
the fabrics. This is true for any statistical test and not just 𝑡-tests. If a number of tests
are carried out on the same set of data, eventually some false significant results will be
obtained. It has been suggested that if you torture data enough, it will confess, whether
or not it is guilty.

One way out of this dilemma is to carry out a single test, an 𝐹 -test, which can be thought
of as giving an average value of the comparisons between treatments. The way it does this
should become clear in the next few sections.
The burn times are plotted in Figure 2.1 in which the scale on the horizontal axis indicates
the number of the fabric. The times for fabrics 2 and 4 appear fairly similar to the times for
fabric 3. But the burn times for fabric 1 appear to be higher.

fabric |>
ggplot() +
aes(x = Fabric, y = burntime) +
geom_hline(aes(yintercept = mean(burntime)), alpha = .7) +
geom_point() +
annotate("text",
x = .7,
y = mean(fabric$burntime) + 0.3,
label = "Overall mean",
alpha=.7
)

6
 18

16
burntime

14

Overall mean
12

10

Fabric 1 Fabric 2 Fabric 3 Fabric 4

Fabric

Figure 2.1: Burn time vs fabric Id

Let 𝑦𝑖𝑗 be the 𝑗𝑡ℎ observed value in the 𝑖𝑡ℎ treatment (fabric type in the above example); 𝑦𝑖̄
be the mean of the 𝑖𝑡ℎ treatment; 𝑦 ̄ be the overall mean of all the observations; 𝑘 is the total
number of treatments being compared. As usual the observed data can be modelled by
observed = fit + residual.
However, the appropriate model for the fit is different for these data. For a treatment 𝑖
observation
fit =𝑦𝑖̄ , the mean of the 𝑖𝑡ℎ treatment
or, adding and subtracting 𝑦 ̄ ,
fit =𝑦 ̄ + (𝑦𝑖̄ − 𝑦)̄ =overall mean + treatment effect
Clearly, residual = observed - fit; so the residual for 𝑦𝑖𝑗 is equal to
residual = 𝑦𝑖𝑗 − (𝑦 ̄ + (𝑦𝑖̄ − 𝑦))
̄ = 𝑦𝑖𝑗 − 𝑦𝑖̄
Since observed = fit + residual, we have

𝑦𝑖𝑗 = 𝑦 ̄ + (𝑦𝑖̄ − 𝑦)̄ + (𝑦𝑖𝑗 − 𝑦𝑖̄ )

observed = overall mean + treatment effect + residual.

7
That is
𝑦𝑖𝑗 = 𝑚 + 𝑡𝑖 + 𝑒𝑖𝑗
where the three terms on the right are:
𝑚 =: the overall mean, 𝑦,̄
𝑡𝑖 =: the treatment effect, adjusted for the mean. i.e. (𝑦𝑖̄ − 𝑦),
̄
𝑒𝑖𝑗 =: the residual or error, (𝑦𝑖𝑗 - 𝑦𝑖̄ ). See Figure 2.2 (produced manually) for an illustration
of the treatment effect for the fabric data.

Figure 2.2: Explanation of factor effects

From the above model we obtain the equation

(𝑦𝑖𝑗 − 𝑦)̄ = (𝑦𝑖̄ − 𝑦)̄ + (𝑦𝑖𝑗 − 𝑦𝑖̄ ).

It can be shown that the sums of squares follow from this equation if each term is squared and
then summed over all the values in the sample. Note, the summation is over both 𝑖 and 𝑗.

2 2 2
∑ (𝑦𝑖𝑗 − 𝑦)̄ = ∑ (𝑦𝑖̄ − 𝑦)̄ + ∑ (𝑦𝑖𝑗 − 𝑦𝑖̄ )
𝑖,𝑗 𝑖,𝑗 𝑖,𝑗

That is, SS TOTAL = SS FACTOR + SS ERROR.

8
Mean squares (MeanSq or MS) are obtained by dividing the sums of squares (SS) by their
respective degrees of freedom (df), as shown below:

SS df MeanSq
FACTOR k-1 FACTOR SS/(n-1)
ERROR n-k ERROR SS/(n-k
TOTAL n-1 TOTAL SS/(n-1)

Finally, the 𝐹 statistic for the FACTOR is obtained by dividing the FACTOR MeanSq by the
ERROR MeanSq. The associated degrees of freedom are 𝑘 − 1 for the numerator and 𝑛 − 𝑘 for
the denominator. We display the SS, MS in the form of a table called the one-way ANOVA
table.
For fabric data, the one-way ANOVA R output is shown below.

oneway.model <- aov(burntime ~ Fabric, data = fabric)

summary(oneway.model)

Df Sum Sq Mean Sq F value Pr(>F)

Fabric 3 120.50 40.17 13.89 0.000102 ***
Residuals 16 46.26 2.89
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

If there is no real difference between the fabrics, we would expect the 𝐹 Statistic to be about 1.
If there is a real difference, we would expect the 𝐹 statistics to be larger than 1. From tables,
the 95th percentile of the 𝐹 statistic with 3 and 16 degrees of freedom is 3.24. As our value
of 13.89 is more than this, the 𝐹 statistic is significant at the 5% level. This is also confirmed
by the 𝑝-value, which is 0.000. So there is a significant difference between the mean burning
times of the fabrics. This obviously doesn’t mean that all the fabrics differ significantly from
each other. It means that there is a significant difference for at least one pair of fabrics.
The individual confidence intervals for the fabric means may be obtained using the pooled
error estimate S of 1.7 (the square root of MS Error of 2.891). For example, the confidence
interval for the mean burn time of fabric 1 is 𝑚𝑒𝑎𝑛 ± 𝑡𝑒𝑟𝑟𝑜𝑟 𝑑𝑓,0.975 × 𝑆 or 16.78 ± 2.12 × 1.7
or (15.17, 18.39).

fabric |>
group_by(Fabric) |>
summarise(

9
 mean = mean(burntime),
sd = sd(burntime),
n = n(),
se = sd / sqrt(n),
ci = qt(0.975, df = n - 1) * se
) |>
ggplot() +
aes(x = Fabric, y = mean, group = factor(1)) +
geom_line() +
geom_point() +
geom_errorbar(aes(ymin = mean - ci,
ymax = mean + ci),
width = .1)

18

16
mean

14

12

10

Fabric 1 Fabric 2 Fabric 3 Fabric 4

Fabric

Figure 2.3: CIs using pooled SD

The 95% confidence intervals shown in Figure 2.3 indicate that fabric 1 differs significantly
from the other three fabrics. Note that each CI in the above figure has individual Type I error
rate, which makes the overall comparison difficult.
For comparing many treatments, we may perform multiple comparison tests. The following R
output shows the adjusted confidence intervals for the difference in fabric means.

10
 TukeyHSD(oneway.model)

Tukey multiple comparisons of means

95% family-wise confidence level

Fit: aov(formula = burntime ~ Fabric, data = fabric)

$Fabric
diff lwr upr p adj
Fabric 2-Fabric 1 -5.02 -8.09676 -1.94324 0.0013227
Fabric 3-Fabric 1 -6.54 -9.61676 -3.46324 0.0000851
Fabric 4-Fabric 1 -4.80 -7.87676 -1.72324 0.0019981
Fabric 3-Fabric 2 -1.52 -4.59676 1.55676 0.5094118
Fabric 4-Fabric 2 0.22 -2.85676 3.29676 0.9968426
Fabric 4-Fabric 3 1.74 -1.33676 4.81676 0.3968476

This adjustment in constructing the confidence interval for the difference in the treatment
means was proposed by Tukey (known as the Tukey’s Honest Significant Difference (HSD)).
The idea behind the multiple comparison test proposed Tukey (or by others such as Duncan)
is that the error rate is controlled for the family of interval as against individual intervals. We
will rely on the software programs to perform such treatment comparisons and obtain plots
for multiple comparison; see Figure 2.4. Note that we used the par() function because the
Y-axis labels are bit long.

par(mar=c(5.1, 9, 4.1, 2.1))

plot(TukeyHSD(oneway.model), las=1 , col="brown")

11
 95% family−wise confidence level

Fabric 2−Fabric 1
Fabric 3−Fabric 1
Fabric 4−Fabric 1
Fabric 3−Fabric 2
Fabric 4−Fabric 2
Fabric 4−Fabric 3

−10 −5 0 5

Differences in mean levels of Fabric

Figure 2.4: Tukey HSD plot

12
3 Assumptions and Transformations

For the one way ANOVA, it is assumed that the burn time variances for each treatment are
the same. Although we can never be sure whether assumptions are valid, we can look for
indications that the assumptions may not be realistic.
The sample standard deviations of the treatment groups could be plotted against the sample
means of the treatment groups. For the fabric example the means and standard deviations of
the fabrics are given below.

summary Fabric 1 Fabric 2 Fabric 3 Fabric 4

Mean 𝑦𝑖̄ 16.78 11.76 10.24 11.98
Standard deviation 𝑆𝑖 1.167 2.330 1.144 1.862

fabric |>
group_by(Fabric) |>
summarise(
mean = mean(burntime),
sd = sd(burntime)
) |>
ggplot() +
aes(x = mean, y = sd, group = factor(1)) +
geom_point()

13
 2.0
sd

1.5

10 12 14 16
mean

Figure 3.1: SD vs mean for four fabrics

The plot of SD vs. mean is shown in Figure 3.1. With only four fabrics in the sample, it is
difficult to make any definitive claim. If the assumptions were valid, we would expect the four
points to fall approximately along a horizontal band indicating constant standard deviations,
and hence variances, regardless of the means of the groups. Figure 3.1 suggests that this is
the case, so the assumption of equal variances appears to be valid.
A formal test for equal variances may also be performed. In Bartlett’s test, the null hy-
pothesis of equal variances is tested. This test requires the response variable to be normally
distributed where as the alternative test known as the Levene’s test is applicable for any
continuous distribution. The 𝑝-value for the Bartlett’s test for the fabric data is 0.447. This
suggests that the null hypothesis of equal variances for the four fabric burn times be accepted.

bartlett.test(burntime ~ Fabric, data = fabric)

Bartlett test of homogeneity of variances

data: burntime by Fabric

Bartlett's K-squared = 2.6606, df = 3, p-value = 0.447

14
 car::leveneTest(burntime ~ Fabric, data = fabric)

Levene's Test for Homogeneity of Variance (center = median)

Df F value Pr(>F)
group 3 0.1788 0.9092
16

If the standard deviations seem to be increasing with the means, a transformation such as
the square root or logarithm could be tried. The comments of chapter 4 also apply to the
one way ANOVA. However, before performing such a data transformation it is important that
the data be checked for outliers. Outliers may inflate the standard deviation for one or more
treatments. Such outliers should be checked for accuracy. Even when there is no obvious
reason for an outlier, it is probably best to delete such a value if it is obvious that this value
is causing a major distortion of the data. This will make our data unbalanced, but that does
not matter for one way ANOVA.
The 𝐹 statistic is based on the null hypothesis that there is no difference (in the population)
between treatment means. As we have noted before, a large value of 𝐹 would indicate that
the null hypothesis is not valid and that differences between treatments do exist. However, if
the variances for the different treatments vary considerably, then this test is no longer valid.

15
4 Two-Way ANOVA

We discuss two-way ANOVA model using the following example. The strength of concrete
(𝑌 , measured in MPa) is affected by the type of aggregate (stone, a blocking variable) and
the type of cement (the treatment factor) used. An experiment was conducted in order to
investigate the effect of aggregate and cement on concrete strength. In all other respects the
concrete was the same. That is, same mixing ratios, the same water and the same mixing
procedure was used. Ignoring any interaction between aggregate and cement the following
model is to be fitted to the data:
fitted = overall effect + aggregate effect + cement effect.
A single testing was done for each cement and each aggregate, producing the balanced set of
results shown in Table 4.1.

concrete <- read_csv("http://www.massey.ac.nz/~anhsmith/data/concrete.txt",

col_types = "dff") # double, factor, factor

In Figure 4.1, the computation of row (cement) and column (Aggregate) effects is explained.
Clearly the rows correspond to the four cements and the columns correspond to the three
aggregates.

Figure 4.1: Explanation of row and column factor effects

The row effect is taken as the additional row effect after the overall value 14.42 has been
fitted. Similarly the column effect is taken as the additional column effect after the overall
value has been fitted. Note the following points:

16
 Table 4.1: Concrete strength data

Strength Cement Aggregate

4 1 1
5 2 1
6 3 1
7 4 1
10 1 2
8 2 2
9 3 2
10 4 2
22 1 3
28 2 3
34 3 3
30 4 3

a.: Overall value is the overall mean, 14.42.

b.: The row effect for Row 1 is 12 − 14.42 = −2.42. In other words, the row effect is the row
mean minus the overall mean. The column effects are calculated similarly.
c.: The row effects add to zero, although in practice, as in this example, there is some rounding
error. Likewise, the column effects add to zero. If the data were not balanced the effects would
not necessarily add to zero.
d.: In each cell, fitted values and residuals could be calculated. For example, for cell (1, 1), we
obtain the fitted value as 14.42 + (−2.42) + (−8.92) = 3.08. Hence, residual = observed-fitted
= 4 − 3.08 = 0.92.
ANOVA tables are a tidy way of writing down the sums of squares, degrees of freedom and
mean squares. We are basically concerned with the variation in the dependent variable about
its mean and the amount of this variation explained by the explanatory variables, which in
this case are the row and column effects. In the SS column in the ANOVA table we break
down the total variation according to its source, namely ROWS, COLUMNS and ERROR.

Figure 4.2: Formation of ANOVA table

17
In the ANOVA table, (given as Figure 4.2) the number of rows is denoted by 𝑟 and the number
of columns is denoted by 𝑐. The Error degrees of freedom are obtained by subtracting the
ROW and COLUMN degrees of freedom from the total degrees of freedom. The mean squares
are obtained by dividing the sums of squares by their respective degrees of freedom. Note that
118.27 (Mean Square corresponding to Total) is the variance of the original observations.
The R output for the two-way ANOVA fit is given below. The entries relating to TOTAL are
not displayed in R.

additive.model <- aov(Strength ~ Cement + Aggregate, data = concrete)

summary(additive.model)

Df Sum Sq Mean Sq F value Pr(>F)

Cement 3 34.9 11.6 1.46 0.317
Aggregate 2 1218.2 609.1 76.40 5.39e-05 ***
Residuals 6 47.8 8.0
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Clearly a large variance (MS) for the rows (Cement) would suggest a significant difference
between the Cement-group means and a large variance (MS) for the columns (Aggregate)
would suggest a significant difference between the Aggregate-group means.
To test whether a factor has a significant influence, we calculate the 𝐹 test statistic. As before,
this statistic is the ratio of two mean squares. Hence, to test whether the rows have the same
means in the population (i.e., there’s no “row effect”), the 𝐹 statistic is
Row MS
𝐹 =
Error MS
with the corresponding numerator and denominator degrees of freedom. Likewise, to test
whether the columns have the same means in the population (i.e., there’s no “coumn effect”),
the 𝐹 statistic is
Column MS
𝐹 =
Error MS
with the corresponding numerator and denominator degrees of freedom.
To test the significance of the Cement effect,
11.64
𝐹 = = 1.5
7.97
with 3 and 6 d.f. Not significant. To test the significance of the Aggregate effect,
609.08
𝐹 = = 76.4
7.97

18
with 2 and 6 d.f. Very significant.
These results wouldn’t be surprising to us had we explored the mean concrete strength for the
3 levels of Aggregate and 4 levels of Cement as shown in Figure 4.3, which are connected by
a line, is known as the main effects plot.

p1 <- concrete |>

group_by(Cement) |>
summarise(Mean = mean(Strength)) |>
ggplot() +
aes(y = Mean,
x = Cement) +
geom_point() +
geom_line(aes(group = 1)) +
xlab("Cement") +
ggtitle("Main effects plot of Cement") +
geom_hline(yintercept = mean(concrete$Strength), alpha = .7) +
ylim(5,30)

p2 <- concrete |>

group_by(Aggregate) |>
summarise(Mean = mean(Strength)) |>
ggplot() +
aes(y = Mean,
x = Aggregate) +
geom_point() +
geom_line(aes(group = 1)) +
xlab("Aggregate") +
ggtitle("Main effects plot of Aggregate") +
geom_hline(yintercept = mean(concrete$Strength), alpha = .7) +
ylim(5,30)

gridExtra::grid.arrange(p1, p2, ncol=2)

19
 Main effects plot of Cement Main effects plot of Aggregate
30 30

20 20
Mean

Mean
10 10

1 2 3 4 1 2 3
Cement Aggregate

Figure 4.3: Main effects plots

20
5 Two Way ANOVA with Interaction

Brook and Arnold [3] provided the following data from a milk mixing time experiment.

paddle <- tibble(

Speed = c(70, 70, 70, 110, 110, 110, 150, 150, 150,
70, 70, 70, 110, 110, 110, 150, 150, 150) |> factor(),
Diameter = c(90, 120, 150, 90, 120, 150, 90, 120, 150,
90, 120, 150, 90, 120, 150, 90, 120, 150) |> factor(),
MixTime = c(1490,780,825,575,385,315,195,117,225,
1100,620,690,480,385,400,230,190,145)
)

paddle

# A tibble: 18 x 3
Speed Diameter MixTime
<fct> <fct> <dbl>
1 70 90 1490
2 70 120 780
3 70 150 825
4 110 90 575
5 110 120 385
6 110 150 315
7 150 90 195
8 150 120 117
9 150 150 225
10 70 90 1100
11 70 120 620
12 70 150 690
13 110 90 480
14 110 120 385
15 110 150 400
16 150 90 230
17 150 120 190
18 150 150 145

21
When whole milk is left standing in a vat, the cream rises to the top, making sampling difficult.
A rotating paddle can be used to mix the milk, but too much mixing can damage it. The
aim of the experiment was to see how paddle size and speed of rotation affect the optimum
mixing time. There were two independent runs at three levels of both speed and paddle size.
The data are set out in a two way table in which the rows and columns relate to different
speeds and diameters of the paddle. Again, we have balanced data in that the same number
of measurements occur in each cell of the table. The experimental data may be treated as
separate one way ANOVAs for the Rotational Speed or Paddle Diameter as shown below:

aov(MixTime ~ Speed, data = paddle) |> summary()

Df Sum Sq Mean Sq F value Pr(>F)

Speed 2 1680304 840152 21.72 3.72e-05 ***
Residuals 15 580184 38679
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

aov(MixTime ~ Diameter, data = paddle) |> summary()

Df Sum Sq Mean Sq F value Pr(>F)

Diameter 2 261871 130936 0.983 0.397
Residuals 15 1998618 133241

Clearly, the rotational speed has more influence than diameter of paddle on optimum mixture
time (𝑝 = 0.000 for Rotational Speed while 𝑝 = 0.397 for Paddle Diameter). Note that the
true effect of Paddle Diameter may be masked due to the overestimate of the Error under the
(incorrect) one-way ANOVA model. The mean mixing time is obviously higher for a Rotational
Speed of 70 rpm, whereas Paddle Diameter appears to have a little effect on the mixing time
(see Figure 5.1).

p1 <- paddle |>

group_by(Speed) |>
summarise(mean = mean(MixTime)) |>
ggplot() +
aes(y = mean, x = Speed) +
geom_point() +
geom_path(aes(group = 1)) +
xlab("Speed") +
ggtitle("Main effects plot of Speed") +
geom_hline(yintercept = mean(paddle$MixTime), alpha = .7) +

22
 ylim(150,1000)

p2 <- paddle |>

group_by(Diameter) |>
summarise(mean = mean(MixTime)) |>
ggplot() +
aes(y = mean, x = Diameter) +
geom_point() +
geom_path(aes(group = 1)) +
xlab("Diameter") +
ggtitle("Main effects plot of Diameter") +
geom_hline(yintercept = mean(paddle$MixTime), alpha = .7) +
ylim(150,1000)

gridExtra::grid.arrange(p1, p2, ncol=2)

Main effects plot of Speed Main effects plot of Diameter

1000 1000

750 750
mean

mean

500 500

250 250

70 110 150 90 120 150

Speed Diameter

Figure 5.1: Main effects plots

The visreg package is useful for automatically plotting linear models, including ANOVA.

23
 library(visreg)

aovs <- aov(MixTime ~ Speed, data = paddle)

aovd <- aov(MixTime ~ Diameter, data = paddle)

p1 <- aovs |>

visreg(gg=T) +
ylim(10,1200)

p2 <- aovd |>

visreg(gg=T) +
ylim(10,1200)

gridExtra::grid.arrange(p1, p2, ncol=2)

Warning: Removed 1 rows containing missing values (`geom_point()`).

Removed 1 rows containing missing values (`geom_point()`).

1250 1250

1000 1000

750 750
MixTime

MixTime

500 500

250 250

0 0
70 110 150 90 120 150
Speed Diameter

Whether the effect of Speed on mixing time is independent of the paddle diameter or not
cannot be explored using the above plot. We can explore interactions graphically using inter-
action plots, as shown in Figure 5.2.

24
pmeans <- paddle |>
group_by(Speed, Diameter) |>
summarise(MixTime = mean(MixTime))

p1 <- pmeans |>

ggplot(aes(Speed, MixTime)) +
geom_line(linewidth = 1, aes(group = Diameter, color = Diameter)) +
geom_point(size = 3, aes(color = Diameter))+
scale_color_brewer(palette="Set1")

p2 <- pmeans |>

ggplot(aes(Diameter, MixTime)) +
geom_line(linewidth = 1, aes(group = Speed, color = Speed)) +
geom_point(size = 3, aes(color = Speed)) +
scale_color_brewer(palette="Set2")

gridExtra::grid.arrange(p1, p2, nrow=2)

25
 1000

Diameter
MixTime

90
120
150

500

70 110 150
Speed

1000

Speed
MixTime

70
110
150

500

90 120 150
Diameter

Figure 5.2: Speed*Diameter interaction plot

26
In Figure 5.2, the mean mixing times have been plotted and connected for all factor level
combinations. In the first plot, we’ve put Speed on the x-axis and coloured the points and
lines by Diameter, and then swapped the roles. The lines in the interaction plots are not
parallel. This suggests that the effect of rotational speed is determined, to some extent, by
the effect of paddle diameter (and vice versa). In other words, the effect of rotational speed
on mixing time is not the same for the various levels of paddle diameter.
These interaction plots suggest that we should allow for an interaction term in our Two-Way
ANOVA model.
A two-way ANOVA interaction model is of the form
fit = overall mean + row effect + column effect + (row×column effect).
This model has been fitted to mixing times using R below. Note the syntax * which fits both
the interaction and main effect terms.

aovdsx <- aov(MixTime ~ Speed * Diameter, data = paddle)

summary(aovdsx)

Df Sum Sq Mean Sq F value Pr(>F)

Speed 2 1680304 840152 67.174 3.89e-06 ***
Diameter 2 261871 130936 10.469 0.00448 **
Speed:Diameter 4 205749 51437 4.113 0.03635 *
Residuals 9 112565 12507
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

With this model object, we can make interaction plots automatically using visreg (Fig-
ure 5.3).

visreg(aovdsx, "Speed", by = "Diameter", gg=T) + theme_bw()

27
 90 120 150
1500

1000
MixTime

500

0
70 110 150 70 110 150 70 110 150
Speed

Figure 5.3: Speed * Diameter interaction plot from visreg

Note that the interaction effect is tested by comparing the interaction (i.e. Speed×Diameter)
MS against the residual (i.e. Error) MS using an 𝐹 statistic with 4 and 9 degrees of freedom
(i.e. 𝐹 = 4.11). This 𝐹 -value exceeds the tabulated value 3.63 at the 5% level, so that this
interaction effect is significant at the 5% level (also note that the corresponding 𝑝-value is
smaller than 0.05). In other words, there is evidence that the row effects (i.e. Speed effects)
are NOT constant over columns (i.e. Diameters), or the column effects are not constant over
rows.
The degrees of freedom, d.f., for the numerator, 4, is the product of 2 times 2.
d.f.(rows×columns) = d.f.(rows)× d.f.(columns)
The error degrees of freedom are obtained by subtraction. That is
d.f.(Error) = d.f.(Total)-d.f.(rows)-d.f.(column)-d.f.(rows×columns) = (𝑛 − 1) − (𝑟 − 1) − (𝑐 −
1) − (𝑟 − 1) × (𝑐 − 1) = 17 − 2 − 2 − 4 = 9.
If it could be assumed that the interaction between rows and columns was not large, an
additive (non-interaction) model could be fitted, namely
observed = fit + residual = (overall mean + row effect + column effect) + e.
Consider the additive ANOVA model fitted below. Note the syntax + which fits only the main
effect terms.

28
 aovds <- aov(MixTime ~ Speed + Diameter, data = paddle)

summary(aovds)

Df Sum Sq Mean Sq F value Pr(>F)

Speed 2 1680304 840152 34.312 6.51e-06 ***
Diameter 2 261871 130936 5.347 0.0202 *
Residuals 13 318313 24486
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Notice that the degrees of freedom for the error term in the additive model is the sum of the
d.f. for error and interaction. Similarly,
SS (Error) of Additive Model = SS (Interaction) + SS (Error) of Interaction Model.
Notice that if there was only ONE observation in each cell, it would not be possible to test for
the significance of an interaction. This is the case with the two-way ANOVA we considered in
the previous section (see concrete strength ANOVA output).
The mixtime experimental setup is known as a factorial design where the factor levels are
crossed to form the treatments. The treatments are usually completely randomised. When
factor levels are quantitative, we can also fit a regression model. The set levels of Speed and
Diameter are quantitative. So we can regress the mixing time on the speed and diameter levels.
The advantage with this approach is that we will be able to fit a response surface of mixing
time so that we can look for optimum settings on some cost or practical grounds. Figure 5.4
shows the contour plot of the regression (response) surface of mixing time. This plot suggests
that both speed and diameter must be set at higher levels in general to reduce the mixing time.
But we can choose practically convenient settings such as higher speed but smaller diameter.
The curvature in the contour plot is due to the interaction effect but it tends to be smaller
at higher speeds. The text by Box, Hunter, and Hunter [2] contains many examples on using
experimental designs for response surface optimisation.

visreg2d(aovdsx, "Speed", "Diameter")

29
 MixTime

1200
150
1000
Diameter

800
120
600
400
90
200

70 110 150

Speed

Figure 5.4: 2d contour visreg plot of mixing time

30
6 Indicator Variables

Indicator variable (also known as a dummy or binary variable) is one whose possible values
are either 1 or zero. A value of 1 means a particular attribute or characteristic is present and
a value of zero means the absence. For example, we may define indicator variables for males
and females. Consider- Indicator variable for the male category
𝐼male = 1 for males
0 for females

Indicator variable for the female category

𝐼female = 1 for females
0 for males

In order identify the gender category, we either need either 𝐼𝑚𝑎𝑙𝑒 or 𝐼𝑓𝑒𝑚𝑎𝑙𝑒 and not both.
This is because for the two gender categories, we have only a single degree of freedom. Using
indicator variables, we will be able to include categorical predictors in a regression model. It is
also possible to approach the ANOVA test for equality of means through linear regression.
Consider the fabric burn time data discussed earlier. For the four fabric types, we define the
following four indicator variables,

𝐼1 = 1 for Fabric 1
0 for Fabric 2, 3 and 4
𝐼2 = 1 for Fabric 2
0 for Fabric 1, 3 and 4
𝐼3 = 1 for Fabric 3
0 for Fabric 1, 2 and 4
𝐼4 = 1 for Fabric 4
0 for Fabric 1, 2 and 3

Note that we need only any three of the above indicator variables to identify the fabric category.
For example, with 𝐼1 , 𝐼2 , and 𝐼3 variables, fabric 4 is identified when 𝐼1 = 𝐼2 = 𝐼3 = 0. See
Table 6.1.
Let us regress the burn times on the indicator variables 𝐼1 , 𝐼2 and 𝐼3 .

31
 Table 6.1: Indicators of Fabrics

burntime Fabric I1 I2 I3 I4
17.8 Fabric 1 1 0 0 0
16.2 Fabric 1 1 0 0 0
17.5 Fabric 1 1 0 0 0
17.4 Fabric 1 1 0 0 0
15.0 Fabric 1 1 0 0 0
11.2 Fabric 2 0 1 0 0
11.4 Fabric 2 0 1 0 0
15.8 Fabric 2 0 1 0 0
10.0 Fabric 2 0 1 0 0
10.4 Fabric 2 0 1 0 0
11.8 Fabric 3 0 0 1 0
11.0 Fabric 3 0 0 1 0
10.0 Fabric 3 0 0 1 0
9.2 Fabric 3 0 0 1 0
9.2 Fabric 3 0 0 1 0
14.9 Fabric 4 0 0 0 1
10.8 Fabric 4 0 0 0 1
12.8 Fabric 4 0 0 0 1
10.7 Fabric 4 0 0 0 1
10.7 Fabric 4 0 0 0 1

fabric <- fabric |>

select(burntime, Fabric) |>
mutate(I1 = as.numeric(Fabric=="Fabric 1"),
I2 = as.numeric(Fabric=="Fabric 2"),
I3 = as.numeric(Fabric=="Fabric 3"),
I4 = as.numeric(Fabric=="Fabric 4")
)

fabric

mdl <- lm(burntime ~ I1 + I2 + I3, data = fabric)

summary(mdl)

Call:

32
lm(formula = burntime ~ I1 + I2 + I3, data = fabric)

Residuals:
Min 1Q Median 3Q Max
-1.780 -1.205 -0.460 0.775 4.040

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 11.9800 0.7604 15.754 3.65e-11 ***
I1 4.8000 1.0754 4.463 0.000392 ***
I2 -0.2200 1.0754 -0.205 0.840485
I3 -1.7400 1.0754 -1.618 0.125206
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.7 on 16 degrees of freedom

Multiple R-squared: 0.7226, Adjusted R-squared: 0.6706
F-statistic: 13.89 on 3 and 16 DF, p-value: 0.0001016

The following points are to be noted on the above regression model:

1. The 𝑦-intercept 11.98 is the mean burn time of the fourth fabric (i.e. the mean response
for the omitted predictor category).
2. The mean burn time of fabrics 1, 2 and 3 can be found from the fitted model. For
fabric 1, 𝐼1 =1, 𝐼2 =0, and 𝐼3 =0. Substituting these values in the fitted model, we get
11.98 + 4.80 × 1 − 0.22 × 0 − 1.74 × 0 = 12 + 4.8 = 16.78, which is mean burn time of fabric
1. For fabric 2, the mean burn time is 11.98 + 4.80 × 0 − 0.22 × 1 − 1.74 × 0 = 11.76. For
fabric 3, the mean burn time is 11.98 + 4.80 × 0 − 0.22 × 0 − 1.74 × 1 = 10.24. In other
words, the fitted coefficient of an indicator variable is the difference between the response
means of the category indicated by the variable and the ‘base’ category (indicated by
the omitted indicator variable).
3. The significance of the slope coefficients implies a significant difference in means. For
example, the coefficient of the indicator variable 𝐼1 is highly significant. This means
that the mean burn time of fabric 1 is significantly different from the mean burn time of
fabric 4. Note that this is not the case when fabrics 2 and 3 are compared with fabric 4.
4. In the above output, a multiple comparison of means is made keeping fabric 4 as the
base. A comparison of the mean burn time of fabrics 2 & 3 is not possible with the
above regression. We need to omit either 𝐼2 or 𝐼3 and fit a regression of burn time on
the predictors 𝐼1 , 𝐼3 , and 𝐼4 or 𝐼1 , 𝐼2 , and 𝐼4 for such a comparison.

33
The ANOVA of the regression model is the same as the one-way ANOVA fit (compare F, mean
squares etc.)

anova(mdl)

Analysis of Variance Table

Response: burntime
Df Sum Sq Mean Sq F value Pr(>F)
I1 1 111.521 111.521 38.5718 1.248e-05 ***
I2 1 1.408 1.408 0.4871 0.4952
I3 1 7.569 7.569 2.6179 0.1252
Residuals 16 46.260 2.891
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1 Another example

Consider the pine tree data discussed earlier. Let us model the Top circumference (numer-
ical response) using Area variable (which is categorical). A plot of the raw data and mean
circumference along with the associated 95% confidence intervals are shown in Figure 6.1.

download.file(
url = "http://www.massey.ac.nz/~anhsmith/data/pinetree.RData",
destfile = "pinetree.RData")

load("pinetree.RData")

pinetree |>
ggplot() +
aes(x = Area, y = Top, color = Area) +
geom_jitter(width = 0.15, height = 0, alpha = .6) +
stat_summary(fun = "mean",
geom = "point",
size = 3,
position = position_nudge(x = 0.3)
) +
stat_summary(fun.data = "mean_cl_normal",
geom = "errorbar",
size = 0.75, width = 0.075,

34
 position = position_nudge(x = 0.3)
)

Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
i Please use `linewidth` instead.

30

25

Area
1
Top

20
2
3

15

10
1 2 3
Area

Figure 6.1: Interval Plot

For the three different areas of the forest, we define the following three indicator variables,

𝐼1 = 1 for Area 1
0 for Areas 2, and 3
𝐼2 = 1 for Area 2
0 for Areas 1, and 3
𝐼3 = 1 for Area 3
0 for Areas 1, and 2

Note that we need only any three of the above indicator variables to identify the Area category.
For example, with 𝐼1 and 𝐼2 variables, Area 3 is identified when 𝐼1 = 𝐼2 = 0.

35
 Table 6.2: Regression of Top Circumference on Area Indicator Variables

term estimate std.error statistic p.value

(Intercept) 20.025 1.11375 17.979805 0.0000000
I2 -1.955 1.57508 -1.241207 0.2196132
I3 -5.925 1.57508 -3.761714 0.0004002

Let us regress the pine tree Top circumference on the indicator variables 𝐼2 and 𝐼3 using the
following R codes.

pinetree1 <- pinetree |>

select(Area, Top) |>
mutate(I1 = as.numeric(Area == "1"),
I2 = as.numeric(Area == "2"),
I3 = as.numeric(Area == "3") )

mdl <- lm(Top ~ I2 + I3, data = pinetree1)

library(broom)

tidy(mdl)

pinetree1 <- pinetree |>

select(Top, Area) |>
mutate(I1 = as.numeric(Area == "1"),
I2 = as.numeric(Area == "2"),
I3 = as.numeric(Area == "3") )

mdl <- lm(Top ~ I2 + I3, data = pinetree1)

tidy(mdl)

The following points are to be noted on the regression model shown in Table 6.2:

1. The 𝑦-intercept 20.025 is the mean Top circumference for Area 1 (i.e. the mean response
for the omitted predictor category).
2. The mean Top circumference 2 and 3 can be found from the fitted model. For Area 2,
𝐼1 =0, 𝐼2 =1, and 𝐼3 =0. Substituting these values in the fitted model, we get 20.025 −
1.955 × 1 − 5.925 × 0 = 20.025 − 1.955 = 18.07, which is mean Top circumference for Area
1. For Area 3, the mean Top circumference for Area 3 is 20.025 − 1.955 × 0 − 5.925 × 1 =
20.025 = 14.1. In other words, the fitted coefficient of an indicator variable is the

36
 Table 6.3: Regression ANOVA

Df Sum Sq Mean Sq F value Pr(>F)

Area 2 364.5903 182.29517 7.348015 0.0014482
Residuals 57 1414.0995 24.80876 NA NA

difference between the response means of the category indicated by the variable and the
‘base’ category (indicated by the omitted indicator variable).
3. The significance of the slope coefficients implies a significant difference in means. For
example, the coefficient of the indicator variable 𝐼2 is highly significant. This means
that the mean Top circumference for Area 2 is significantly different from the mean Top
circumference for Area 1. The negative sign of the coefficient means that Area 2 mean
is significantly lower when compared Area 1 mean. The same is true when Area 3 is
compared with Area 1.
4. In the above output, a multiple comparison of means is made keeping Area 1 as the
base. A comparison of the mean Top circumference for Areas 2 & 3 is not possible with
the above regression. We need to omit either 𝐼2 or 𝐼3 and fit a regression for such a
comparison.

In practice, you will NOT be creating any indicator variables to perform the analysis and R
does it for us when we use the lm() function but we have to make sure that categorical factors
are stored as factors, not numerical variables.
The ANOVA of the regression model shown in Table 6.3 has a highly significant F value which
means that at least one Area is different in terms of mean Top circumference.

lm(Top ~ Area, data=pinetree) |> anova()

37
7 Analysis of Covariance (ANCOVA)

Indicator variables are particular useful when both a dependent variable and an independent
variable are measured. One would like to use regression to show the relationship between the
dependent or response variable and the explanatory variable (covariate) separately for each
factor level. However, both the slope and the intercept may differ for the various factor levels.
What sort of model does one fit to such data? Consider the Restaurant Sales Data presented
in the first four columns of Table 7.1. This dataset is from Neter and Whitmore [4].
A study for a chain of fast-food restaurants examined the relationship between restaurant sales
(𝑌 , in thousands of dollars) and the number of households in the restaurant’s trading area (𝑋,
in thousands) and location of restaurant (Highway, shopping Mall, Street).

restaurant <-
read_table("http://www.massey.ac.nz/~anhsmith/data/restaurant.txt",
col_types = "fddf") |>
mutate(Restaurant = factor(Restaurant),
I1 = as.numeric(Location=="Mall"),
I2 = as.numeric(Location=="Street"),
I3 = as.numeric(Location=="Highway"),
I1.X = I1 * Sales,
I2.X = I2 * Sales)

restaurant

Table 7.1 also shows the indicator variables for the Location factor. Just two indicator variables
(say 𝐼1 and 𝐼2 ) are needed in order to define the three different locations uniquely. In order
to permit a separate line for each location we need a model of the following form

𝑌 = 𝛽0 + 𝛽1 𝐼1 + 𝛽2 𝐼2 + (𝛽3 + 𝛽4 𝐼1 + 𝛽5 𝐼2 )𝑋

This model provides a separate model for each location as well as allows for the interaction
between the location of the restaurant and the number of households through the slope coef-
ficients.
For Highway locations, 𝐼1 and 𝐼2 are both equal to zero. Hence the model simplifies to
𝑌 = 𝛽0 + (𝛽3 )𝑋. For Mall locations, 𝐼1 is equal to one and 𝐼2 is equal to zero. So the model

38
 Table 7.1: Restaurant Sales Data

Restaurant Sales Households Location I1 I2 I3 I1.X I2.X

1 135.27 155 Highway 0 0 1 0.00 0.00
2 72.74 93 Highway 0 0 1 0.00 0.00
3 114.95 128 Highway 0 0 1 0.00 0.00
4 102.93 114 Highway 0 0 1 0.00 0.00
5 131.77 158 Highway 0 0 1 0.00 0.00
6 160.91 183 Highway 0 0 1 0.00 0.00
7 179.86 178 Mall 1 0 0 179.86 0.00
8 220.14 215 Mall 1 0 0 220.14 0.00
9 179.64 172 Mall 1 0 0 179.64 0.00
10 185.92 197 Mall 1 0 0 185.92 0.00
11 207.82 207 Mall 1 0 0 207.82 0.00
12 113.51 95 Mall 1 0 0 113.51 0.00
13 203.98 224 Street 0 1 0 0.00 203.98
14 174.48 199 Street 0 1 0 0.00 174.48
15 220.43 240 Street 0 1 0 0.00 220.43
16 93.19 100 Street 0 1 0 0.00 93.19

Table 7.2: Analysis of Covariance (ANCOVA)

term estimate std.error statistic p.value

(Intercept) 1.491 11.688 0.128 0.901
Households 0.854 0.082 10.370 0.000
I1 26.588 19.999 1.329 0.213
I2 -0.597 16.447 -0.036 0.972
I1.X 0.009 0.122 0.074 0.942
I2.X 0.053 0.111 0.479 0.642

becomes 𝑌 = (𝛽0 + 𝛽1 ) + (𝛽3 + 𝛽4 )𝑋. For Street locations, 𝐼1 is equal to zero and 𝐼2 is equal
to one. So the model becomes 𝑌 = (𝛽0 + 𝛽2 ) + (𝛽3 + 𝛽5 )𝑋.
The newly created product variables 𝐼1 .𝑋 = 𝐼1 × 𝑋 and 𝐼2 .𝑋 = 𝐼2 × 𝑋 shown in Table 7.1
allow us to fit separate slopes for the Locations. R does not require creation of data for the
interaction terms 𝐼1 ×𝑋 and 𝐼2 ×𝑋 and it does internally. The regression of Sales (𝑌 ) on
Households (𝑋), 𝐼1 , 𝐼2 , 𝐼1 × 𝑋 and 𝐼2 × 𝑋 is shown in Table 7.2.

ancova.model <- lm(Sales ~ Households + I1 + I2 + I1.X + I2.X,

data=restaurant)

tidy(ancova.model)

39
This R output suggests that the coefficients for 𝐼2 , 𝐼1 × 𝑋 and 𝐼2 × 𝑋 are not significantly
different from zero. This suggests that a simpler model can be fitted to these data omitting
the category indicated by 𝐼2 . The significance of the 𝐼1 coefficient means that the 𝑦-intercept
of the model for Mall location is different. The significance of the coefficients of the product
variables will imply significant differences in slopes for the locations but this is not the case
here. In general, a stepwise regression is needed to obtain a simpler model having the best
subset of predictors (rather than judging from the multiple regression model given here).
The final or simpler model suggested after step-wise analysis (results not shown) is:
𝑌 = −3.298 + 0.906𝑋 + 23.8 × 𝐼1 .
Because 𝐼2 does not appear in this equation, it means that the same regression line can be
used to relate sales to number of households for the Highway and Street Locations. The fact
that 𝐼1 is included in the final model but 𝐼1 ×𝑋 is excluded means that the line for Malls has
a different intercept but the same slope as the Highway/Street Line.
𝐼1 =0 for both Highway and Street locations so the fitted values for Highway/Street locations
is,
𝑌 = −3.298 + 0.906𝑋.
𝐼1 =1 for Mall locations so the fitted model for Mall locations is,
𝑌 = (−3.298 + 23.81) + (0.906 − 0.074)𝑋 = 20.512 + 0.832𝑋.
These two lines are plotted in Figure 7.1. The top line is (obviously) the fitted model for Mall
locations and the bottom one for Highway and Street locations.

restaurant |>
mutate(`Mall location` = Location == "Mall") |>
ggplot() +
aes(y = Sales, x = Households, linetype = `Mall location`) +
geom_point(aes(shape = Location)) +
geom_smooth(method = lm)

`geom_smooth()` using formula = 'y ~ x'

40
 200 Location
Highway
Mall
Street
Sales

150

Mall location
FALSE
100 TRUE

100 150 200

Households

Figure 7.1: Plot of Fitted Lines

In practice, you will NOT be creating any indicator variables to perform the analysis of
covariance and R does it for us when we use the lm() with the syntax * which stands for
interaction. Try-

mdl <- lm(Top ~ First * Area, data = pinetree)

tidy(mdl) # also summary(mdl) or anova(mdl)

41
8 Summary

Various ANOVA models have been considered in this chapter. The goodness of fit is indicated
by the 𝑅-Squared value or 𝐹 statistic. Most of the ANOVA examples given in this chapter are
based on experimental data but ANOVA models can also be fitted to survey data, provided
that the observations represent a random sample. When the observations are time series or
other data forms chosen in a non-random fashion, the assumptions of these models may not
be satisfied. In particular it is unlikely that the residuals will be independent, following no
clear pattern. It is important that such assumptions be checked; otherwise the results of these
analyses may be misleading. It is also important that the residual variances are reasonably
similar for all treatment levels. If this is not the case, some transformation of the response
variable may be required in order to ensure that the ANOVA 𝐹 tests are valid.
Indicator variables can be used to perform ANOVA using regression. However, it is more
common to use indicator variables when one wants to use both a categorical factor and a
continuous measurement variable 𝑋 to model the 𝑌 responses. Such an analysis is called
an ANCOVA and the model fitted using regression may consist of a separate model for each
treatment.

42
Bibliography
[1] G.K. Bhattacharyya and R.A. Johnson. Statistical Concepts and Methods. NY: Wiley,
1977.
[2] G.E.P. Box, J.S. Hunter, and W.G. Hunter. Statistics for experimenters: design, innova-
tion, and discovery. Wiley series in probability and statistics. Wiley-Interscience, 2005.
[3] R. J. Brook and G. C. Arnold. Applied Regression Analysis and Experimental Design.
NY: Marcel Dekker, 1985.
[4] Wasserman W. Neter J. and G. A. Whitmore. Applied Statistics. Boston: Allyn and Ba-
con., 1993.

43