# Two way ANOVA - overview

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Two way ANOVA
Sign test
Two sample $z$ test
Paired sample $t$ test
Independent/grouping variablesIndependent variableIndependent/grouping variableIndependent variable
Two categorical, the first with $I$ independent groups and the second with $J$ independent groups ($I \geqslant 2$, $J \geqslant 2$)2 paired groupsOne categorical with 2 independent groups2 paired groups
Dependent variableDependent variableDependent variableDependent variable
One quantitative of interval or ratio levelOne of ordinal levelOne quantitative of interval or ratio levelOne quantitative of interval or ratio level
Null hypothesisNull hypothesisNull hypothesisNull hypothesis
ANOVA $F$ tests:
• H0 for main and interaction effects together (model): no main effects and interaction effect
• H0 for independent variable A: no main effect for A
• H0 for independent variable B: no main effect for B
• H0 for the interaction term: no interaction effect between A and B
Like in one way ANOVA, we can also perform $t$ tests for specific contrasts and multiple comparisons. This is more advanced stuff.
• H0: P(first score of a pair exceeds second score of a pair) = P(second score of a pair exceeds first score of a pair)
If the dependent variable is measured on a continuous scale, this can also be formulated as:
• H0: the population median of the difference scores is equal to zero
A difference score is the difference between the first score of a pair and the second score of a pair.
H0: $\mu_1 = \mu_2$

Here $\mu_1$ is the population mean for group 1, and $\mu_2$ is the population mean for group 2.
H0: $\mu = \mu_0$

Here $\mu$ is the population mean of the difference scores, and $\mu_0$ is the population mean of the difference scores according to the null hypothesis, which is usually 0. A difference score is the difference between the first score of a pair and the second score of a pair.
Alternative hypothesisAlternative hypothesisAlternative hypothesisAlternative hypothesis
ANOVA $F$ tests:
• H1 for main and interaction effects together (model): there is a main effect for A, and/or for B, and/or an interaction effect
• H1 for independent variable A: there is a main effect for A
• H1 for independent variable B: there is a main effect for B
• H1 for the interaction term: there is an interaction effect between A and B
• H1 two sided: P(first score of a pair exceeds second score of a pair) $\neq$ P(second score of a pair exceeds first score of a pair)
• H1 right sided: P(first score of a pair exceeds second score of a pair) > P(second score of a pair exceeds first score of a pair)
• H1 left sided: P(first score of a pair exceeds second score of a pair) < P(second score of a pair exceeds first score of a pair)
If the dependent variable is measured on a continuous scale, this can also be formulated as:
• H1 two sided: the population median of the difference scores is different from zero
• H1 right sided: the population median of the difference scores is larger than zero
• H1 left sided: the population median of the difference scores is smaller than zero
H1 two sided: $\mu_1 \neq \mu_2$
H1 right sided: $\mu_1 > \mu_2$
H1 left sided: $\mu_1 < \mu_2$
H1 two sided: $\mu \neq \mu_0$
H1 right sided: $\mu > \mu_0$
H1 left sided: $\mu < \mu_0$
AssumptionsAssumptionsAssumptionsAssumptions
• Within each of the $I \times J$ populations, the scores on the dependent variable are normally distributed
• The standard deviation of the scores on the dependent variable is the same in each of the $I \times J$ populations
• For each of the $I \times J$ groups, the sample is an independent and simple random sample from the population defined by that group. That is, within and between groups, observations are independent of one another
• Equal sample sizes for each group make the interpretation of the ANOVA output easier (unequal sample sizes result in overlap in the sum of squares; this is advanced stuff)
• Sample of pairs is a simple random sample from the population of pairs. That is, pairs are independent of one another
• Within each population, the scores on the dependent variable are normally distributed
• Population standard deviations $\sigma_1$ and $\sigma_2$ are known
• Group 1 sample is a simple random sample (SRS) from population 1, group 2 sample is an independent SRS from population 2. That is, within and between groups, observations are independent of one another
• Difference scores are normally distributed in the population
• Sample of difference scores is a simple random sample from the population of difference scores. That is, difference scores are independent of one another
Test statisticTest statisticTest statisticTest statistic
For main and interaction effects together (model):
• $F = \dfrac{\mbox{mean square model}}{\mbox{mean square error}}$
For independent variable A:
• $F = \dfrac{\mbox{mean square A}}{\mbox{mean square error}}$
For independent variable B:
• $F = \dfrac{\mbox{mean square B}}{\mbox{mean square error}}$
For the interaction term:
• $F = \dfrac{\mbox{mean square interaction}}{\mbox{mean square error}}$
Note: mean square error is also known as mean square residual or mean square within.
$W =$ number of difference scores that is larger than 0$z = \dfrac{(\bar{y}_1 - \bar{y}_2) - 0}{\sqrt{\dfrac{\sigma^2_1}{n_1} + \dfrac{\sigma^2_2}{n_2}}} = \dfrac{\bar{y}_1 - \bar{y}_2}{\sqrt{\dfrac{\sigma^2_1}{n_1} + \dfrac{\sigma^2_2}{n_2}}}$
Here $\bar{y}_1$ is the sample mean in group 1, $\bar{y}_2$ is the sample mean in group 2, $\sigma^2_1$ is the population variance in population 1, $\sigma^2_2$ is the population variance in population 2, $n_1$ is the sample size of group 1, and $n_2$ is the sample size of group 2. The 0 represents the difference in population means according to the null hypothesis.

The denominator $\sqrt{\frac{\sigma^2_1}{n_1} + \frac{\sigma^2_2}{n_2}}$ is the standard deviation of the sampling distribution of $\bar{y}_1 - \bar{y}_2$. The $z$ value indicates how many of these standard deviations $\bar{y}_1 - \bar{y}_2$ is removed from 0.

Note: we could just as well compute $\bar{y}_2 - \bar{y}_1$ in the numerator, but then the left sided alternative becomes $\mu_2 < \mu_1$, and the right sided alternative becomes $\mu_2 > \mu_1$.
$t = \dfrac{\bar{y} - \mu_0}{s / \sqrt{N}}$
Here $\bar{y}$ is the sample mean of the difference scores, $\mu_0$ is the population mean of the difference scores according to the null hypothesis, $s$ is the sample standard deviation of the difference scores, and $N$ is the sample size (number of difference scores).

The denominator $s / \sqrt{N}$ is the standard error of the sampling distribution of $\bar{y}$. The $t$ value indicates how many standard errors $\bar{y}$ is removed from $\mu_0$.
Pooled standard deviationn.a.n.a.n.a.
\begin{aligned} s_p &= \sqrt{\dfrac{\sum\nolimits_{subjects} (\mbox{subject's score} - \mbox{its group mean})^2}{N - (I \times J)}}\\ &= \sqrt{\dfrac{\mbox{sum of squares error}}{\mbox{degrees of freedom error}}}\\ &= \sqrt{\mbox{mean square error}} \end{aligned} ---
Sampling distribution of $F$ if H0 were trueSampling distribution of $W$ if H0 were trueSampling distribution of $z$ if H0 were trueSampling distribution of $t$ if H0 were true
For main and interaction effects together (model):
• $F$ distribution with $(I - 1) + (J - 1) + (I - 1) \times (J - 1)$ (df model, numerator) and $N - (I \times J)$ (df error, denominator) degrees of freedom
For independent variable A:
• $F$ distribution with $I - 1$ (df A, numerator) and $N - (I \times J)$ (df error, denominator) degrees of freedom
For independent variable B:
• $F$ distribution with $J - 1$ (df B, numerator) and $N - (I \times J)$ (df error, denominator) degrees of freedom
For the interaction term:
• $F$ distribution with $(I - 1) \times (J - 1)$ (df interaction, numerator) and $N - (I \times J)$ (df error, denominator) degrees of freedom
Here $N$ is the total sample size.
The exact distribution of $W$ under the null hypothesis is the Binomial($n$, $P$) distribution, with $n =$ number of positive differences $+$ number of negative differences, and $P = 0.5$.

If $n$ is large, $W$ is approximately normally distributed under the null hypothesis, with mean $nP = n \times 0.5$ and standard deviation $\sqrt{nP(1-P)} = \sqrt{n \times 0.5(1 - 0.5)}$. Hence, if $n$ is large, the standardized test statistic $$z = \frac{W - n \times 0.5}{\sqrt{n \times 0.5(1 - 0.5)}}$$ follows approximately the standard normal distribution if the null hypothesis were true.
Standard normal distribution$t$ distribution with $N - 1$ degrees of freedom
Significant?Significant?Significant?Significant?
• Check if $F$ observed in sample is equal to or larger than critical value $F^*$ or
• Find $p$ value corresponding to observed $F$ and check if it is equal to or smaller than $\alpha$
If $n$ is small, the table for the binomial distribution should be used:
Two sided:
• Check if $W$ observed in sample is in the rejection region or
• Find two sided $p$ value corresponding to observed $W$ and check if it is equal to or smaller than $\alpha$
Right sided:
• Check if $W$ observed in sample is in the rejection region or
• Find right sided $p$ value corresponding to observed $W$ and check if it is equal to or smaller than $\alpha$
Left sided:
• Check if $W$ observed in sample is in the rejection region or
• Find left sided $p$ value corresponding to observed $W$ and check if it is equal to or smaller than $\alpha$

If $n$ is large, the table for standard normal probabilities can be used:
Two sided:
Right sided:
Left sided:
Two sided:
Right sided:
Left sided:
Two sided:
Right sided:
Left sided:
n.a.n.a.$C\%$ confidence interval for \mu_1 - \mu_2$$C\% confidence interval for \mu --(\bar{y}_1 - \bar{y}_2) \pm z^* \times \sqrt{\dfrac{\sigma^2_1}{n_1} + \dfrac{\sigma^2_2}{n_2}} where the critical value z^* is the value under the normal curve with the area C / 100 between -z^* and z^* (e.g. z^* = 1.96 for a 95% confidence interval). The confidence interval for \mu_1 - \mu_2 can also be used as significance test. \bar{y} \pm t^* \times \dfrac{s}{\sqrt{N}} where the critical value t^* is the value under the t_{N-1} distribution with the area C / 100 between -t^* and t^* (e.g. t^* = 2.086 for a 95% confidence interval when df = 20). The confidence interval for \mu can also be used as significance test. Effect sizen.a.n.a.Effect size • Proportion variance explained R^2: Proportion variance of the dependent variable y explained by the independent variables and the interaction effect together:$$ \begin{align} R^2 &= \dfrac{\mbox{sum of squares model}}{\mbox{sum of squares total}} \end{align} $$R^2 is the proportion variance explained in the sample. It is a positively biased estimate of the proportion variance explained in the population. • Proportion variance explained \eta^2: Proportion variance of the dependent variable y explained by an independent variable or interaction effect:$$ \begin{align} \eta^2_A &= \dfrac{\mbox{sum of squares A}}{\mbox{sum of squares total}}\\ \\ \eta^2_B &= \dfrac{\mbox{sum of squares B}}{\mbox{sum of squares total}}\\ \\ \eta^2_{int} &= \dfrac{\mbox{sum of squares int}}{\mbox{sum of squares total}} \end{align} $$\eta^2 is the proportion variance explained in the sample. It is a positively biased estimate of the proportion variance explained in the population. • Proportion variance explained \omega^2: Corrects for the positive bias in \eta^2 and is equal to:$$ \begin{align} \omega^2_A &= \dfrac{\mbox{sum of squares A} - \mbox{degrees of freedom A} \times \mbox{mean square error}}{\mbox{sum of squares total} + \mbox{mean square error}}\\ \\ \omega^2_B &= \dfrac{\mbox{sum of squares B} - \mbox{degrees of freedom B} \times \mbox{mean square error}}{\mbox{sum of squares total} + \mbox{mean square error}}\\ \\ \omega^2_{int} &= \dfrac{\mbox{sum of squares int} - \mbox{degrees of freedom int} \times \mbox{mean square error}}{\mbox{sum of squares total} + \mbox{mean square error}}\\ \end{align} $$\omega^2 is a better estimate of the explained variance in the population than \eta^2. Only for balanced designs (equal sample sizes). • Proportion variance explained \eta^2_{partial}:$$ \begin{align} \eta^2_{partial\,A} &= \frac{\mbox{sum of squares A}}{\mbox{sum of squares A} + \mbox{sum of squares error}}\\ \\ \eta^2_{partial\,B} &= \frac{\mbox{sum of squares B}}{\mbox{sum of squares B} + \mbox{sum of squares error}}\\ \\ \eta^2_{partial\,int} &= \frac{\mbox{sum of squares int}}{\mbox{sum of squares int} + \mbox{sum of squares error}} \end{align} $$--Cohen's d: Standardized difference between the sample mean of the difference scores and \mu_0:$$d = \frac{\bar{y} - \mu_0}{s}$Cohen's$d$indicates how many standard deviations$s$the sample mean of the difference scores$\bar{y}$is removed from$\mu_0.$n.a.n.a.Visual representationVisual representation -- ANOVA tablen.a.n.a.n.a. --- Equivalent toEquivalent ton.a.Equivalent to OLS regression with two categorical independent variables and the interaction term, transformed into$(I - 1)$+$(J - 1)$+$(I - 1) \times (J - 1)$code variables. Two sided sign test is equivalent to - • One sample$t$test on the difference scores. • Repeated measures ANOVA with one dichotomous within subjects factor. Example contextExample contextExample contextExample context Is the average mental health score different between people from a low, moderate, and high economic class? And is the average mental health score different between men and women? And is there an interaction effect between economic class and gender?Do people tend to score higher on mental health after a mindfulness course?Is the average mental health score different between men and women? Assume that in the population, the standard devation of the mental health scores is$\sigma_1 = 2$amongst men and$\sigma_2 = 2.5$amongst women.Is the average difference between the mental health scores before and after an intervention different from$\mu_0 = 0$? SPSSSPSSn.a.SPSS Analyze > General Linear Model > Univariate... • Put your dependent (quantitative) variable in the box below Dependent Variable and your two independent (grouping) variables in the box below Fixed Factor(s) Analyze > Nonparametric Tests > Legacy Dialogs > 2 Related Samples... • Put the two paired variables in the boxes below Variable 1 and Variable 2 • Under Test Type, select the Sign test -Analyze > Compare Means > Paired-Samples T Test... • Put the two paired variables in the boxes below Variable 1 and Variable 2 JamoviJamovin.a.Jamovi ANOVA > ANOVA • Put your dependent (quantitative) variable in the box below Dependent Variable and your two independent (grouping) variables in the box below Fixed Factors Jamovi does not have a specific option for the sign test. However, you can do the Friedman test instead. The$p$value resulting from this Friedman test is equivalent to the two sided$p\$ value that would have resulted from the sign test. Go to:

ANOVA > Repeated Measures ANOVA - Friedman
• Put the two paired variables in the box below Measures
-T-Tests > Paired Samples T-Test
• Put the two paired variables in the box below Paired Variables, one on the left side of the vertical line and one on the right side of the vertical line
• Under Hypothesis, select your alternative hypothesis
Practice questionsPractice questionsPractice questionsPractice questions