# Cochran's Q test - overview

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Cochran's Q test
One sample $z$ test for the mean
McNemar's test
Two way ANOVA
Independent/grouping variableIndependent variableIndependent variableIndependent/grouping variables
One within subject factor ($\geq 2$ related groups)None2 paired groupsTwo categorical, the first with $I$ independent groups and the second with $J$ independent groups ($I \geqslant 2$, $J \geqslant 2$)
Dependent variableDependent variableDependent variableDependent variable
One categorical with 2 independent groupsOne quantitative of interval or ratio levelOne categorical with 2 independent groupsOne quantitative of interval or ratio level
Null hypothesisNull hypothesisNull hypothesisNull hypothesis
H0: $\pi_1 = \pi_2 = \ldots = \pi_I$

Here $\pi_1$ is the population proportion of 'successes' for group 1, $\pi_2$ is the population proportion of 'successes' for group 2, and $\pi_I$ is the population proportion of 'successes' for group $I.$
H0: $\mu = \mu_0$

Here $\mu$ is the population mean, and $\mu_0$ is the population mean according to the null hypothesis.

Let's say that the scores on the dependent variable are scored 0 and 1. Then for each pair of scores, the data allow four options:

1. First score of pair is 0, second score of pair is 0
2. First score of pair is 0, second score of pair is 1 (switched)
3. First score of pair is 1, second score of pair is 0 (switched)
4. First score of pair is 1, second score of pair is 1
The null hypothesis H0 is that for each pair of scores, P(first score of pair is 0 while second score of pair is 1) = P(first score of pair is 1 while second score of pair is 0). That is, the probability that a pair of scores switches from 0 to 1 is the same as the probability that a pair of scores switches from 1 to 0.

Other formulations of the null hypothesis are:

• H0: $\pi_1 = \pi_2$, where $\pi_1$ is the population proportion of ones for the first paired group and $\pi_2$ is the population proportion of ones for the second paired group
• H0: for each pair of scores, P(first score of pair is 1) = P(second score of pair is 1)

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.
Alternative hypothesisAlternative hypothesisAlternative hypothesisAlternative hypothesis
H1: not all population proportions are equalH1 two sided: $\mu \neq \mu_0$
H1 right sided: $\mu > \mu_0$
H1 left sided: $\mu < \mu_0$

The alternative hypothesis H1 is that for each pair of scores, P(first score of pair is 0 while second score of pair is 1) $\neq$ P(first score of pair is 1 while second score of pair is 0). That is, the probability that a pair of scores switches from 0 to 1 is not the same as the probability that a pair of scores switches from 1 to 0.

Other formulations of the alternative hypothesis are:

• H1: $\pi_1 \neq \pi_2$
• H1: for each pair of scores, P(first score of pair is 1) $\neq$ P(second score of pair is 1)

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
AssumptionsAssumptionsAssumptionsAssumptions
• Sample of 'blocks' (usually the subjects) is a simple random sample from the population. That is, blocks are independent of one another
• Scores are normally distributed in the population
• Population standard deviation $\sigma$ is known
• Sample is a simple random sample from the population. That is, observations are independent of one another
• Sample of pairs is a simple random sample from the population of pairs. That is, pairs are independent of one another
• 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)
Test statisticTest statisticTest statisticTest statistic
If a failure is scored as 0 and a success is scored as 1:

$Q = k(k - 1) \dfrac{\sum_{groups} \Big (\mbox{group total} - \frac{\mbox{grand total}}{k} \Big)^2}{\sum_{blocks} \mbox{block total} \times (k - \mbox{block total})}$

Here $k$ is the number of related groups (usually the number of repeated measurements), a group total is the sum of the scores in a group, a block total is the sum of the scores in a block (usually a subject), and the grand total is the sum of all the scores.

Before computing $Q$, first exclude blocks with equal scores in all $k$ groups.
$z = \dfrac{\bar{y} - \mu_0}{\sigma / \sqrt{N}}$
Here $\bar{y}$ is the sample mean, $\mu_0$ is the population mean according to the null hypothesis, $\sigma$ is the population standard deviation, and $N$ is the sample size.

The denominator $\sigma / \sqrt{N}$ is the standard deviation of the sampling distribution of $\bar{y}$. The $z$ value indicates how many of these standard deviations $\bar{y}$ is removed from $\mu_0$.
$X^2 = \dfrac{(b - c)^2}{b + c}$
Here $b$ is the number of pairs in the sample for which the first score is 0 while the second score is 1, and $c$ is the number of pairs in the sample for which the first score is 1 while the second score is 0.
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.
n.a.n.a.n.a.Pooled standard deviation
---\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 $Q$ if H0 were trueSampling distribution of $z$ if H0 were trueSampling distribution of $X^2$ if H0 were trueSampling distribution of $F$ if H0 were true
If the number of blocks (usually the number of subjects) is large, approximately the chi-squared distribution with $k - 1$ degrees of freedomStandard normal distribution

If $b + c$ is large enough (say, > 20), approximately the chi-squared distribution with 1 degree of freedom.

If $b + c$ is small, the Binomial($n$, $P$) distribution should be used, with $n = b + c$ and $P = 0.5$. In that case the test statistic becomes equal to $b$.

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.
Significant?Significant?Significant?Significant?
If the number of blocks is large, the table with critical $X^2$ values can be used. If we denote $X^2 = Q$:
• Check if $X^2$ observed in sample is equal to or larger than critical value $X^{2*}$ or
• Find $p$ value corresponding to observed $X^2$ and check if it is equal to or smaller than $\alpha$
Two sided:
Right sided:
Left sided:
For test statistic $X^2$:
• Check if $X^2$ observed in sample is equal to or larger than critical value $X^{2*}$ or
• Find $p$ value corresponding to observed $X^2$ and check if it is equal to or smaller than $\alpha$
If $b + c$ is small, the table for the binomial distribution should be used, with as test statistic $b$:
• Check if $b$ observed in sample is in the rejection region or
• Find two sided $p$ value corresponding to observed $b$ and check if it is equal to or smaller than $\alpha$
• 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 $\alpha$
n.a.$C\%$ confidence interval for $\mu$n.a.n.a.
-$\bar{y} \pm z^* \times \dfrac{\sigma}{\sqrt{N}}$
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 $\mu$ can also be used as significance test.
--
n.a.Effect sizen.a.Effect size
-Cohen's $d$:
Standardized difference between the sample mean and $\mu_0$: $$d = \frac{\bar{y} - \mu_0}{\sigma}$$ Cohen's $d$ indicates how many standard deviations $\sigma$ the sample mean $\bar{y}$ is removed from $\mu_0.$
-
• 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}
n.a.Visual representationn.a.n.a.
---
n.a.n.a.n.a.ANOVA table
---
Equivalent ton.a.Equivalent toEquivalent to
Friedman test, with a categorical dependent variable consisting of two independent groups.-
OLS regression with two categorical independent variables and the interaction term, transformed into $(I - 1)$ + $(J - 1)$ + $(I - 1) \times (J - 1)$ code variables.
Example contextExample contextExample contextExample context
Subjects perform three different tasks, which they can either perform correctly or incorrectly. Is there a difference in task performance between the three different tasks?Is the average mental health score of office workers different from $\mu_0 = 50$? Assume that the standard deviation of the mental health scores in the population is $\sigma = 3.$Does a tv documentary about spiders change whether people are afraid (yes/no) of spiders?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?
SPSSn.a.SPSSSPSS
Analyze > Nonparametric Tests > Legacy Dialogs > K Related Samples...
• Put the $k$ variables containing the scores for the $k$ related groups in the white box below Test Variables
• Under Test Type, select Cochran's Q test
-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 McNemar test
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)
Jamovin.a.JamoviJamovi
Jamovi does not have a specific option for the Cochran's Q test. However, you can do the Friedman test instead. The $p$ value resulting from this Friedman test is equivalent to the $p$ value that would have resulted from the Cochran's Q test. Go to:

ANOVA > Repeated Measures ANOVA - Friedman
• Put the $k$ variables containing the scores for the $k$ related groups in the box below Measures
-Frequencies > Paired Samples - McNemar test
• Put one of the two paired variables in the box below Rows and the other paired variable in the box below Columns
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
Practice questionsPractice questionsPractice questionsPractice questions