# Cochran's Q test - overview

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Cochran's Q test
Pearson correlation
One sample $t$ test for the mean
Two way ANOVA
Independent/grouping variableVariable 1Independent variableIndependent/grouping variables
One within subject factor ($\geq 2$ related groups)One quantitative of interval or ratio levelNoneTwo categorical, the first with $I$ independent groups and the second with $J$ independent groups ($I \geqslant 2$, $J \geqslant 2$)
Dependent variableVariable 2Dependent variableDependent variable
One categorical with 2 independent groupsOne quantitative of interval or ratio levelOne quantitative of interval or ratio levelOne 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: $\rho = \rho_0$

Here $\rho$ is the Pearson correlation in the population, and $\rho_0$ is the Pearson correlation in the population according to the null hypothesis (usually 0). The Pearson correlation is a measure for the strength and direction of the linear relationship between two variables of at least interval measurement level.
H0: $\mu = \mu_0$

Here $\mu$ is the population mean, and $\mu_0$ is the population mean according to the null 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.
Alternative hypothesisAlternative hypothesisAlternative hypothesisAlternative hypothesis
H1: not all population proportions are equalH1 two sided: $\rho \neq \rho_0$
H1 right sided: $\rho > \rho_0$
H1 left sided: $\rho < \rho_0$
H1 two sided: $\mu \neq \mu_0$
H1 right sided: $\mu > \mu_0$
H1 left sided: $\mu < \mu_0$
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
AssumptionsAssumptions of test for correlationAssumptionsAssumptions
• Sample of 'blocks' (usually the subjects) is a simple random sample from the population. That is, blocks are independent of one another
• In the population, the two variables are jointly normally distributed (this covers the normality, homoscedasticity, and linearity assumptions)
• Sample of pairs is a simple random sample from the population of pairs. That is, pairs are independent of one another
Note: these assumptions are only important for the significance test and confidence interval, not for the correlation coefficient itself. The correlation coefficient just measures the strength of the linear relationship between two variables.
• Scores are normally distributed in the population
• Sample is a simple random sample from the population. That is, observations 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.
Test statistic for testing H0: $\rho = 0$:
• $t = \dfrac{r \times \sqrt{N - 2}}{\sqrt{1 - r^2}}$
where $r$ is the sample correlation $r = \frac{1}{N - 1} \sum_{j}\Big(\frac{x_{j} - \bar{x}}{s_x} \Big) \Big(\frac{y_{j} - \bar{y}}{s_y} \Big)$ and $N$ is the sample size
Test statistic for testing values for $\rho$ other than $\rho = 0$:
• $z = \dfrac{r_{Fisher} - \rho_{0_{Fisher}}}{\sqrt{\dfrac{1}{N - 3}}}$
• $r_{Fisher} = \dfrac{1}{2} \times \log\Bigg(\dfrac{1 + r}{1 - r} \Bigg )$, where $r$ is the sample correlation
• $\rho_{0_{Fisher}} = \dfrac{1}{2} \times \log\Bigg( \dfrac{1 + \rho_0}{1 - \rho_0} \Bigg )$, where $\rho_0$ is the population correlation according to H0
$t = \dfrac{\bar{y} - \mu_0}{s / \sqrt{N}}$
Here $\bar{y}$ is the sample mean, $\mu_0$ is the population mean according to the null hypothesis, $s$ is the sample standard deviation, and $N$ is the sample size.

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 $\mu_0$.
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 $t$ and of $z$ if H0 were trueSampling distribution of $t$ 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 freedomSampling distribution of $t$:
• $t$ distribution with $N - 2$ degrees of freedom
Sampling distribution of $z$:
• Approximately the standard normal distribution
$t$ distribution with $N - 1$ degrees of freedomFor 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 $\alpha$
$t$ Test two sided:
$t$ Test right sided:
$t$ Test left sided:
$z$ Test two sided:
$z$ Test right sided:
$z$ Test left sided:
Two sided:
Right sided:
Left sided:
• 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.Approximate $C$% confidence interval for \rho$$C\% confidence interval for \mun.a. -First compute the approximate C% confidence interval for \rho_{Fisher}: • lower_{Fisher} = r_{Fisher} - z^* \times \sqrt{\dfrac{1}{N - 3}} • upper_{Fisher} = r_{Fisher} + z^* \times \sqrt{\dfrac{1}{N - 3}} where r_{Fisher} = \frac{1}{2} \times \log\Bigg(\dfrac{1 + r}{1 - r} \Bigg ) and 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). Then transform back to get the approximate C% confidence interval for \rho: • lower bound = \dfrac{e^{2 \times lower_{Fisher}} - 1}{e^{2 \times lower_{Fisher}} + 1} • upper bound = \dfrac{e^{2 \times upper_{Fisher}} - 1}{e^{2 \times upper_{Fisher}} + 1} \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. - n.a.Properties of the Pearson correlation coefficientEffect sizeEffect size - • The Pearson correlation coefficient is a measure for the linear relationship between two quantitative variables. • The Pearson correlation coefficient squared reflects the proportion of variance explained in one variable by the other variable. • The Pearson correlation coefficient can take on values between -1 (perfect negative relationship) and 1 (perfect positive relationship). A value of 0 means no linear relationship. • The absolute size of the Pearson correlation coefficient is not affected by any linear transformation of the variables. However, the sign of the Pearson correlation will flip when the scores on one of the two variables are multiplied by a negative number (reversing the direction of measurement of that variable). For example: • the correlation between x and y is equivalent to the correlation between 3x + 5 and 2y - 6. • the absolute value of the correlation between x and y is equivalent to the absolute value of the correlation between -3x + 5 and 2y - 6. However, the signs of the two correlation coefficients will be in opposite directions, due to the multiplication of x by -3. • The Pearson correlation coefficient does not say anything about causality. • The Pearson correlation coefficient is sensitive to outliers. Cohen's d: Standardized difference between the sample mean and \mu_0:$$d = \frac{\bar{y} - \mu_0}{s}$$Cohen's d indicates how many standard deviations s the sample mean \bar{y} is removed from \mu_0. • Proportion variance explained R^2: Proportion variance of the dependent variable y explained by the independent variables and the interaction effect together:$$ \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}$n.a.n.a.Visual representationn.a. --- n.a.n.a.n.a.ANOVA table --- Equivalent toEquivalent ton.a.Equivalent to Friedman test, with a categorical dependent variable consisting of two independent groups.OLS regression with one independent variable: •$b_1 = r \times \frac{s_y}{s_x}$• Results significance test ($t$and$p$value) testing$H_0$:$\beta_1 = 0$are equivalent to results significance test testing$H_0$:$\rho = 0$-OLS regression with two categorical independent variables and the interaction term, transformed into$(I - 1)$+$(J - 1)$+$(I - 1) \times (J - 1)$code variables. Example contextExample contextExample contextExample context Subjects perform three different tasks, which they can either perform correctly or incorrectly. Is there a difference in task performance between the three different tasks?Is there a linear relationship between physical health and mental health?Is the average mental health score of office workers different from$\mu_0 = 50$?Is the average mental health score different between people from a low, moderate, and high economic class? And is the average mental health score different between men and women? And is there an interaction effect between economic class and gender? SPSSSPSSSPSSSPSS Analyze > Nonparametric Tests > Legacy Dialogs > K Related Samples... • Put the$k$variables containing the scores for the$k$related groups in the white box below Test Variables • Under Test Type, select Cochran's Q test Analyze > Correlate > Bivariate... • Put your two variables in the box below Variables Analyze > Compare Means > One-Sample T Test... • Put your variable in the box below Test Variable(s) • Fill in the value for$\mu_0$in the box next to Test Value Analyze > General Linear Model > Univariate... • Put your dependent (quantitative) variable in the box below Dependent Variable and your two independent (grouping) variables in the box below Fixed Factor(s) JamoviJamoviJamoviJamovi Jamovi does not have a specific option for the Cochran's Q test. However, you can do the Friedman test instead. The$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$related groups in the box below Measures Regression > Correlation Matrix • Put your two variables in the white box at the right • Under Correlation Coefficients, select Pearson (selected by default) • Under Hypothesis, select your alternative hypothesis T-Tests > One Sample T-Test • Put your variable in the box below Dependent Variables • Under Hypothesis, fill in the value for$\mu_0\$ in the box next to Test Value, and select your alternative hypothesis
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
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