# Regarding flattening a 3 variables experiment to conduct one-way repeated measures ANOVA

I recently conducted an experiment where I had participants experience 8 conditions in a 2x2 manner (two variables and their combinations). This was primarily to give us an opportunity to observe how they work in different situations while under the same condition. My primary dependent variable is completion time. However, I am less interested in studying how completion time was moderated in the 2x2 case quantitatively (more so qualitatively). Instead, I am more broadly interested in whether completion time differed between the conditions (combining the scores from the 2x2 trials). Is it considered acceptable in such a scenario to conduct a one-way repeated measures ANOVA as opposed to studying the three-way interaction?

EDIT: to add a bit more context, upon conducting the three-way repeated measures there is a statistically signifiicant three-way interaction effect, as well as one statistically significant two-way interaction effect, and all three variables are statistically significant on their own.

• You may want to search CV for lsmeans or contrasts which could clue you in on how you might approach this: stats.stackexchange.com/tags/lsmeans/hot Aug 29, 2020 at 1:38
• Thanks for the suggestion, I will have a look! Aug 31, 2020 at 0:09

This situation may be a little simpler than yours, but I hope it points the way to some useful possibilities. Suppose two drugs A and B are under study for treatment of a condition. One hundred subjects exhibiting the condition are recruited and randomly assigned, 25 each, to four different 'treatments': A only, B only, both A & B, and neither: for short A, B, AB, and N.

Simulated data might be as follows:

set.seed(2020)
x1 = rnorm(25, 104, 10)
x2 = rnorm(25, 106, 10)
x3 = rnorm(25, 110, 10)
x4 = rnorm(25, 100, 10)
x = c(x1,x2,x3,x4);  gp = rep(1:4, each=25)
stripchart(x~gp, ylim=c(.7, 4.3), pch="|") You could analyze this as a one-way ANOVA with treatment levels as the factor. You would have the choice of a standard one-way ANOVA, assuming variances equal in each of the four groups, or by using the procedure oneway.test in R. For my fake data, there are significant differences among the four group population means, as shown by the P-value 0.0067.

Then you could use Welch two-sample t tests ad hoc to explore differences of particular interest: for example, A vs. B, various treatments using drugs vs. the placebo, and so on. If you are going to look at all six pairs of the four levels, you should use some method (perhaps Bonferroni) to protect against 'false discovery'.

oneway.test(x~gp)

One-way analysis of means (not assuming equal variances)

data:  x and gp
F = 4.5322, num df = 3.000, denom df = 52.201, p-value = 0.006741


However, if it seems clear in advance that the four groups should have equal variances, you could use a standard ANOVA that assumes equal variances.

lm.out = lm(x ~ as.factor(gp))
anova(lm.out)
Analysis of Variance Table

Response: x
Df  Sum Sq Mean Sq F value  Pr(>F)
as.factor(gp)  3  1824.4  608.14  4.7253 0.00405 **
Residuals     96 12355.2  128.70
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1


Notice that you have three DF for Factor. As suggested in a comment by @StatStudentm you could look into contrasts. You could use "three pre-planned" orthogonal contrasts, perhaps ones with coefficients $$(1,-1,0,0)$$ [to see if drug A is better than B], $$(0,0,1,-1)$$ [to see if two drugs are better than none], and $$(1,1,-1,-1)$$ [to see if one drug is better than two or none].

Alternatively, you could look at a two-way ANOVA, with factors Drug A (levels Yes and No) and Drug B (levels Yes and No). Then the first three lines of the ANOVA table would be for Drug A, Drug B, and Interaction. These three would have one DF each, with an F-test for each. [In the one-way ANOVA, you could find three orthogonal contrasts that correspond to these three lines of the two-way table: $$c(1,-1,1-1),$$ $$(-1,1,1,-1),$$ $$(-1,-1,1,1),$$ respectively.]

A comparison of the standard one-way ANOVA (with contrasts for A, B, and Interaction) and the standard two-way ANOVA (in which these comparisons are lines in the table). shows that you can 'flatten' a two-way ANOVA to a one-way ANOVA without losing options for comparisons. In many cases, it is simpler to do the two-way ANOVA, especially if the comparisons of interest correspond to the effects.

If there is concern about unequal group variances, then it seems better to use oneway.test to adjust for unequal variances, and then do ad hoc Welch t tests. (As far as I know, the Satterthwaite correction used by one-way.test and Welch t tests has not yet been implemented for two and more factors.)

• Thank you for the detailed response! This is very helpful. Aug 31, 2020 at 0:12