How to do Pairwise Comparisons in R, To evaluate if there is a statistically significant difference between the means of three or more independent groups, a one-way ANOVA is utilized.
The following null and alternate hypotheses are used in a one-way ANOVA.
H0: All group means are equal. HA: Not all group means are equal.
We reject the null hypothesis and come to the conclusion that not all of the group means are equal if the overall p-value of the ANOVA is less than a predetermined significance level (for example, =.05.
We can next conduct post hoc pairwise comparisons to determine which group means are different.
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Example: One-Way ANOVA in R
Consider a teacher who is curious about whether or not the use of three different study methods affects pupils’ exam results.
She distributes ten students to each study method at random in order to test this, then she tracks their exam results.
To conduct a one-way ANOVA in R and check for variations in the mean exam scores among the three groups, use the following code:
Let’s create a data frame
df <- data.frame(technique = rep(c("tech1", "tech2", "tech3"), each=10), score = c(276, 377, 407, 581, 182, 112, 483, 484, 185, 289, 81, 82, 183, 183, 183, 584, 187, 190, 192, 193, 77, 78, 177, 178, 179, 140, 178, 195, 145, 158))
technique score 1 tech1 176 2 tech1 177 3 tech1 107 4 tech1 181 5 tech1 182 6 tech1 112
Now we can perform one-way ANOVA
model <- aov(score ~ technique, data = df)
View output of ANOVA
Df Sum Sq Mean Sq F value Pr(>F) technique 2 184786 92393 6.159 0.00626 ** Residuals 27 405053 15002 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
We will reject the null hypothesis that the mean exam score is the same for each studying method because the overall p-value of the ANOVA (.00626) is less than =.05.
We can now conduct posthoc pairwise comparisons to identify the groups with various means.
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The Tukey Method
When the sample sizes of each group are equal, the Tukey posthoc method performs the best.
The built-in TukeyHSD() function in R can be used to implement the Tukey posthoc method:
Let’s use the Tukey post-hoc analysis
Tukey multiple comparisons of means 95% family-wise confidence level Fit: aov(formula = score ~ technique, data = df) $technique diff lwr upr p adj tech2-tech1 -131.8 -267.6121 4.012102 0.0584488 tech3-tech1 -187.1 -322.9121 -51.287898 0.0055676 tech3-tech2 -55.3 -191.1121 80.512102 0.5773136
From the output, we can see that the only p-value (“p adj“) less than 0.05 those pairs are significantly different from each other.
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The Scheffe Method
When comparing group means, the Scheffe technique yields the largest confidence intervals and is the most conservative posthoc pairwise comparison method.
To implement the Scheffe post-hoc approach in R, use the ScheffeTest() function from the DescTools package:
Now ready to perform the Scheffe post-hoc method
Posthoc multiple comparisons of means: Scheffe Test 95% family-wise confidence level $technique diff lwr.ci upr.ci pval tech2-tech1 -131.8 -273.671 10.07105 0.0726 . tech3-tech1 -187.1 -328.971 -45.22895 0.0078 ** tech3-tech2 -55.3 -197.171 86.57105 0.6064 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
From the output we can see that the only p-value (“p adj“) less than 0.05 those pairs are significantly different from each other.
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The Bonferroni Method
When you want to make a set of pre-planned pairwise comparisons, the Bonferroni method is the best to apply.
To use the Bonferroni post-hoc procedure, we can use the R syntax shown below:
Let’s use the Bonferroni post-hoc analysis
pairwise.t.test(df$score, df$technique, p.adj='bonferroni')
Pairwise comparisons using t tests with pooled SD data: df$score and df$technique tech1 tech2 tech2 0.0697 - tech3 0.0061 0.9650 P value adjustment method: bonferroni
The Holm Method
When you want to make a set of planned pairwise comparisons in advance, you can also use the Holm technique because it frequently has even higher power than the Bonferroni approach.
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The Holm post-hoc approach can be used in R using the syntax shown below:
Holm post-hoc approach should be used.
pairwise.t.test(df$score, df$technique, p.adj='holm')
Pairwise comparisons using t tests with pooled SD data: df$score and df$technique tech1 tech2 tech2 0.0465 - tech3 0.0061 0.3217 P value adjustment method: holm
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Comment on “How to do Pairwise Comparisons in R?”
No! Multiple contrast tests are the best way. See the R-packages lsmeans, multcomp, nparcomp, …!