emmeans_test {rstatix} | R Documentation |
Pairwise Comparisons of Estimated Marginal Means
Description
Performs pairwise comparisons between groups using the estimated
marginal means. Pipe-friendly wrapper arround the functions emmans() +
contrast()
from the emmeans
package, which need to be installed
before using this function. This function is useful for performing post-hoc
analyses following ANOVA/ANCOVA tests.
Usage
emmeans_test(
data,
formula,
covariate = NULL,
ref.group = NULL,
comparisons = NULL,
p.adjust.method = "bonferroni",
conf.level = 0.95,
model = NULL,
detailed = FALSE
)
get_emmeans(emmeans.test)
Arguments
data |
a data.frame containing the variables in the formula. |
formula |
a formula of the form |
covariate |
(optional) covariate names (for ANCOVA) |
ref.group |
a character string specifying the reference group. If specified, for a given grouping variable, each of the group levels will be compared to the reference group (i.e. control group). If |
comparisons |
A list of length-2 vectors specifying the groups of
interest to be compared. For example to compare groups "A" vs "B" and "B" vs
"C", the argument is as follow: |
p.adjust.method |
method to adjust p values for multiple comparisons. Used when pairwise comparisons are performed. Allowed values include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". If you don't want to adjust the p value (not recommended), use p.adjust.method = "none". |
conf.level |
confidence level of the interval. |
model |
a fitted-model objects such as the result of a call to
|
detailed |
logical value. Default is FALSE. If TRUE, a detailed result is shown. |
emmeans.test |
an object of class |
Value
return a data frame with some the following columns:
-
.y.
: the y variable used in the test. -
group1,group2
: the compared groups in the pairwise tests. -
statistic
: Test statistic (t.ratio) used to compute the p-value. -
df
: degrees of freedom. -
p
: p-value. -
p.adj
: the adjusted p-value. -
method
: the statistical test used to compare groups. -
p.signif, p.adj.signif
: the significance level of p-values and adjusted p-values, respectively. -
estimate
: estimate of the effect size, that is the difference between the two emmeans (estimated marginal means). -
conf.low,conf.high
: Lower and upper bound on a confidence interval of the estimate.
The returned object has an attribute called args, which is a list holding the test arguments. It has also an attribute named "emmeans", a data frame containing the groups emmeans.
Functions
-
get_emmeans()
: returns the estimated marginal means from an object of classemmeans_test
Examples
# Data preparation
df <- ToothGrowth
df$dose <- as.factor(df$dose)
# Pairwise comparisons
res <- df %>%
group_by(supp) %>%
emmeans_test(len ~ dose, p.adjust.method = "bonferroni")
res
# Display estimated marginal means
attr(res, "emmeans")
# Show details
df %>%
group_by(supp) %>%
emmeans_test(len ~ dose, p.adjust.method = "bonferroni", detailed = TRUE)