wilcox_test.Rd
Provides a pipe-friendly framework to performs one and two sample Wilcoxon tests.
wilcox_test(data, formula, comparisons = NULL, ref.group = NULL, p.adjust.method = "holm", paired = FALSE, exact = NULL, alternative = "two.sided", mu = 0, conf.level = 0.95, detailed = FALSE) pairwise_wilcox_test(data, formula, comparisons = NULL, ref.group = NULL, p.adjust.method = "holm", detailed = FALSE, ...)
data | a data.frame containing the variables in the formula. |
---|---|
formula | a formula of the form |
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: |
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 |
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". |
paired | a logical indicating whether you want a paired test. |
exact | a logical indicating whether an exact p-value should be computed. |
alternative | a character string specifying the alternative
hypothesis, must be one of |
mu | a number specifying an optional parameter used to form the null hypothesis. |
conf.level | confidence level of the interval. |
detailed | logical value. Default is FALSE. If TRUE, a detailed result is shown. |
... | other arguments to be passed to the function
|
return a data frame with some of the following columns:
.y.
: the y variable used in the test.
group1,group2
: the compared groups in the pairwise tests.
n,n1,n2
: Sample counts.
statistic
: Test statistic used
to compute the p-value.
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.
The returned object has an attribute called args, which is a list holding the test arguments.
- pairwise_wilcox_test()
applies the standard two sample
Wilcoxon test to all possible pairs of groups. This method calls the
wilcox.test()
, so extra arguments are accepted.
- If a list of comparisons is specified, the result of the pairwise tests is filtered to keep only the comparisons of interest.The p-value is adjusted after filtering.
- For a grouped data, if pairwise test is performed, then the p-values are adjusted for each group level independently.
wilcox_test
: Wilcoxon test
pairwise_wilcox_test
: performs pairwise two sample Wilcoxon test.
# Load data #::::::::::::::::::::::::::::::::::::::: data("ToothGrowth") df <- ToothGrowth # One-sample test #::::::::::::::::::::::::::::::::::::::::: df %>% wilcox_test(len ~ 1, mu = 0)#> Error in UseMethod("wilcox_test"): pas de méthode pour 'wilcox_test' applicable pour un objet de classe "data.frame"# Two-samples unpaired test #::::::::::::::::::::::::::::::::::::::::: df %>% wilcox_test(len ~ supp)#> Error in UseMethod("wilcox_test"): pas de méthode pour 'wilcox_test' applicable pour un objet de classe "data.frame"# Two-samples paired test #::::::::::::::::::::::::::::::::::::::::: df %>% wilcox_test (len ~ supp, paired = TRUE)#> Error in UseMethod("wilcox_test"): pas de méthode pour 'wilcox_test' applicable pour un objet de classe "data.frame"# Compare supp levels after grouping the data by "dose" #:::::::::::::::::::::::::::::::::::::::: df %>% group_by(dose) %>% wilcox_test(data =., len ~ supp) %>% adjust_pvalue(method = "bonferroni") %>% add_significance("p.adj")#> Error in add_significance(., "p.adj"): The column p.adj does not exist in the data# pairwise comparisons #:::::::::::::::::::::::::::::::::::::::: # As dose contains more than two levels ==> # pairwise test is automatically performed. df %>% wilcox_test(len ~ dose)#> Error in UseMethod("wilcox_test"): pas de méthode pour 'wilcox_test' applicable pour un objet de classe "data.frame"# Comparison against reference group #:::::::::::::::::::::::::::::::::::::::: # each level is compared to the ref group df %>% wilcox_test(len ~ dose, ref.group = "0.5")#> Error in UseMethod("wilcox_test"): pas de méthode pour 'wilcox_test' applicable pour un objet de classe "data.frame"# Comparison against all #:::::::::::::::::::::::::::::::::::::::: df %>% wilcox_test(len ~ dose, ref.group = "all")#> Error in UseMethod("wilcox_test"): pas de méthode pour 'wilcox_test' applicable pour un objet de classe "data.frame"