fisher_test {rstatix} | R Documentation |
Fisher's Exact Test for Count Data
Description
Performs Fisher's exact test for testing the null of independence of rows and columns in a contingency table.
Wrappers around the R base function fisher.test()
but
have the advantage of performing pairwise and row-wise fisher tests, the
post-hoc tests following a significant chi-square test of homogeneity for 2xc
and rx2 contingency tables.
Usage
fisher_test(
xtab,
workspace = 2e+05,
alternative = "two.sided",
conf.int = TRUE,
conf.level = 0.95,
simulate.p.value = FALSE,
B = 2000,
detailed = FALSE,
...
)
pairwise_fisher_test(xtab, p.adjust.method = "holm", detailed = FALSE, ...)
row_wise_fisher_test(xtab, p.adjust.method = "holm", detailed = FALSE, ...)
Arguments
xtab |
a contingency table in a matrix form. |
workspace |
an integer specifying the size of the workspace
used in the network algorithm. In units of 4 bytes. Only used for
non-simulated p-values larger than |
alternative |
indicates the alternative hypothesis and must be
one of |
conf.int |
logical indicating if a confidence interval for the
odds ratio in a |
conf.level |
confidence level for the returned confidence
interval. Only used in the |
simulate.p.value |
a logical indicating whether to compute
p-values by Monte Carlo simulation, in larger than |
B |
an integer specifying the number of replicates used in the Monte Carlo test. |
detailed |
logical value. Default is FALSE. If TRUE, a detailed result is shown. |
... |
Other arguments passed to the function |
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". |
Value
return a data frame with some the following columns:
-
group
: the categories in the row-wise proportion tests. -
p
: p-value. -
p.adj
: the adjusted p-value. -
method
: the used statistical test. -
p.signif, p.adj.signif
: the significance level of p-values and adjusted p-values, respectively. -
estimate
: an estimate of the odds ratio. Only present in the 2 by 2 case. -
alternative
: a character string describing the alternative hypothesis. -
conf.low,conf.high
: a confidence interval for the odds ratio. Only present in the 2 by 2 case and if argument conf.int = TRUE.
The returned object has an attribute called args, which is a list holding the test arguments.
Functions
-
fisher_test()
: performs Fisher's exact test for testing the null of independence of rows and columns in a contingency table with fixed marginals. Wrapper around the functionfisher.test()
. -
pairwise_fisher_test()
: pairwise comparisons between proportions, a post-hoc tests following a significant Fisher's exact test of homogeneity for 2xc design. -
row_wise_fisher_test()
: performs row-wise Fisher's exact test of count data, a post-hoc tests following a significant chi-square test of homogeneity for rx2 contingency table. The test is conducted for each category (row).
Examples
# Comparing two proportions
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Data: frequencies of smokers between two groups
xtab <- as.table(rbind(c(490, 10), c(400, 100)))
dimnames(xtab) <- list(
group = c("grp1", "grp2"),
smoker = c("yes", "no")
)
xtab
# compare the proportion of smokers
fisher_test(xtab, detailed = TRUE)
# Homogeneity of proportions between groups
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# H0: the proportion of smokers is similar in the four groups
# Ha: this proportion is different in at least one of the populations.
#
# Data preparation
grp.size <- c( 106, 113, 156, 102 )
smokers <- c( 50, 100, 139, 80 )
no.smokers <- grp.size - smokers
xtab <- as.table(rbind(
smokers,
no.smokers
))
dimnames(xtab) <- list(
Smokers = c("Yes", "No"),
Groups = c("grp1", "grp2", "grp3", "grp4")
)
xtab
# Compare the proportions of smokers between groups
fisher_test(xtab, detailed = TRUE)
# Pairwise comparison between groups
pairwise_fisher_test(xtab)
# Pairwise proportion tests
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Data: Titanic
xtab <- as.table(rbind(
c(122, 167, 528, 673),
c(203, 118, 178, 212)
))
dimnames(xtab) <- list(
Survived = c("No", "Yes"),
Class = c("1st", "2nd", "3rd", "Crew")
)
xtab
# Compare the proportion of survived between groups
pairwise_fisher_test(xtab)
# Row-wise proportion tests
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Data: Titanic
xtab <- as.table(rbind(
c(180, 145), c(179, 106),
c(510, 196), c(862, 23)
))
dimnames(xtab) <- list(
Class = c("1st", "2nd", "3rd", "Crew"),
Gender = c("Male", "Female")
)
xtab
# Compare the proportion of males and females in each category
row_wise_fisher_test(xtab)
# A r x c table Agresti (2002, p. 57) Job Satisfaction
Job <- matrix(c(1,2,1,0, 3,3,6,1, 10,10,14,9, 6,7,12,11), 4, 4,
dimnames = list(income = c("< 15k", "15-25k", "25-40k", "> 40k"),
satisfaction = c("VeryD", "LittleD", "ModerateS", "VeryS")))
fisher_test(Job)
fisher_test(Job, simulate.p.value = TRUE, B = 1e5)