chisq_test: Chi-squared Test for Count Data

In kassambara/rstatix: Pipe-Friendly Framework for Basic Statistical Tests

Chi-squared Test for Count Data

Description

Performs chi-squared tests, including goodness-of-fit, homogeneity and independence tests.

Usage

chisq_test(
  x,
  y = NULL,
  correct = TRUE,
  p = rep(1/length(x), length(x)),
  rescale.p = FALSE,
  simulate.p.value = FALSE,
  B = 2000
)

pairwise_chisq_gof_test(x, p.adjust.method = "holm", ...)

pairwise_chisq_test_against_p(
  x,
  p = rep(1/length(x), length(x)),
  p.adjust.method = "holm",
  ...
)

chisq_descriptives(res.chisq)

expected_freq(res.chisq)

observed_freq(res.chisq)

pearson_residuals(res.chisq)

std_residuals(res.chisq)

Arguments

x	a numeric vector or matrix. x and y can also both be factors.
y	a numeric vector; ignored if x is a matrix. If x is a factor, y should be a factor of the same length.
correct	a logical indicating whether to apply continuity correction when computing the test statistic for 2 by 2 tables: one half is subtracted from all |O - E| differences; however, the correction will not be bigger than the differences themselves. No correction is done if simulate.p.value = TRUE.
p	a vector of probabilities of the same length of x. An error is given if any entry of p is negative.
rescale.p	a logical scalar; if TRUE then p is rescaled (if necessary) to sum to 1. If rescale.p is FALSE, and p does not sum to 1, an error is given.
simulate.p.value	a logical indicating whether to compute p-values by Monte Carlo simulation.
B	an integer specifying the number of replicates used in the Monte Carlo test.
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".
...	other arguments passed to the function {chisq_test}().
res.chisq	an object of class chisq_test.

Value

return a data frame with some the following columns:

• n: the number of participants.

• group, group1, group2: the categories or groups being compared.

• statistic: the value of Pearson's chi-squared test statistic.

• df: the degrees of freedom of the approximate chi-squared distribution of the test statistic. NA if the p-value is computed by Monte Carlo simulation.

• 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.

• observed: observed counts.

• expected: the expected counts under the null hypothesis.

The returned object has an attribute called args, which is a list holding the test arguments.

Functions

• chisq_test(): performs chi-square tests including goodness-of-fit, homogeneity and independence tests.

• pairwise_chisq_gof_test(): perform pairwise comparisons between groups following a global chi-square goodness of fit test.

• pairwise_chisq_test_against_p(): perform pairwise comparisons after a global chi-squared test for given probabilities. For each group, the observed and the expected proportions are shown. Each group is compared to the sum of all others.

• chisq_descriptives(): returns the descriptive statistics of the chi-square test. These include, observed and expected frequencies, proportions, residuals and standardized residuals.

• expected_freq(): returns the expected counts from the chi-square test result.

• observed_freq(): returns the observed counts from the chi-square test result.

• pearson_residuals(): returns the Pearson residuals, (observed - expected) / sqrt(expected).

• std_residuals(): returns the standardized residuals

Examples

# Chi-square goodness of fit test
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
tulip <- c(red = 81, yellow = 50, white = 27)
# Q1: Are the colors equally common?
chisq_test(tulip)
pairwise_chisq_gof_test(tulip)
# Q2: comparing observed to expected proportions
chisq_test(tulip, p = c(1/2, 1/3, 1/6))
pairwise_chisq_test_against_p(tulip, p = c(0.5, 0.33, 0.17))

# Homogeneity of proportions between groups
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Data: Titanic
xtab <- as.table(rbind(
  c(203, 118, 178, 212),
  c(122, 167, 528, 673)
))
dimnames(xtab) <- list(
  Survived = c("Yes", "No"),
  Class = c("1st", "2nd", "3rd", "Crew")
)
xtab
# Chi-square test
chisq_test(xtab)
# Compare the proportion of survived between groups
pairwise_prop_test(xtab)

kassambara/rstatix documentation built on Feb. 6, 2023, 3:36 a.m.