chisqPostHoc: Post-hoc Chi Square Tests

In cdeterman/HGTools: HG Tools

Description

Post-hoc tests for which pairs of populations differ following a significant chi-square test can be constructed by performing all chi-square tests for all pairs of populations and then adjusting the resulting p-values for inflation due to multiple comparisons. The adjusted p-values can be computed with a wide variety of methods – fdr, BH, BY, bonferroni, holm, hochberg, and hommel. This function basically works as a wrapper function that sends the unadjusted “raw” p-values from each pair-wise chi-square test to the p.adjust function in the base R program. The p.adjust function should be consulted for further description of the methods used.

Usage

chisqPostHoc(chi, control = c("fdr", "BH", "BY", "bonferroni", "holm",
  "hochberg", "hommel"), digits = 4)

Arguments

chi	A chisq.test object.
control	A string indicating the method of control to use. See details.
digits	A numeric that controls the number of digits to print.
popsInRows	A logical indicating whether the populations form the rows (default; =TRUE) of the table or not (=FALSE).
...	Other arguments sent to print.

Value

A data.frame with a description of the pairwise comparisons, the raw p-values, and the adjusted p-values.

See Also

chisq.test and p.adjust.

Examples

# Makes a table of observations -- similar to first example in chisq.test
M <- as.table(rbind(c(76, 32, 46), c(48,23,47), c(45,34,78)))
dimnames(M) <- list(sex=c("Male","Female","Juv"),loc=c("Lower","Middle","Upper"))
M
# Fits chi-square test and shows summary
( chi1 <- chisq.test(M) )
# Shows post-hoc pairwise comparisons using fdr method
chisqPostHoc(chi1)

# Transpose the observed table to demonstrate use of popsInRows=FALSE
( chi2 <- chisq.test(t(M)) )
chisqPostHoc(chi2,popsInRows=FALSE)

cdeterman/HGTools documentation built on May 13, 2019, 2:34 p.m.