Pairwise tests of independence for nominal data with matrix output

Conducts pairwise tests for a 2-dimensional matrix, in which at at least one dimension has more than two levels, as a post-hoc test. Conducts Fisher exact, Chi-square, or G-test.

Usage

pairwiseNominalMatrix(
  x,
  compare = "row",
  fisher = TRUE,
  gtest = FALSE,
  chisq = FALSE,
  method = "fdr",
  correct = "none",
  digits = 3,
  ...
)

Arguments

x: A two-way contingency table. At least one dimension should have more than two levels.
compare: If "row", treats the rows as the grouping variable. If "column", treats the columns as the grouping variable.
fisher: If "TRUE", conducts fisher exact test.
gtest: If "TRUE", conducts G-test.
chisq: If "TRUE", conducts Chi-square test of association.
method: The method to adjust multiple p-values. See p.adjust.
correct: The correction method to pass to DescTools::GTest.
digits: The number of significant digits in the output.
...: Additional arguments, passed to stats::fisher.test, DescTools::GTest, or stats::chisq.test.

Value

A list consisting of: the test used, a matrix of unadjusted p-values, the p-value adjustment method used, and a matrix of adjusted p-values.

References

https://rcompanion.org/handbook/H_04.html

Author

Salvatore Mangiafico, mangiafico@njaes.rutgers.edu

Examples

### Independence test for a 4 x 2 matrix
data(Anderson)
fisher.test(Anderson)
#> 
#> 	Fisher's Exact Test for Count Data
#> 
#> data:  Anderson
#> p-value = 0.000668
#> alternative hypothesis: two.sided
#> 
Anderson = Anderson[(c("Heimlich", "Bloom", "Dougal", "Cobblestone")),]
PT = pairwiseNominalMatrix(Anderson,
                           fisher = TRUE,
                           gtest  = FALSE,
                           chisq  = FALSE)$Adjusted
PT
#>             Heimlich  Bloom Dougal Cobblestone
#> Heimlich     1.00000 0.7400 0.0262     0.00596
#> Bloom        0.74000 1.0000 0.0564     0.01190
#> Dougal       0.02620 0.0564 1.0000     0.74000
#> Cobblestone  0.00596 0.0119 0.7400     1.00000
library(multcompView)
multcompLetters(PT)
#>    Heimlich       Bloom      Dougal Cobblestone 
#>         "a"        "ab"        "bc"         "c"