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.

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.

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"