Post-hoc tests for Cochran-Mantel-Haenszel test

Conducts groupwise tests of association on a three-way contingency table.

Usage

groupwiseCMH(
  x,
  group = 3,
  fisher = TRUE,
  gtest = FALSE,
  chisq = FALSE,
  method = "fdr",
  correct = "none",
  digits = 3,
  ...
)

Arguments

x: A three-way contingency table.
group: The dimension of the table to use as the grouping variable. Will be 1, 2, or 3.
fisher: If TRUE, conducts Fisher exact test.
gtest: If TRUE, conducts G test of association.
chisq: If TRUE, conducts Chi-square test of association.
method: The method to use to adjust p-values. See ?p.adjust.
correct: The correction to apply to the G test. See GTest.
digits: The number of digits for numbers in the output.
...: Other arguments passed to chisq.test or GTest.

Value

A data frame of groups, test used, p-values, and adjusted p-values.

Details

If more than one of fisher, gtest, or chisq is set to TRUE, only one type of test of association will be conducted.

References

https://rcompanion.org/handbook/H_06.html

Author

Salvatore Mangiafico, mangiafico@njaes.rutgers.edu

Examples

### Post-hoc for Cochran-Mantel-Haenszel test
data(AndersonBias)
Table = xtabs(Count ~ Gender + Result + County,
              data=AndersonBias)
ftable(Table)
#>               County Bloom Cobblestone Dougal Heimlich
#> Gender Result                                         
#> Female Pass              9          11      9       15
#>        Fail              5           4      7        8
#> Male   Pass              7           9     19       14
#>        Fail             17          21      9       17
mantelhaen.test(Table)
#> 
#> 	Mantel-Haenszel chi-squared test with continuity correction
#> 
#> data:  Table
#> Mantel-Haenszel X-squared = 6.7314, df = 1, p-value = 0.009473
#> alternative hypothesis: true common odds ratio is not equal to 1
#> 95 percent confidence interval:
#>  1.248399 4.260003
#> sample estimates:
#> common odds ratio 
#>          2.306119 
#> 
groupwiseCMH(Table,
             group   = 3,
             fisher  = TRUE,
             gtest   = FALSE,
             chisq   = FALSE,
             method  = "fdr",
             correct = "none",
             digits  = 3)
#> 
#>         Group   Test p.value  adj.p
#> 1       Bloom Fisher  0.0468 0.0936
#> 2 Cobblestone Fisher  0.0102 0.0408
#> 3      Dougal Fisher  0.5230 0.5230
#> 4    Heimlich Fisher  0.1750 0.2330