contTables: Contingency Tables
In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

contTables

R Documentation

Contingency Tables

Description

The X² test of association (not to be confused with the X² goodness of fit) is used to test whether two categorical variables are independent or associated. If the p-value is low, it suggests the variables are not independent, and that there is a relationship between the two variables.

Usage

contTables(
  data,
  rows,
  cols,
  counts = NULL,
  layers = NULL,
  chiSq = TRUE,
  chiSqCorr = FALSE,
  likeRat = FALSE,
  fisher = FALSE,
  contCoef = FALSE,
  phiCra = FALSE,
  logOdds = FALSE,
  odds = FALSE,
  relRisk = FALSE,
  ci = TRUE,
  ciWidth = 95,
  gamma = FALSE,
  taub = FALSE,
  obs = TRUE,
  exp = FALSE,
  pcRow = FALSE,
  pcCol = FALSE,
  pcTot = FALSE,
  formula
)

Arguments

`data`	the data as a data frame
`rows`	the variable to use as the rows in the contingency table (not necessary when providing a formula, see the examples)
`cols`	the variable to use as the columns in the contingency table (not necessary when providing a formula, see the examples)
`counts`	the variable to use as the counts in the contingency table (not necessary when providing a formula, see the examples)
`layers`	the variables to use to split the contingency table (not necessary when providing a formula, see the examples)
`chiSq`	`TRUE` (default) or `FALSE`, provide X²
`chiSqCorr`	`TRUE` or `FALSE` (default), provide X² with continuity correction
`likeRat`	`TRUE` or `FALSE` (default), provide the likelihood ratio
`fisher`	`TRUE` or `FALSE` (default), provide Fisher's exact test
`contCoef`	`TRUE` or `FALSE` (default), provide the contingency coefficient
`phiCra`	`TRUE` or `FALSE` (default), provide Phi and Cramer's V
`logOdds`	`TRUE` or `FALSE` (default), provide the log odds ratio (only available for 2x2 tables)
`odds`	`TRUE` or `FALSE` (default), provide the odds ratio (only available for 2x2 tables)
`relRisk`	`TRUE` or `FALSE` (default), provide the relative risk (only available for 2x2 tables)
`ci`	`TRUE` or `FALSE` (default), provide confidence intervals for the comparative measures
`ciWidth`	a number between 50 and 99.9 (default: 95), width of the confidence intervals to provide
`gamma`	`TRUE` or `FALSE` (default), provide gamma
`taub`	`TRUE` or `FALSE` (default), provide Kendall's tau-b
`obs`	`TRUE` or `FALSE` (default), provide the observed counts
`exp`	`TRUE` or `FALSE` (default), provide the expected counts
`pcRow`	`TRUE` or `FALSE` (default), provide row percentages
`pcCol`	`TRUE` or `FALSE` (default), provide column percentages
`pcTot`	`TRUE` or `FALSE` (default), provide total percentages
`formula`	(optional) the formula to use, see the examples

Value

A results object containing:

`results$freqs`					a table of proportions
`results$chiSq`					a table of X² test results
`results$odds`					a table of comparative measures
`results$nom`					a table of the 'nominal' test results
`results$gamma`					a table of the gamma test results
`results$taub`					a table of the Kendall's tau-b test results

Tables can be converted to data frames with asDF or as.data.frame. For example:

results$freqs$asDF

as.data.frame(results$freqs)

Examples


# data('HairEyeColor')
# dat <- as.data.frame(HairEyeColor)

# contTables(formula = Freq ~ Hair:Eye, dat)

#
#  CONTINGENCY TABLES
#
#  Contingency Tables
#  -----------------------------------------------------
#    Hair     Brown    Blue    Hazel    Green    Total
#  -----------------------------------------------------
#    Black       68      20       15        5      108
#    Brown      119      84       54       29      286
#    Red         26      17       14       14       71
#    Blond        7      94       10       16      127
#    Total      220     215       93       64      592
#  -----------------------------------------------------
#
#
#  X² Tests
#  -------------------------------
#          Value    df    p
#  -------------------------------
#    X²      138     9    < .001
#    N       592
#  -------------------------------
#

# Alternatively, omit the left of the formula (`Freq`) if each row
# represents a single observation:

# contTables(formula = ~ Hair:Eye, dat)

sbalci/ClinicoPathJamoviModule documentation built on June 13, 2025, 9:34 a.m.