Contingency Tables — contTables • ClinicoPath

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,
  riskDiff = FALSE,
  nnt = FALSE,
  ci = FALSE,
  ciWidth = 95,
  gamma = FALSE,
  taub = FALSE,
  trendTest = FALSE,
  trendDirection = "twosided",
  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)
riskDiff: TRUE or FALSE (default), provide the risk difference (only available for 2x2 tables)
nnt: TRUE or FALSE (default), provide the number needed to treat (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
trendTest: TRUE or FALSE (default), provide Cochran-Armitage test for trend for ordered categorical variables
trendDirection: Direction of trend test: two-sided (default), increasing, or decreasing
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
`results$trendTest`					Cochran-Armitage trend 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)