eudysbiome (version 1.2.0)

contingencyTest: Contingency test for count data

Description

Performs Chi-squared test or Fisher's exact test for testing the significance of association between conditions and eubiotic/dysbiotic impacts in a contingency table.

Usage

contingencyTest(microCount, chisq = TRUE, fisher = TRUE, alternative = c("greater"))

Arguments

microCount

a m by 2 data frame or numeric matrix of contingency table with frequencies under each condition-impact term; could be produced from contingencyCount.

chisq, fisher

logical indicating if the Chi-squared test or Fisher's exact test should be performed.

alternative

parameter specifying for alternative hypothesis, only used when fisher is TRUE; see fisher.test.

Value

A list with following components: Chisq Chi-squared test results for each pair-wise condition. Chisq.p the p-values of the Chi-squared tests for all pair-wise conditions. Fisher Fisher's exact test results for each pair-wise condition. Fisher.p the p-values of the Fisher's exact tests for all pair-wise conditions.

Details

Chi-squared test for testing the probability that the proportions of eubiotic frequencies are different between two conditions; furtherly, the Fisher's exact test for testing whether one condition is more likely to be associated to eubiotic impact. More details, refer to chisq.test and fisher.test

See Also

contingencyCount, fisher.test, chisq.test

Examples

data(microCount)

test = contingencyTest(microCount,chisq = TRUE,fisher = TRUE,
           alternative = "greater")
chisq.p = test[["Chisq.p"]]
fisher.p = test[["Fisher.p"]]