contingencyTest: Contingency test for count data
In eudysbiome: Cartesian plot and contingency test on 16S Microbial data

Description Usage Arguments Details Value See Also Examples

View source: R/contingencyTest.R

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.

1 2	contingencyTest(microCount, chisq = TRUE, fisher = TRUE, alternative = c("greater"))

`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`.

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

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.

contingencyCount, fisher.test, chisq.test

data(microCount)

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