contingencyTest {eudysbiome} | R Documentation

## 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`.

### 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`

### 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.

### 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"]]

[Package eudysbiome version 1.16.0 Index]