diversity_beta_test {animalcules} | R Documentation

## Beta diversity test (by default we use bray-curtis distance)

### Description

Beta diversity test (by default we use bray-curtis distance)

### Usage

    diversity_beta_test(
      MAE,
      tax_level,
      input_beta_method,
      input_select_beta_condition,
      input_select_beta_stat_method,
      input_num_permutation_permanova = 999
    )

### Arguments

`MAE` | A multi-assay experiment object
`tax_level` | The taxon level used for organisms
`input_beta_method` | bray, jaccard
`input_select_beta_condition` | Which condition to group samples
`input_select_beta_stat_method` | PERMANOVA,Kruskal-Wallis,Wilcoxon test
`input_num_permutation_permanova` | number of permutations

### Value

A plotly object

### Examples

    data_dir = system.file('extdata/MAE.rds', package = 'animalcules')
    toy_data <- readRDS(data_dir)
    p <- diversity_beta_test(toy_data,
                             tax_level = 'genus',
                             input_beta_method = 'bray',
                             input_select_beta_condition = 'DISEASE',
                             input_select_beta_stat_method = 'PERMANOVA',
                             input_num_permutation_permanova = 999)
    p

[Package animalcules version 1.8.1 Index]