pairwise_adonis: Pairwise multilevel comparison using adonis

In gauravsk/ranacapa: Utility Functions and 'shiny' App for Simple Environmental DNA Visualizations and Analyses

Description

This is a wrapper function for multilevel pairwise comparison using adonis() from package 'vegan'. The function returns adjusted p-values using p.adjust().

Usage

pairwise_adonis(x, factors, sim_method = "bray",
  p_adjust_m = "bonferroni", reduce = NULL)

Arguments

x	Data frame (the community table).
factors	Vector (a column or vector with the levels to be compared pairwise).
sim_method	Similarity method from vegdist, default is 'bray'
p_adjust_m	The p.value correction method, one of the methods supported by p.adjust(), default is 'bonferroni'.
reduce	String. Restrict comparison to pairs including these factors. If more than one factor, separate by pipes like: reduce = 'setosa|versicolor'

Value

Table with the pairwise factors, F-values, R^2, p.value and adjusted p.value.

Examples

data(iris)
pairwise_adonis(iris[, 1:4], iris$Species)

pairwise_adonis(iris[, 1:4], iris$Species, reduce = 'setosa')

# similarity euclidean from vegdist and holm correction
pairwise_adonis(x = iris[, 1:4], factors = iris$Species,
sim_method = 'euclidian', p_adjust_m = 'holm')

#similarity manhattan from daisy and bonferroni correction
pairwise_adonis(x = iris[, 1:4], factors = iris$Species,
sim_method = 'manhattan', p_adjust_m = 'bonferroni')

gauravsk/ranacapa documentation built on June 7, 2019, 4:03 a.m.