pairwise.adonis: Pairwise multilevel comparison using adonis (from...

In erifa1/ExploreMetabar: ExploreMetabar

Pairwise multilevel comparison using adonis (from https://github.com/pmartinezarbizu/pairwiseAdonis)

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.function = "vegdist",
  sim.method = "bray",
  p.adjust.m = "bonferroni",
  reduce = NULL,
  perm = 999
)

Arguments

x	Data frame (the community table), or "dist" object (user-supplied distance matrix).
factors	Vector (a column or vector with the levels to be compared pairwise).
sim.function	Function used to calculate the similarity matrix, one of 'daisy' or 'vegdist' default is 'vegdist'. Ignored if x is a distance matrix.
sim.method	Similarity method from daisy or vegdist, default is 'bray'. Ignored if x is a distance matrix.
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, Df, SumsOfSqs, F-values, R^2, p.value and adjusted p.value.

Author(s)

Pedro Martinez Arbizu & Sylvain Monteux

Examples

data(iris)
pairwise.adonis(iris[,1:4],iris$Species)


#similarity euclidean from vegdist and holm correction
pairwise.adonis(x=iris[,1:4],factors=iris$Species,sim.function='vegdist',
sim.method='euclidian',p.adjust.m='holm')

#identical example using a distance matrix as an input
dist_matrix=vegdist(iris[,1:4],method="euclidean")
pairwise.adonis(dist_matrix,factors=iris$Species,
p.adjust.m='holm')

#similarity manhattan from daisy and bonferroni correction
pairwise.adonis(x=iris[,1:4],factors=iris$Species,sim.function='daisy',
sim.method='manhattan',p.adjust.m='bonferroni')

#Restrict comparison to only some factors
pairwise.adonis(iris[,1:4],iris$Species, reduce='setosa')

#for more than one factor separate by pipes
pairwise.adonis(iris[,1:4],iris$Species, reduce='setosa|versicolor')

erifa1/ExploreMetabar documentation built on Jan. 12, 2023, 1:51 a.m.