my_ordination: Customized function for PCoA and NMDS

In kun-ecology/ecoloop: Loop for ecological data analysis

Customized function for PCoA and NMDS

Description

Customized function for PCoA and NMDS

Usage

my_ordination(sp.df, sp.dist = NULL, method = NULL, axes = NULL, ...)

Arguments

sp.df	Species abundance data, row as sites while column as species
sp.dist	WHich distance should be used, by default, bray distance will be used
method	Either PCoA or NMDS should be conducted, by default, PCoA will be performed with ape::pcoa. Since it is recommended that PCoA are suitable for most of the applications.
axes	Indicating the numbers of axes interested, by default axes=2.
...	More arguments can be passed to vegan::metaMDS or ape::pcoa

Value

A list including 1) the ordination model and 2) the summary for further visualizations

kun-ecology/ecoloop documentation built on Jan. 9, 2025, 10:20 a.m.