tidy_cap: Constrained Ordination on Tidy Data

In bulksoil/tidyMB: A Set of Tools for Tidy Microbiome Analysis

Description

This function is a wrapper around Vegan's capscale function for performing PCoA on tidy (long) data.

Usage

tidy_cap(x, samples = "SampleID", otus = "variable", value = "RA",
  dist = "bray", formula = NULL)

Arguments

samples	The column header for your sample identifiers. Defaults to SampleID
otus	The column header for your OTU identifiers. Defaults to variable
value	The column header for the OTU abundances. Defaults to RA
dist	The distance metric options from vegan's vegdist(). Defaults to bray
formula	The formula to feed into the capscale function

Value

A list containing the axes, the eigenvalues, and loadings (optional)

Examples

tidy_cap()

bulksoil/tidyMB documentation built on May 29, 2019, 2:27 p.m.