phyloseq: cca-rda-phyloseq-methods – R documentation

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cca-rda-phyloseq-methods

Constrained Correspondence Analysis and Redundancy Analysis.

Description

This is the internal function that simplifies getting phyloseq data into the constrained ordination functions, cca and rda. Unlike capscale.phyloseq, the formula argument to these methods is optional, and results in an unconstrained ordination.

Usage

cca.phyloseq(physeq, formula = NULL, method = "CCA", ...)

## S4 method for signature 'phyloseq,formula'
cca.phyloseq(physeq, formula = NULL,
  method = "CCA", ...)

## S4 method for signature 'otu_table,ANY'
cca.phyloseq(physeq, formula = NULL,
  method = "CCA", ...)

## S4 method for signature 'phyloseq,'NULL''
cca.phyloseq(physeq, formula = NULL,
  method = "CCA", ...)

Arguments

`physeq`	(Required). Phylogenetic sequencing data (`phyloseq-class`). The data on which you want to perform the ordination.
`formula`	(Optional). A `formula`, specifying the contraining variable(s) format, with variable names corresponding to `sample_data` (RHS) from within `physeq`.
`method`	(Optional). A single `character` string, specifying `"RDA"` or `"CCA"`. Default is `"CCA"`.
`...`	(Optional). Additional named arguments passed to `capscale`.

Value

same output as cca or rda, respectively.

Examples

#
# cca.phyloseq(physeq, formula, method, ...)

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23