cca.phyloseq

cca.phyloseq,otu_table,ANY-method

cca.phyloseq,otu_table-method

cca.phyloseq,phyloseq,NULL-method

cca.phyloseq,phyloseq,formula-method

rda.phyloseq

(Required). Phylogenetic sequencing data
(<code><a href="/link/phyloseq-class?package=phyloseq&version=1.16.2" rd-options="" data-mini-rdoc="phyloseq::phyloseq-class">phyloseq-class</a></code>).
The data on which you want to perform the ordination.

physeq

(Optional). A <code><a href="/link/formula?package=phyloseq&version=1.16.2" rd-options="" data-mini-rdoc="phyloseq::formula">formula</a></code>, 
specifying the contraining variable(s) format,
with variable names corresponding to <code><a href="/link/sample_data?package=phyloseq&version=1.16.2" rd-options="" data-mini-rdoc="phyloseq::sample_data">sample_data</a></code> (RHS)
from within <code>physeq</code>.

formula

(Optional). A single <code><a href="/link/character?package=phyloseq&version=1.16.2" rd-options="" data-mini-rdoc="phyloseq::character">character</a></code> string,
specifying <code>"RDA"</code> or <code>"CCA"</code>. Default is <code>"CCA"</code>.

method

(Optional). Additional named arguments passed to 
<code><a href="/link/capscale?package=phyloseq&version=1.16.2&to=vegan" rd-options="vegan" data-mini-rdoc="vegan::capscale">capscale</a></code>.

This is the internal function that simplifies getting phyloseq data
into the constrained ordination functions, 
<code><a href="/link/cca?package=phyloseq&version=1.16.2&to=vegan" rd-options="vegan" data-mini-rdoc="vegan::cca">cca</a></code> and <code><a href="/link/rda?package=phyloseq&version=1.16.2&to=vegan" rd-options="vegan" data-mini-rdoc="vegan::rda">rda</a></code>.
Unlike <code><a href="/link/capscale.phyloseq?package=phyloseq&version=1.16.2&to=phyloseq" rd-options="phyloseq" data-mini-rdoc="phyloseq::capscale.phyloseq">capscale.phyloseq</a></code>, the formula argument
to these methods is optional, and results in an unconstrained ordination.

internal

phyloseq provides a set of classes and tools
    to facilitate the import, storage, analysis, and
    graphical display of microbiome census data.

Paul McMurdie

phyloseq

Handling and analysis of high-throughput microbiome
    census data

cca.phyloseq function

(Required). Phylogenetic sequencing data
(<code><a href="phyloseq-class" rd-options="">phyloseq-class</a></code>).
The data on which you want to perform the ordination.

(Optional). A <code><a href="formula" rd-options="">formula</a></code>, 
specifying the contraining variable(s) format,
with variable names corresponding to <code><a href="sample_data" rd-options="">sample_data</a></code> (RHS)
from within <code>physeq</code>.

(Optional). A single <code><a href="character" rd-options="">character</a></code> string,
specifying <code>"RDA"</code> or <code>"CCA"</code>. Default is <code>"CCA"</code>.

(Optional). Additional named arguments passed to 
<code><a href="capscale" rd-options="vegan">capscale</a></code>.

This is the internal function that simplifies getting phyloseq data
into the constrained ordination functions, 
<code><a href="cca" rd-options="vegan">cca</a></code> and <code><a href="rda" rd-options="vegan">rda</a></code>.
Unlike <code><a href="capscale.phyloseq" rd-options="phyloseq">capscale.phyloseq</a></code>, the formula argument
to these methods is optional, and results in an unconstrained ordination.

cca.phyloseq: Constrained Correspondence Analysis and Redundancy Analysis.

Description

Usage

Arguments

Value

See Also

Examples