physeq_wrap

Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 'breakaway' is the premier package for statistical analysis of microbial diversity. 'breakaway' implements the latest and greatest estimates of species richness, described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, Willis et al. (2017) <doi:10.1111/rssc.12206>, and Willis (2016) <arXiv:1604.02598>, as well as the most commonly used estimates, including the objective Bayes approach described in Barger and Bunge (2010) <doi:10.1214/10-BA527>.

Amy D Willis

breakaway

Species Richness Estimation and Modeling

Bryan D Martin

Pauline Trinh

Sarah Teichman

David Clausen

Kathryn Barger

John Bunge

physeq_wrap function

<dl><dt>fn</dt>
<dd>alpha diversity estimator function with <code>breakaway</code> to be applied to <code>physeq</code></dd>
<dt>physeq</dt>
<dd>A <code>phyloseq</code> object, or an object of class <code>otu_table</code></dd>
<dt>...</dt>
<dd>Additional arguments for fn</dd></dl>

Arguments

Wrapper for phyloseq objects — physeq_wrap

<dl>

<dt>fn</dt>
<dd>alpha diversity estimator function with <code>breakaway</code> to be applied to <code>physeq</code></dd>


<dt>physeq</dt>
<dd>A <code>phyloseq</code> object, or an object of class <code>otu_table</code></dd>


<dt>...</dt>
<dd>Additional arguments for fn</dd>

</dl>

Wrapper for phyloseq objects

physeq_wrap: Wrapper for phyloseq objects

Description

Usage

Value

Arguments