chao1

This function implements the Chao1 richness estimate, which is often
mistakenly referred to as an index.

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

chao1 function

<dl><dt>input_data</dt>
<dd>An input type that can be processed by <code>convert()</code> or a <code>phyloseq</code> object</dd>
<dt>output</dt>
<dd>Deprecated; only for backwards compatibility</dd>
<dt>answers</dt>
<dd>Deprecated; only for backwards compatibility</dd></dl>

Arguments

Author

Chao1 species richness estimator — chao1

<dl>

<dt>input_data</dt>
<dd>An input type that can be processed by <code>convert()</code> or a <code>phyloseq</code> object</dd>


<dt>output</dt>
<dd>Deprecated; only for backwards compatibility</dd>


<dt>answers</dt>
<dd>Deprecated; only for backwards compatibility</dd>

</dl>

chao1: Chao1 species richness estimator

Description

Usage

Value

Arguments

Author

Examples