alpha_estimate

Build objects of class alpha_estimate from their components. <code>alpha_estimate()</code> is a constructor method

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

alpha_estimate function

<dl><dt>estimate</dt>
<dd>The estimate</dd>
<dt>error</dt>
<dd>The standard error in the estimate</dd>
<dt>estimand</dt>
<dd>What is the estimate trying to estimate? (richness, Shannon...)</dd>
<dt>name</dt>
<dd>The name of the method</dd>
<dt>interval</dt>
<dd>An interval estimate</dd>
<dt>interval_type</dt>
<dd>Type of interval estimate</dd>
<dt>type</dt>
<dd>TODO(Amy): Deprecate?</dd>
<dt>model</dt>
<dd>What model is fit</dd>
<dt>warnings</dt>
<dd>Any warnings?</dd>
<dt>frequentist</dt>
<dd>Logical. Frequentist or Bayesian?</dd>
<dt>parametric</dt>
<dd>Logical. Parametric or not?</dd>
<dt>plot</dt>
<dd>A ggplot associated with the estimate</dd>
<dt>reasonable</dt>
<dd>Is the estimate likely to be reasonable?</dd>
<dt>other</dt>
<dd>Any other relevant objects</dd>
<dt>...</dt>
<dd>Any other objects</dd></dl>

Arguments

alpha_estimate — alpha_estimate

<dl>

<dt>estimate</dt>
<dd>The estimate</dd>


<dt>error</dt>
<dd>The standard error in the estimate</dd>


<dt>estimand</dt>
<dd>What is the estimate trying to estimate? (richness, Shannon...)</dd>


<dt>name</dt>
<dd>The name of the method</dd>


<dt>interval</dt>
<dd>An interval estimate</dd>


<dt>interval_type</dt>
<dd>Type of interval estimate</dd>


<dt>type</dt>
<dd>TODO(Amy): Deprecate?</dd>


<dt>model</dt>
<dd>What model is fit</dd>


<dt>warnings</dt>
<dd>Any warnings?</dd>


<dt>frequentist</dt>
<dd>Logical. Frequentist or Bayesian?</dd>


<dt>parametric</dt>
<dd>Logical. Parametric or not?</dd>


<dt>plot</dt>
<dd>A ggplot associated with the estimate</dd>


<dt>reasonable</dt>
<dd>Is the estimate likely to be reasonable?</dd>


<dt>other</dt>
<dd>Any other relevant objects</dd>


<dt>...</dt>
<dd>Any other objects</dd>

</dl>

alpha_estimate: alpha_estimate

Description

Usage

Value

Arguments