soil_phylum_small_sample

A small subset of <code>soil_phylo_sample</code> used for examples. A data frame made from the `phyloseq` object with only sample data.

datasets

Statistical modeling for correlated count data using the beta-binomial distribution, described in Martin et al. (2020) <doi:10.1214/19-AOAS1283>. It allows for both mean and overdispersion covariates.

Amy D Willis

corncob

Count Regression for Correlated Observations with the
Beta-Binomial

Bryan D Martin

Daniela Witten

Sarah Teichman

Thomas W Yee

Xiangjie Xue

soil_phylum_small_sample function

A phyloseq-class experiment-level object with sample data.<dl>
<dt>sam_data</dt>
<dd>sample data with the following covariates:<ul>
<li><code>Plants</code>, values <code>0</code> and <code>1</code>. Index for different plants</li>
<li><code>Day</code>, values <code>0</code> (initial sampling point), <code>1</code> (12 days after treatment additions), and <code>2</code> (82 days after treatment additions). Index for different days of measurement</li>
<li><code>Amdmt</code>, values <code>0</code> (no additions), <code>1</code> (biochar additions), and <code>2</code> (fresh biomass additions). Index for different soil additives.</li>
<li><code>DayAmdmt</code>, values <code>00</code>, <code>01</code>, <code>02</code>, <code>10</code>, <code>11</code>, <code>12</code>, <code>20</code>, <code>21</code>, and <code>22</code>. A single index for the combination of <code>Day</code> and <code>Amdmt</code> with <code>Day</code> as the first digit and <code>Amdmt</code> as the second digit.</li>
<li><code>ID</code>, values <code>A</code>, <code>B</code>, <code>C</code>, <code>D</code>, and <code>F</code>. Index for different soil plots.</li>
</ul></dd>
</dl>

Format

Small soil phylum data for examples, sample data as data frame — soil_phylum_small_sample

A phyloseq-class experiment-level object with sample data.<dl>
<dt>sam_data</dt>
<dd>sample data with the following covariates:<ul>
<li><code>Plants</code>, values <code>0</code> and <code>1</code>. Index for different plants</li>
<li><code>Day</code>, values <code>0</code> (initial sampling point), <code>1</code> (12 days after treatment additions), and <code>2</code> (82 days after treatment additions). Index for different days of measurement</li>
<li><code>Amdmt</code>, values <code>0</code> (no additions), <code>1</code> (biochar additions), and <code>2</code> (fresh biomass additions). Index for different soil additives.</li>
<li><code>DayAmdmt</code>, values <code>00</code>, <code>01</code>, <code>02</code>, <code>10</code>, <code>11</code>, <code>12</code>, <code>20</code>, <code>21</code>, and <code>22</code>. A single index for the combination of <code>Day</code> and <code>Amdmt</code> with <code>Day</code> as the first digit and <code>Amdmt</code> as the second digit.</li>
<li><code>ID</code>, values <code>A</code>, <code>B</code>, <code>C</code>, <code>D</code>, and <code>F</code>. Index for different soil plots.</li>
</ul></dd>


</dl>

soil_phylum_small_sample: Small soil phylum data for examples, sample data as data frame

Description

Usage

Arguments

Format

References