lozupone_tree

lozupone_panel_a

lozupone_panel_b

This example was used to illustrate unweighted UniFrac distance in Lozupone
and Knight (2005).

datasets

A collection of measures for measuring ecological diversity.
Ecological diversity comes in two flavors: alpha diversity measures the
diversity within a single site or sample, and beta diversity measures the
diversity across two sites or samples. This package overlaps considerably
with other R packages such as 'vegan', 'gUniFrac', 'betapart', and 'fossil'.
We also include a wide range of functions that are implemented in software
outside the R ecosystem, such as 'scipy', 'Mothur', and 'scikit-bio'.  The
implementations here are designed to be basic and clear to the reader.

Kyle Bittinger

abdiv

Alpha and Beta Diversity Measures

lozupone_tree function

<code>lozupone_tree</code> is a phylogenetic tree with 14 tips, labeled
A-N. It was created with the <code>ape</code> library.
The data frames <code>lozupone_panel_a</code> and <code>lozupone_panel_b</code> are
transcribed from Figure 1 of the paper. They have the following columns:<dl class="dl-horizontal">
 <dt>Species</dt><dd>The species label, matching to the phylogenetic tree.</dd>
 <dt>SampleID</dt><dd>The community, either "Circle" or "Square".</dd>
 <dt>Counts</dt><dd>The number of organisms counted per species, always 1 for this
 example.</dd>
</dl>

Format

Example data for UniFrac distance — lozupone_tree

<code>lozupone_tree</code> is a phylogenetic tree with 14 tips, labeled
A-N. It was created with the <code>ape</code> library.
The data frames <code>lozupone_panel_a</code> and <code>lozupone_panel_b</code> are
transcribed from Figure 1 of the paper. They have the following columns:<dl class='dl-horizontal'>
 <dt>Species</dt><dd>The species label, matching to the phylogenetic tree.</dd>
 <dt>SampleID</dt><dd>The community, either "Circle" or "Square".</dd>
 <dt>Counts</dt><dd>The number of organisms counted per species, always 1 for this
 example.</dd>
</dl>

lozupone_tree: Example data for UniFrac distance

Description

Usage

Arguments

Format