xue_species_similarity

<p>A similarity matrix, with entry (i,j) corresponding to the pairwise similarity
between species i and species j. This similarity matrix was derived from a
phylogenetic distance matrix, inferred from the tree xue_species_tree,
using the expression s(i,j) = exp(-d(i,j)), where d(i,j) is the phylogenetic
distance between species i and j.</p>

datasets

Implements the statistic FAVA, an Fst-based Assessment of Variability across
vectors of relative Abundances, as well as a suite of helper functions which enable the
visualization and statistical analysis of relative abundance data. The 'FAVA' R package
accompanies the paper, “Quantifying compositional variability in microbial communities
with FAVA” by Morrison, Xue, and Rosenberg (2025) <doi:10.1073/pnas.2413211122>.

Maike Morrison

FAVA

Quantify Compositional Variability Across Relative Abundance
Vectors

xue_species_similarity function


<div class="section" id="xue-species-similarity">
<h3><code>xue_species_similarity</code></h3><p></p><p>
</p><p>A data frame with 524 rows and 524 columns, each corresponding to one species.</p>
</div>


Format

Species similarity matrix for the species included in xue_microbiome_sample — xue_species_similarity


<div class='section' id='xue-species-similarity'>
<h3><code>xue_species_similarity</code></h3>


<p>A data frame with 524 rows and 524 columns, each corresponding to one species.</p>
</div>


xue_species_similarity: Species similarity matrix for the species included in xue_microbiome_sample

Description

Usage

Arguments

Format

`xue_species_similarity`