phylolm_summary

Runs basic case of single x and y variables (dummy or continuous). Note that the ordering of the input vectors
and the tree tip labels needs to be checked by the user beforehand:
this script does not require that the y and x variables are named, and so no name check is performed.

Code to identify functional enrichments across diverse taxa
in phylogenetic tree, particularly where these taxa differ in
abundance across samples in a non-random pattern. The motivation for
this approach is to identify microbial functions encoded by diverse
taxa that are at higher abundance in certain samples compared to
others, which could indicate that such functions are broadly adaptive
under certain conditions. See 'GitHub' repository for tutorial and
examples: <https://github.com/gavinmdouglas/POMS/wiki>. Citation: Gavin M. Douglas, Molly G. Hayes, Morgan G. I. Langille, Elhanan Borenstein (2022) <doi:10.1093/bioinformatics/btac655>.

Gavin Douglas

POMS

Phylogenetic Organization of Metagenomic Signals

phylolm_summary function

<dl><dt>y</dt>
<dd>variable to use for y component of model.</dd>
<dt>x</dt>
<dd>variable to use for x component of model.</dd>
<dt>in_tree</dt>
<dd>phylo object. Tip label order is assumed to match the y and x variables.</dd>
<dt>model_type</dt>
<dd>length-one character vector specifying which phylogenetic model to use (must be a possible setting of the model argument to the phylolm function).</dd></dl>

Arguments

Wrapper for running phylogenetic regression with phylolm — phylolm_summary

<dl>

<dt>y</dt>
<dd>variable to use for y component of model.</dd>


<dt>x</dt>
<dd>variable to use for x component of model.</dd>


<dt>in_tree</dt>
<dd>phylo object. Tip label order is assumed to match the y and x variables.</dd>


<dt>model_type</dt>
<dd>length-one character vector specifying which phylogenetic model to use (must be a possible setting of the model argument to the phylolm function).</dd>

</dl>

phylolm_summary: Wrapper for running phylogenetic regression with phylolm

Description

Usage

Value

Arguments