calcRF

<code>calcRF</code> Calculates the RF distance between two phylogenetic trees with 
 the same tips and tip labels.

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

Kenneth Hoehn

dowser

B Cell Receptor Phylogenetics Toolkit

Cole Jensen

Jessie Fielding

Hunter Melton

Susanna Marquez

Jason Vander Heiden

Erick Matsen

Steven Kleinstein

calcRF function

<dl><dt>tree_1</dt>
<dd>A <code>phylo</code> object</dd>
<dt>tree_2</dt>
<dd>A <code>phylo</code> object</dd>
<dt>nproc</dt>
<dd>Number of cores to use for calculations.</dd>
<dt>normalize</dt>
<dd>Normalize RF by maximum RF distance</dd>
<dt>include_root</dt>
<dd>If TRUE include root split in denominator when
normalize=TRUE. If FALSE root split won't be counted 
as a possible split if trees are rooted at same tip.</dd></dl>

Arguments

Finds the Robinson-Fould's cluster distance between phylogenies. — calcRF

<dl>

<dt>tree_1</dt>
<dd>A <code>phylo</code> object</dd>


<dt>tree_2</dt>
<dd>A <code>phylo</code> object</dd>


<dt>nproc</dt>
<dd>Number of cores to use for calculations.</dd>


<dt>normalize</dt>
<dd>Normalize RF by maximum RF distance</dd>


<dt>include_root</dt>
<dd>If TRUE include root split in denominator when
normalize=TRUE. If FALSE root split won't be counted 
as a possible split if trees are rooted at same tip.</dd>

</dl>

calcRF: Finds the Robinson-Fould's cluster distance between phylogenies.

Description

Usage

Value

Arguments