getTimeTreesIterate

<code>getTimeTreesIterate</code> Iteratively resume getTimeTrees til convergence.

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

Steven Kleinstein

getTimeTreesIterate function

<dl><dt>clones</dt>
<dd>a tibble of <code>airrClone</code> objects, the output of
formatClones</dd>
<dt>iterations</dt>
<dd>Maximum number of times to resume MCMC chain</dd>
<dt>ess_cutoff</dt>
<dd>Minimum number of ESS for all parameters</dd>
<dt>ignore</dt>
<dd>Vector of parameters to ignore for ESS calculation</dd>
<dt>quiet</dt>
<dd>quiet notifications if &gt; 0</dd>
<dt>...</dt>
<dd>Additional arguments for getTimeTrees</dd></dl>

Arguments

Iteratively resume getTimeTrees until convergence, as defined by 
all parameters (except those in ignore vector) having ESS 
greater than or equal to the specified ess_cutoff — getTimeTreesIterate

<dl>

<dt>clones</dt>
<dd>a tibble of <code>airrClone</code> objects, the output of
formatClones</dd>


<dt>iterations</dt>
<dd>Maximum number of times to resume MCMC chain</dd>


<dt>ess_cutoff</dt>
<dd>Minimum number of ESS for all parameters</dd>


<dt>ignore</dt>
<dd>Vector of parameters to ignore for ESS calculation</dd>


<dt>quiet</dt>
<dd>quiet notifications if &gt; 0</dd>


<dt>...</dt>
<dd>Additional arguments for getTimeTrees</dd>

</dl>

Iteratively resume getTimeTrees until convergence, as defined by 
all parameters (except those in <code>ignore</code> vector) having ESS 
greater than or equal to the specified ess_cutoff

getTimeTreesIterate: Iteratively resume getTimeTrees until convergence, as defined by all parameters (except those in `ignore` vector) having ESS greater than or equal to the specified ess_cutoff

Description

Usage

Value

Arguments

Details