plot_marg_liks

'BEAST2' (<https://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'mcbette' allows to do a Bayesian model comparison over some
site and clock models,
using 'babette' (<https://github.com/ropensci/babette/>).

Richèl J.C. Bilderbeek

mcbette

Model Comparison Using 'babette'

Joëlle Barido-Sottani

Vikram Baliga

plot_marg_liks function

<dl><dt>marg_liks</dt>
<dd>a table of (estimated) marginal likelihoods,
as, for example, created by est_marg_liks.
This <a href="/link/data.frame?package=mcbette&version=1.15.3" data-mini-rdoc="mcbette::data.frame">data.frame</a> has the following columns:<ul>
<li><code>site_model_name</code>: name of the site model,
 must be an element of get_site_model_names</li>
<li><code>clock_model_name</code>: name of the clock model,
 must be an element of get_clock_model_names</li>
<li><code>tree_prior_name</code>: name of the tree prior,
 must be an element of get_tree_prior_names</li>
<li><code>marg_log_lik</code>: estimated marginal (natural) log likelihood</li>
<li><code>marg_log_lik_sd</code>: estimated error of <code>marg_log_lik</code></li>
<li><code>weight</code>: relative model weight, a value from 1.0 (all
 evidence is in favor of this model combination) to 0.0 (no
 evidence in favor of this model combination)</li>
<li><code>ess</code>: effective sample size of the marginal likelihood
 estimation</li>
</ul>Use get_test_marg_liks to get a test <code>marg_liks</code>.
Use is_marg_liks to determine if a <code>marg_liks</code> is valid.
Use check_marg_liks to check that a <code>marg_liks</code> is valid.</dd></dl>

Arguments

Plot the marg_liks — plot_marg_liks

<dl>

<dt>marg_liks</dt>
<dd>a table of (estimated) marginal likelihoods,
as, for example, created by est_marg_liks.
This <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> has the following columns:<ul>
<li><code>site_model_name</code>: name of the site model,
 must be an element of get_site_model_names</li>
<li><code>clock_model_name</code>: name of the clock model,
 must be an element of get_clock_model_names</li>
<li><code>tree_prior_name</code>: name of the tree prior,
 must be an element of get_tree_prior_names</li>
<li><code>marg_log_lik</code>: estimated marginal (natural) log likelihood</li>
<li><code>marg_log_lik_sd</code>: estimated error of <code>marg_log_lik</code></li>
<li><code>weight</code>: relative model weight, a value from 1.0 (all
 evidence is in favor of this model combination) to 0.0 (no
 evidence in favor of this model combination)</li>
<li><code>ess</code>: effective sample size of the marginal likelihood
 estimation</li>
</ul>Use get_test_marg_liks to get a test <code>marg_liks</code>.
Use is_marg_liks to determine if a <code>marg_liks</code> is valid.
Use check_marg_liks to check that a <code>marg_liks</code> is valid.</dd>

</dl>

plot_marg_liks: Plot the `marg_liks`

Description

Usage

Value

Arguments

Examples