estimate_marginal_models

estimate_marginal_models estimates the marginal likelihood of
both the strict and the relaxed clock model, given the JC69 substitution
model, using the NS package in BEAST, made available via the babette R
package. The NS package performs nested sampling, and uses an MCMC approach
to estimate the marginal likelihood. Sampling is performed until convergence
of the MCMC chain. Unfortunately, currently the babette package is unavailable
on CRAN, requiring installation through GitHub to enjoy the full
functionality of this function.

Simulate DNA sequences for the node substitution model.
In the node substitution model, substitutions accumulate additionally
during a speciation event, providing a potential mechanistic explanation for
substitution rate variation. This package provides tools to simulate
such a process, simulate a reference process with only substitutions along
the branches, and provides tools to infer phylogenies from alignments. More
information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.

Thijs Janzen

nodeSub

Simulate DNA Alignments Using Node Substitutions

estimate_marginal_models function

<dl><dt>fasta_filename</dt>
<dd>file name of fasta file holding alignment for which the
marginal likelihood is to be estimated</dd>
<dt>use_yule_prior</dt>
<dd>by default, a birth-death prior is used as tree prior,
but if use_yule_prior is set to TRUE, a pure-birth prior will be used.</dd>
<dt>rng_seed</dt>
<dd>seed of pseudo-random number generator</dd>
<dt>sub_rate</dt>
<dd>substitution rate</dd>
<dt>verbose</dt>
<dd>boolean indicating if verbose intermediate output is to be
generated</dd></dl>

Arguments

estimate the marginal likelihood of the relaxed and strict clock model for
a provided alignment — estimate_marginal_models

<dl>

<dt>fasta_filename</dt>
<dd>file name of fasta file holding alignment for which the
marginal likelihood is to be estimated</dd>


<dt>use_yule_prior</dt>
<dd>by default, a birth-death prior is used as tree prior,
but if use_yule_prior is set to TRUE, a pure-birth prior will be used.</dd>


<dt>rng_seed</dt>
<dd>seed of pseudo-random number generator</dd>


<dt>sub_rate</dt>
<dd>substitution rate</dd>


<dt>verbose</dt>
<dd>boolean indicating if verbose intermediate output is to be
generated</dd>

</dl>

estimate_marginal_models: estimate the marginal likelihood of the relaxed and strict clock model for a provided alignment

Description

Usage

Value

Arguments