check_file_and_model_agree

Will <a href="/link/stop?package=beautier&version=2.6.12" data-mini-rdoc="beautier::stop">stop</a> if not

'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.
'BEAUti 2' (which is part of 'BEAST2') is a GUI tool
that allows users to specify the many possible setups
and generates the XML file 'BEAST2' needs to run.
This package provides a way to create 'BEAST2' input
files without active user input, but using
R function calls instead.

Richèl J.C. Bilderbeek

beautier

'BEAUti' from R

Joëlle Barido-Sottani

David Winter

Paul Van Els

Raphael Scherrer

Yacine B. Chehida

Katharine S. Walter

Gary Napier

Jason Griffiths

Thijs Janzen

Pedro Taucce

Olivier Roy

Jana Riederer

check_file_and_model_agree function

<dl><dt>input_filename</dt>
<dd>A FASTA filename.
Use <code>get_fasta_filename</code> to obtain a testing FASTA filename.</dd>
<dt>inference_model</dt>
<dd>a Bayesian phylogenetic inference model.
An inference model is the complete model setup in which a site model,
clock model, tree prior and more are specified.
Use create_inference_model to create an inference model.
Use check_inference_model to check if an inference model is valid.
Use rename_inference_model_filenames to rename the files in an
inference model.</dd></dl>

Arguments

Will <a href='https://rdrr.io/r/base/stop.html'>stop</a> if not

Checks if the input FASTA file and the inference model agree. — check_file_and_model_agree

<dl>

<dt>input_filename</dt>
<dd>A FASTA filename.
Use <code>get_fasta_filename</code> to obtain a testing FASTA filename.</dd>


<dt>inference_model</dt>
<dd>a Bayesian phylogenetic inference model.
An inference model is the complete model setup in which a site model,
clock model, tree prior and more are specified.
Use create_inference_model to create an inference model.
Use check_inference_model to check if an inference model is valid.
Use rename_inference_model_filenames to rename the files in an
inference model.</dd>

</dl>

Checks if the input FASTA file and the inference model agree.

check_file_and_model_agree: Checks if the input FASTA file and the inference model agree.

Description

Usage

Value

Arguments