init_experiment: Initialize the 'experiment'.

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

Initialize the experiment.

Description

A normal user should never need to call this function.

Usage

init_experiment(experiment, alignment_params)

Arguments

experiment	a pirouette experiment, as can be created by create_experiment
alignment_params	parameters to simulate an alignment, as can be created by create_alignment_params

Details

It does the following:

• if an MCMC's treelog filename is $(tree).trees, replace it to by a full path using complete_treelog_filename

• if an MCMC's tracelog filename is NA, replace it to [alignment_folder]/[alignment_id].log

Both is done for the regular MCMC in experiment$inference_model and in experiment$est_evidence_mcmc.

[alignment_id] is obtained by using get_alignment_id on the alignment_params$fasta_filename. [alignment_folder] is obtained by using dirname on alignment_params$fasta_filename

Value

an 'experiment'

richelbilderbeek/pirouette documentation built on Oct. 18, 2023, 3:09 p.m.