run_pipeline: Run the pipeline for a single parameter set

In Neves-P/phylometricsims: Simulate DAISIE Islands for Phylogenetic Metric Comparison

Description

Runs the full pipeline one parameter set (i.e., one row of the param_space.csv file). DAISIE simulations are generated, the first lineage, if any, is extracted. Associated branching times are converted to a phylo object which is then saved as a .tre file to the /trees folder, if there are more than 20 tips. Intermediate objects are saved as they are generated to output folder, as a list. See details in the Return section.

Usage

run_pipeline(n_param_sets_to_run, save_to_file = TRUE, test_seed = FALSE)

Arguments

n_param_sets_to_run	Integer with number of parameter sets (i.e., columns in the parameter space file) should be simulated.
save_to_file	Boolean stating if output of pipeline should be saved as an .rds file in ./output/
test_seed	A boolean, which sets the seed to 1. Defaults to FALSE, should only be set to TRUE for testing.

Value

Saves output object to output and trees folder. Generate .tree file if > 20 tips are created. Output object is a list containing the following elements:

• DAISIE IW simulation objects

• Corresponding vector of branching times

• Corresponding branching times converted to phylo objects

Author(s)

Pedro Neves

Neves-P/phylometricsims documentation built on June 3, 2021, 3:21 p.m.