readTrees: Read trees

In revbayes/RevGadgets: Visualization and Post-Processing of 'RevBayes' Analyses

Read trees

Description

Reads in a tree file containing one or multiple trees

Usage

readTrees(paths, tree_name = "psi", burnin = 0, n_cores = 1L, verbose = TRUE)

Arguments

paths	(vector of character strings; no default) File path(s) to tree(s).
tree_name	(character string; default psi) Name of the tree variable.
burnin	(single numeric value; default = 0.1) Fraction of generations to discard (if value provided is between 0 and 1) or number of generations (if value provided is greater than 1).
n_cores	(integer; default 1) Number of cores for parallelizing.
verbose	(logical; default true) Display a status bar?

Details

Reads in a tree file in either nexus or newick format, and containing a single tree or multiple trees (as in the results of a Bayesian analysis). For reading in annotated tree files of continuous character evolution, the parameter must be considered a node parameter rather than branch parameter. Set isNodeParameter = TRUE in the extended newick monitor (mnExtNewick)

Value

A list (across runs) of lists (across samples) of treedata objects.

Examples

# read in a single nexus file

# download the example dataset to working directory
url_nex <-
 "https://revbayes.github.io/tutorials/intro/data/primates_cytb_GTR_MAP.tre"
dest_path_nex <- "primates_cytb_GTR_MAP.tre"
download.file(url_nex, dest_path_nex)

# to run on your own data, change this to the path to your data file
file <- dest_path_nex
tree_single_old <- readTrees(paths = file)

# remove file
# WARNING: only run for example dataset!
# otherwise you might delete your data!
file.remove(dest_path_nex)

# read in a single newick string

# download the example dataset to working directory
url_new <-
 "https://revbayes.github.io/tutorials/intro/data/primates.tre"
dest_path_new <- "primates.tre"
download.file(url_new, dest_path_new)

# to run on your own data, change this to the path to your data file
file_new <- dest_path_new
tree_new <- readTrees(paths = file_new)

# remove file
# WARNING: only run for example dataset!
# otherwise you might delete your data!
file.remove(dest_path_new)


# read in a tree trace (may take a few seconds)

# download the example dataset to working directory
url_multi <-
 "https://revbayes.github.io/tutorials/intro/data/primates_cytb_GTR.trees"
dest_path_multi <- "primates_cytb_GTR.trees"
download.file(url_multi, dest_path_multi)

# to run on your own data, change this to the path to your data file
file_multi <- dest_path_multi
tree_multi <- readTrees(paths = file_multi)

# remove file
# WARNING: only run for example dataset!
# otherwise you might delete your data!
file.remove(dest_path_multi)

revbayes/RevGadgets documentation built on Jan. 19, 2024, 3:29 p.m.