read_nexus_phylo: Read phylogenetic trees from files

In rncl: An Interface to the Nexus Class Library

Read phylogenetic trees from files

Description

Create phylo objects from NEXUS or Newick files

Usage

read_nexus_phylo(
  file,
  simplify = FALSE,
  missing_edge_length = NA,
  show_progress = TRUE,
  ...
)

read_newick_phylo(
  file,
  simplify = FALSE,
  missing_edge_length = NA,
  show_progress = TRUE,
  ...
)

make_phylo(file, simplify = FALSE, missing_edge_length = NA, ...)

Arguments

file	Path of NEXUS or Newick file
simplify	If the file includes more than one tree, returns only the first tree; otherwise, returns a multiPhylo object
missing_edge_length	If the tree contains missing edge lengths, the value to be attributed to these edge lengths. By default, (missing_edge_length = NA) if at least edge length is missing, they are all removed. Otherwise, the value must be a single numeric value. In any case, a warning will be generated if the tree contains missing edge lengths.
show_progress	If TRUE (default)), a progress bar is displayed during the possibly time consuming step of removing the singletons from the tree.
...	additional parameters to be passed to the rncl function

Details

These functions read NEXUS or Newick files and return an object of class phylo/multiPhylo.

Value

A phylo or a multiPhylo object

Note

make_phylo will soon be deprecated, use read_nexus_phylo or read_newick_phylo instead.

Author(s)

Francois Michonneau

See Also

rncl-package

rncl documentation built on Jan. 9, 2023, 1:28 a.m.