rncl (version 0.8.7)

read_nexus_phylo: 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, ...)

Value

A phylo or a multiPhylo object

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

Author

Francois Michonneau

Details

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

See Also

rncl-package