TreeSearch (version 0.3.2)

ReadTntTree: Parse TNT Tree

Description

Reads a tree from TNT's paranthetical output.

Usage

ReadTntTree(filename, relativePath = NULL, keepEnd = 1L,
  tipLabels = NULL)
TNTText2Tree(treeText)

Arguments

filename

character string specifying path to TNT .tre file.

relativePath

(optional) character string specifying location of the matrix file used to generate the TNT results, relative to the current working directory, for portability. Taxon names will be read from this file if they are not specified by tipLabels.

keepEnd

(optional, default 1) integer specifying how many elements of the file path to conserve when creating relative path (see examples).

tipLabels

(optional) character vector specifying the names of the taxa, in the sequence that they appear in the TNT file. If not specified, taxon names will be loaded from the data file linked in the first line of the .tre file specified in filename.

treeText

Character string describing a tree, in the parenthetical format output by TNT.

Value

a tree of class phylo.

Functions

• TNTText2Tree: Converts text representation of a tree in TNT to an object of class phylo

Examples

# NOT RUN {
{
  
# }
# NOT RUN {
  # TNT read a matrix from c:/myproject/tnt/coding1/dataset.nex
  # The results of an analysis were written to c:/myproject/tnt/output/results1.tnt
  # results1.tnt will contain a hard-coded reference to 
  # "c:/myproject/tnt/coding1/dataset.nex"
  
  getwd() # Gives the current working directory
  
  # Say that working directory is c:/myproject, which perhaps corresponds to a
  # Git repository.
  # This directory may be saved into another location by collaborators, or on a 
  # different filesystem by a continuous integration platform.
  
  # Works on local machine but not elsewhere:
  ReadTntTree('tnt/output/results1.tnt')
  
  # Takes only the filename from the results
  ReadTntTree('tnt/output.results1.tnt', 'tnt/coding1')
  
  # Uses the last three elements of c:/myproject/tnt/coding1/dataset.nex
  #                                               3     2       1
  # '.' means "relative to the current directory", which is c:/myproject
  ReadTntTree('tnt/output/results1.tnt', '.', 3)
  
  # If the current working directory was c:/myproject/rscripts/testing,
  # you could navigate up the directory path with '..':
  ReadTntTree('../../tnt/output/results1.tnt', '../..', 3)
  
  
# }
# NOT RUN {
}

# }