Read a tree from TNT's parenthetical output.
ReadTntTree(filepath, relativePath = NULL, keepEnd = 1L, tipLabels = NULL) TntText2Tree(treeText) TNTText2Tree(treeText)
character string specifying path to TNT
relative to the R working directory (visible with
(discouraged) character string specifying location of the
matrix file used to generate the TNT results, relative to the current working
directory. Taxon names will be read from this file if they are not specified
(optional, default 1) integer specifying how many elements of the file path to conserve when creating relative path (see examples).
(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
Character string describing one or more trees, in the parenthetical format output by TNT.
ReadTntTree() returns a tree of class
to the tree in
filepath, or NULL if no trees are found.
TNT is software for parsimony analysis. Whilst its implementation of tree search is extremely rapid, analysis of results in TNT is made difficult by its esoteric and scantly documented scripting language.
ReadTntTree() aims to aid the user by facilitating the import of trees
generated in TNT into R for further analysis.
The function depends on tree files being saved by TNT in parenthetical
notation, using the TNT command
Trees are easiest to load into R if taxa have been saved using their names
taxname=). In this case, the TNT
contains tip labels and can be parsed directly. The downside is that the
.tre files will have a larger file size.
ReadTntTree() can also read
.tre files in which taxa have been saved
using their numbers (
taxname-). Such files contain a hard-coded link to
the matrix file that was used to generate the trees, in the first line of the
.tre file. This poses problems for portability: if the matrix file is
moved, or the
.tre file is accessed on another computer, the taxon names
may be lost. As such, it is important to check that the matrix file
exists in the expected location -- if it does not,
either use the
relativePath argument to point to its new location, or
tipLabels to manually specify the tip labels.
TntText2Tree() converts text representation of a tree in TNT to an
object of class
# In the examples below, TNT has read a matrix from # "c:/TreeTools/input/dataset.nex" # The results of an analysis were written to # "c:/TreeTools/output/results1.tnt" # # results1.tnt will contain a hard-coded reference to # "c:/TreeTools/input/dataset.nex". # On the original machine (but not elsewhere), it would be possible to read # this hard-coded reference from results.tnt: # ReadTntTree("output/results1.tnt") # These datasets are provided with the "TreeTools" package, which will # probably not be located at c:/TreeTools on your machine: oldWD <- getwd() # Remember the current working directory setwd(system.file(package = "TreeTools")) # If taxon names were saved within the file (using `taxname=` in TNT), # then our job is easy: ReadTntTree("extdata/output/named.tre") #> #> Phylogenetic tree with 5 tips and 4 internal nodes. #> #> Tip labels: #> taxon_a, taxon_b, taxon_c, taxon_d, taxon_e #> #> Rooted; no branch lengths. # But if taxa were compressed to numbers (using `taxname-`), we need to # look up the original matrix in order to dereference the tip names. # # We need to extract the relevant file path from the end of the # hard-coded path in the original file. # # We are interested in the last two elements of # c:/TreeTools/input/dataset.nex # 2 1 # # "." means "relative to the current directory" ReadTntTree("extdata/output/numbered.tre", "./extdata", 2) #> 2 phylogenetic trees # If working in a lower subdirectory setwd("./extdata/otherfolder") # then it will be necessary to navigate up the directory path with "..": ReadTntTree("../output/numbered.tre", "..", 2) #> 2 phylogenetic trees setwd(oldWD) # Restore original working directory TNTText2Tree("(A (B (C (D E ))));") #> #> Phylogenetic tree with 5 tips and 4 internal nodes. #> #> Tip labels: #> A, B, C, D, E #> #> Rooted; no branch lengths.