tnt2newick {tbea}

tnt2newick: Function for converting from TNT tree format to newick parenthetical format

Description

tnt2newick: Function for converting from TNT tree format to newick parenthetical format

Usage

tnt2newick(
  file,
  output = NULL,
  string = NULL,
  return = FALSE,
  subsetting = FALSE,
  name.sep = NULL
)

Arguments

file

A vector of type 'character' with the path to the original TNT tree file.

output

A vector of type 'character' with the path to output files to contain the tree in newick format.

string

A vector of type 'character' which can be either an object in memory or a string for interactive transformation, in TNT format. Use file in case your tree(s) are stored in a file instead.

return

A 'logical' expression indicating whether to write the newick tree(s) to a file in 'output' (if FALSE, the default), or whether to return to the screen (if TRUE), potentially to be stored in a vector via the '<-' operator.

subsetting

A vector of type 'logical' indicating whether subsetting (i.e., chopping at once the first and last line of the TNT tree file) should be done. Otherwise, explicit text replacements removing such lines are used. The default is false because it does not play well with multi-tree TNT files. Only use subsetting = TRUE if you are sure that there is only one tree in the file with the commands, tread and proc as first and last lines.

name.sep

A vector of length 2 and type 'character' for carrying out separator conversion in the names of terminals. For instance, if the terminals have names composed of two words separated by an underscore (_) and you want them to be separated by space ( ) then use name.sep = c("_", " "). This does not support regular expressions.

Details

This function has been tested for cases where only one tree is in the original tnt tree file. Please be careful with files containing multiple trees.

Value

This function writes to the disk a text file containing the tree converted to newick format. Alternatively, it returns the output to the screen or writes it to an object in memory thanks to the argument 'string'.

Author(s)

Gustavo A. Ballen

Examples

## Not run: 
tnt2newick(file = "someTrees.tre", return = TRUE)

## End(Not run)