splitstree: Convert an object to SplitsTree-compatible NEXUS input and...

In IVS-UZH/RSplitsTree: SplitsTree file generation and invoking from R

Description

Convert an object to SplitsTree-compatible NEXUS input and launch SplitsTree if required

Usage

splitstree(dist, nexus.file = NULL, plot = FALSE,
  splitstree.path = getOption("splitstree.path", NULL))

Arguments

dist	A distance object (usually of class 'dist')
nexus.file	A name of the file where the NEXUS file will be written to (see notes)
plot	Set this to 'PDF' or 'SVG' to automatically invoke SplitsTree4 and generate a graphics file
splitstree.path	Path to the SplitsTree4 binary (see notes)

Value

The name of the generated NEXUS file

Note

If the name of the output file (nexus.file) is omitted, the function attempts to derive the file name automatically. Beware that if the file with this name already exists, it will be overwritten without a warning — so extra care needs to be taken if you have extra '.nex' files in the output directory.

If you are generating graphical output, the splitstree.path neeeds to point to the command-line executable of the SplitsTree4 package. The location and name of the executable is system- and installation-dependent. The package attempts to guess the standard location for your system, but if it fails, please provide the path explicitly. Note that on as OS X, a suitable executable is located within the SpltisTree.app application bundle, with the path 'SplitsTree.app/Contents/MacOS/JavaApplicationStub' (or alternatively, you can install the Linux SplitsTree4 package on Mac to get an executable in /usr/local/bin/SplitsTree)

Examples

library(cluster)
data(agriculture)
agriculture.dist <- daisy(agriculture)
splitstree(agriculture.dist, plot='PDF')

IVS-UZH/RSplitsTree documentation built on May 8, 2019, 1:26 p.m.