Getting started: Installing R and TreeSearch

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Martin R. Smith

2024-05-23

“TreeSearch” is an R package that allows parsimony search on morphological datasets.

Installation

Simple installation

To use “TreeSearch” you will first need to install R. RStudio (overview) is a popular front-end that makes several of R’s features easier to use.

The “TreeSearch” package can be installed as any other package. To get the latest stable version from CRAN, type

install.packages("TreeSearch")

into the R (or RStudio) command line.

Once installed, load the “TreeSearch” package into R using

library("TreeSearch")

Activate the graphical user interface by typing EasyTrees().

In Jan 2022, some users are reporting issues after loading trees from Nexus files. These arise due to an issue in the underlying “ape” package. To install a patched version, close and re-launch R and run:

if (!require("remotes")) install.packages("remotes")
remotes::install_github("ms609/ape@patch-3")

Windows users may need to install Rtools before installing from the GitHub source.

For advanced users

To get the latest development version from GitHub, type

remotes::install_github("ms609/TreeSearch")

What next?

You might want to:

Load data from a Nexus file or spreadsheet
Conduct parsimony search using Brazeau, Guillerme & Smith’s approach to inapplicable data, or using Profile parsimony.
Conduct parsimony search using custom optimality criteria.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.