Getting started: Installing R and TreeSearch

Martin R. Smith

2021-09-23

“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().

Some features of the graphical user interface require up-to-date versions of the “ape” and “TreeTools” packages, due on CRAN in late 2021. Until then, install the latest versions using

if (!require('remotes')) install.packages('remotes')
remotes::install_github('emmanuelparadis/ape')
packageVersion('ape') # Should be at least 5.5.2
remotes::install_github('ms609/TreeTools@Rogue')
packageVersion('TreeTools') # Should be > 1.5.0 or end in .91XX

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: