Getting started: Installing R and TreeSearch
Martin R. Smith
2024-08-26
Source:vignettes/getting-started.Rmd
getting-started.Rmd“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
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.