# Installing R and TreeSearch

#### Martin R. Smith

#### 2019-03-21

`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. Many people like to use Rstudio (overview), which is a 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.

### For advanced users

To get the latest development version from GitHub, type

    if (!require('devtools')) install.packages('devtools')
    devtools::install_github('ms609/TreeSearch')

You’ll probably need to install Rtools before installing from the GitHub source code, which may be complicated.

If you do already have Rtools installed, then you may wish to install a byte-compiled version of `ape` for additional speed:

    install.packages('ape', type='source', INSTALL_opts='--byte-compile')

Once installed, load the inapplicable package into R using

    library('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.