---
title: "Getting started: Installing R and TreeSearch"
author: "Martin R. Smith"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Getting started: Installing R and TreeSearch}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---


"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](https://CRAN.R-project.org/). 
[RStudio](https://www.rstudio.com/)
([overview](https://dss.princeton.edu/training/RStudio101.pdf)) 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
```r
install.packages('TreeSearch')
```
into the R (or RStudio) command line.

Once installed, load the "TreeSearch" package into R using
```r
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:

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

Windows users may need to install 
[Rtools](https://cran.r-project.org/bin/windows/Rtools/) before
installing from the GitHub source.

### For advanced users

To get the latest development version from
[GitHub](https://github.com/ms609/TreeSearch/), type
```r
remotes::install_github('ms609/TreeSearch')
```

## What next?

You might want to:

- [Load data](https://ms609.github.io/TreeTools/articles/load-data.html) from a Nexus file or spreadsheet
- Conduct parsimony search using Brazeau, Guillerme & Smith's [approach to inapplicable data](tree-search.html), or using [Profile parsimony](profile.html).
- Conduct parsimony search using [custom optimality criteria](custom.html).
