---
title: "File system navigation in R"
author: "Martin R. Smith <martin.smith@durham.ac.uk>"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
bibliography: ../inst/REFERENCES.bib
csl: ../inst/apa-old-doi-prefix.csl
vignette: >
  %\VignetteIndexEntry{File system navigation in R}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

Before you can open a file, you need to tell R where to find it. 
You can do this by providing the full path to the file on your system.
Be careful to use forward slashes (`/`, not `\`, which you'll get if you
copy file paths in Windows).

```r
filename <- "C:/nexus/matrix.nex"
```

You can save typing by giving R a working directory.  You can 
think of R as having a file explorer window open invisibly in the
background.

You can see the folder that's open at the moment by typing `getwd()` at the console.

`setwd()` tells R to open a different folder instead.

`setwd('../')` tells R to go up to a parent directory.
(You can [do this using the  Graphical User Interface ](https://dss.princeton.edu/training/RStudio101.pdf) in RStudio).

By setting the directory that your files are in as the working directory, 
you only need to specify the filename:

```r 
setwd("C:/nexus/") # You only need to do this once
filename <- "matrix.nex"
# Do something with this file
#

filename <- "tree.nex"
# Do something with this file
#
```

## What next?

Now you know how to locate files, you might want to load a
[dataset](load-data.html) or [phylogenetic tree](load-trees.html) into R.