---
title: "Pre-Workshop Setup"
tutorial:
  id: "intro-r-data-analysis_lesson_0"
  version: 1.0
output: 
  learnr::tutorial:
    theme: "lumen"
    progressive: true
    allow_skip: true
runtime: shiny_prerendered
description: >
  Learn how to set up R and RStudio on your machine. We will also demonstrate
  how to install R packages from CRAN, and install the tidyverse package.
---

```{r setup, include=FALSE}
library(learnr)
learnr::tutorial_options(exercise.timelimit = 10)
```

## Introduction

This guide will help you get set up for <ins>Intro to R Data Analysis</ins>. There are just a few steps to make sure you'll have the necessary software installed and ready to go on day 1. **Please ensure that you've completed each step by running the validation test prior to the start of the workshop**. 

This guide will walk you through how to install R, RStudio, and some additional tools that we’ll be using in the course. By rough analogy to a car, R is like the car’s engine and RStudio is like the dashboard. More precisely, R is a programming language and Rstudio is an ‘integrated development environment’ (IDE), which is basically a nice software interface for interacting with R. For our purposes, you will only ever interact directly with RStudio, but it needs to have R installed to work (like a car needing its engine). 

Please complete the following steps (must be done in this order). If you already have R and Rstudio installed you can skip ahead. Make sure you complete step 5 though!

1. [Install R](#install-r)
2. [Install RStudio](#install-rstudio)
3. [Check you have recent versions of R](#check-you-have-a-recent-version-of-r)
4. [Install required packages](#install-required-packages)
5. [Run verification test](#run-verification-test)

Please consult the links provided for additional tips, and feel free to reach out for help by email [me](mailto:natalie.elphick@gladstone.ucsf.edu) if you get stuck.

## Install R

Please watch this quick video guide on how to install R, and then use the link below.

**NOTE MacOS users: With the new MacOS updates, updating R might require you to re-install your packages. While not in issue for many people, you have been warned**
![](https://vimeo.com/203516510)
https://cloud.r-project.org/

## Install RStudio
Please watch this quick video on how to install Rstudio, and then use the link below.
![](https://vimeo.com/203516968)
https://www.rstudio.com/products/rstudio/download/


## Install Required Packages
Many of the tools we will want to use do not come prepackaged with R, but rather need to be installed as ‘packages’. There are a few key packages we will be using. Watch the following video on how to install packages in Rstudio:
![](https://vimeo.com/203516241)
You can also refer to [this site](https://moderndive.netlify.app/1-getting-started.html#packages) for more info on what packages are and how to install them (including a ‘GUI’ installation method if you prefer that).
Please install the [`tidyverse`](https://www.tidyverse.org/) R package, which we’ll be relying on extensively throughout the course. No need to worry about what exactly this is yet, but you can read more [here](https://www.tidyverse.org/) if you like.

## Run verification test
Now it’s time to make sure you have everything installed properly!
First, open Rstudio (remember, you want to open Rstudio, not R). You should see a window that looks something like this:

<center>
<img src="images/rstudio_screenshot.png" width="40%">
</center>

The pane with the ‘>’ symbol is the Console. This is where you enter R commands. 
Copy and paste the following code into your Rstudio console and hit return.

```{r, eval=F}
R_version <- as.numeric(R.version['major']$major)
if (R_version >= 4) {
    library(ggplot2)
    ggplot(iris, aes(x=Sepal.Length, y=Sepal.Width, color=Species)) + 
        geom_point()
} else {
    print('R version is too old')
}
```
You should see a plot that looks like this appear:

<center>
<img src="images/ggplot_output.png" width="40%">
</center>


If you see an error that says “R version is too old” that means you need to update your R version. The update process is the same as the installation process. It will update your R installation. If you see an error that says “There is no package called ggplot2” that means you need to install the tidyverse package (see above).
