An introductory eco-data science course for R markdown
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An introductory eco-data science course for R markdown


From workshop

External resources

Getting started

Before we get to play with R markdown, we need to make sure you have the latest versions of R and R Studio. Then, I'll give a list of basic R packages that we will use, and then some instructions on how to download the materials in this repository (the stuff you see above).

Although it may seem like a lot, it is important that you follow these instructions. This will reduce the chances of running into errors during the workshop, and will help us get through the material. It will not take more than 5 minutes, but make sure you do it well in advance of the workshop. We don't want surprises right before we start, do we?

R and R Studio

Remember that R and R Studio are two separate things. For now, let's say R is the engine that runs the code, and R Studio is the IDE (Integrated Development Environment... which is a fancy User Interface) that allows you to interact with R.

Check for updates

  1. First, make sure you have the latest releases of R and R Studio. If you have never installed them, skip this and go to the next step.
  • Open R Studio
  • In the Console, type sessionInfo() to see which version of R you have. You should be running on R version 3.4.2 or later. In my case, typing that looks like this, and I am only interested in the first line:



You get:

R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

... some other technical stuff follows this
  • To see if you are running the latest version of R Studio, use your toolbar to navigate to Help/Check for Updates

Navigate to Help/Check for Updates In my case, I am up to date

Get the updates

  1. If you have never installed R and R Studio, or need to update them, here are the links. If for any reason they don't work, you can always ask Google.

R packages that you will need

As you will see later, we will need some R packages to do some of the things with R Markdown. By now, I assume that you have the latest version of R and R Studio, and you should not run into any problems.

The basic packages we will need are:

  • rmarkdown: Dynamic Documents for R
  • stargazer: Well-Formatted Regression and Summary Statistics Tables
  • knitr: A General-Purpose Package for Dynamic Report Generation in R
  • kableExtra: Construct Complex Table with 'kable' and Pipe Syntax

To install them, one by one, copy-paste the following lines of code into your console and hit "Enter". You want to wait for a package to finish installing before you install the next one just to make sure there are no problems, This will also make it easier to troubleshoot anything on a a package-by-package basis. This might take a couple of minutes, but be patient.


Getting the course materials

If you have made it this far, it means you are ready to download the course materials. However, you might want to wait until Tuesday afternoon / night before you do this, as I will be adding and modifying the materials right until before the workshop.

So, getting the materials...

  • If you are familiar with git and github, you can just go ahead and fork/clone this repository.
  • If you have no idea what that means, it's OK. We will have an intro to git and github soon. In the mean time, you can go to the green button that says "Clone or Download"
  • Click in "Download zip", and a compressed folder will download to your computer.
  • Extract those files and you should be good to go!

Clone or Download

Feeling ready?

If you think you want to get a head start on R markdown, that is great! Here are some links you might find interesting to start playing with this.