Reproducible Research Course by Eric C. Anderson for (NOAA/SWFSC)


Here is the outline of the topics, readings, and assignments for our course. Readings should be done before the session that they are listed for. For example, if it says Reading X is for Tuesday Oct 14, then you should have done that reading prior to coming to the class at 3:30 on Oct 14.

Most assignments will be “turned in” on GitHub, and will be due at the time stated. Don’t let this get your blood pressure up. This course is not for credit and you will not be graded. But you will learn a lot more and you will be far more likely to benefit from using R and git and GitHub if you do the assignments.

Week 1

Tuesday, October 7, 2014

Introduction and Welcome. R and Rstudio very basics

Thursday, October 9, 2014

An introduction to R markdown

  • Assignment Due: Assignment 2. There is nothing to turn in, but I want everyone to do this.
  • Assignment Given (Please finish by Wednesday night next week!): Assignment 3. You will write about yourself and your research using R markdown.
  • Lectures:

Week 2

Tuesday, October 14, 2014

Atomic data types, Vectorization, Indexing in R

  • Reading: By this class, I would like you to have read the Introduction to Hadley Wickham’s advanced R book, up to, but not including, “Meta-techniques”. Then, please read through Data structures up to “Attributes”. This is very terse and will likely feel foreign to most newcomers to R, but precisely because it is short and compact (and very informative) it is worth coming back to frequently. We will go over the topics in more detail.
  • Lectures:

Thursday, October 16, 2014

git Overview. Configuring git

  • Reading: Read sections 1.1 through 1.3 in the Pro Git Book which is online and free.
  • Assignment Due: Assignment 3. You should have completed this the day before this course session.
  • Lectures:

Week 3

Tuesday, October 21, 2014

Attributes. Length of vectors. Names

  • Assignment Due: Exercise Set 1, named Trial Homework. I emailed this out to people Saturday night. I would like everyone to try to complete it by Tuesday. At least give it a whirl. It is called Trial Homework because it is not very long. Mostly the goal is to figure out how to commit your changes and make a GitHub pull request. It would be good to be able to discuss it in class after everyone has at least tried to complete it.
  • Lectures:

Thursday, October 23, 2014

git: Branching and Merging

  • Reading: I don’t expect people to have finished this reading before class because I didn’t post it till Thursday. We will be covering material in these readings, so it would be good for you to read one or both of them to solidify ideas. Either:
  • Lecture:

Week 4

Tuesday, October 28, 2014

Lists: aka “recursive vectors”

Thursday, October 30, 2014

Merge conflicts, stashing, remotes

Week 5

Tuesday, November 4, 2014

Data Frames. Reading in data, etc

Thursday, November 6, 2014

Factors. Some GitHub Basics

Week 6

Tuesday, November 11, 2014


Thursday, November 13, 2014

NO CLASS. * There was a conflict with the room and this seemed like a good time for everyone to start loading their own data into R and working with it.

Week 7

Tuesday, November 18, 2014

Plotting. ggplot and the grammar of graphics

Thursday, November 20, 2014

Plotting with ggplot

Week 8

Tuesday, November 25, 2014

NO CLASS. THANKSGIVING WEEK * Reading: Download the Tidy Data article by Hadley and read it. * Watch a Video! Take 45 minutes to watch the video tutorial on the dplyr package that we will take about after we come back from Thanksgiving. It is on this page:

Thursday, November 27, 2014


Week 9

Tuesday, December 2, 2014

String Manipulation and Text Processing in R

Thursday, December 4, 2014

A more formal look at functions. lapply()

Week 10

Tuesday, December 9, 2014

Plotting on top of maps in R

Thursday, December 11, 2014


Week 11

Tuesday, December 9, 2014


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