Syllabus

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

• Assignment Due: Assignment 0. Please have all software installed before showing up to the first class.
• Assignment Given (Due by noon on Wednesday): Assignment 1
• Lectures:
  • Introduction
  • Rstudio Orientation

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:
  • R Markdown in an Hour

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:
  • Atomic Data Modes and Coercion
  • Vectorization, Recycling, and Indexing

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:
  • Git Basics

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:
  • length() and names()
  • Comments on the homework

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:
  • Read chapter 3 of the Pro Git Book.
  • OR
  • Read this excellent tutorial on branching and merging
    
  • OR read them both.
• Lecture:
  • Branching and merging

Week 4

Tuesday, October 28, 2014

Lists: aka “recursive vectors”

• Reading: In case you were wondering why you are going through the grueling work of learning R and git, Devon Pearse found this excellent post from Carly Strasser at the California Digital Library that makes a good case for sticking with it! http://datapub.cdlib.org/2014/10/14/the-10-things-every-new-grad-student-should-do/ Everyone, please read this!
• Lecture:
  • An introduction to lists

Thursday, October 30, 2014

Merge conflicts, stashing, remotes

• Reading:
  • Hilarious analogizing between git and “X-men: Days of Future Past”. This is worth a read, even if we haven’t explored all these layers of git. Thanks to Anthony Clemento for finding this. +ProGit Book: git password caching If you are tired of typing your password in every time you push or pull. Read this!
• Assignment Due: Exercise Set 2, named Homework 2. A collection of exercises on vectorization, recycling, indexing, and names. Instructions are on the page. I emailed this out on Sunday night. It’s another GitHub submission.
• Lecture:
  • Merge conflicts, stashing, remotes

Week 5

Tuesday, November 4, 2014

Data Frames. Reading in data, etc

• Lecture:
  • Introduction to Data Frames

Thursday, November 6, 2014

Factors. Some GitHub Basics

• Reading: please download The R Inferno and read the Preface on page 8 and the first few paragraphs of Chapter 1 (because it is fun to do so—we have all been in R hell at one time or another), then read from section 8.2 through 8.2.8, which covers factor hell.
• Lecture:
  • More about factors
  • Putting your own repositories on GitHub

Week 6

Tuesday, November 11, 2014

NO CLASS. VETERANS DAY

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

• Lecture:
  • Introduction to ggplot

Thursday, November 20, 2014

Plotting with ggplot

• Lecture:
  • More ggplot. Reshaping

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: http://www.dataschool.io/dplyr-tutorial-for-faster-data-manipulation-in-r/

Thursday, November 27, 2014

NO CLASS. THANKSGIVING WEEK

Week 9

Tuesday, December 2, 2014

String Manipulation and Text Processing in R

• Lecture:
  • String Manipulation

Thursday, December 4, 2014

A more formal look at functions. lapply()

• Lecture:
  • Functions and lapply

Week 10

Tuesday, December 9, 2014

Plotting on top of maps in R

• Lecture:
  • Making maps with R

Thursday, December 11, 2014

NO CLASS. NMFS LAB PARTY

Week 11

Tuesday, December 9, 2014

NO CLASS

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