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.
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
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.
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.
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.
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.
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:
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!
Thursday, October 30, 2014
Merge conflicts, stashing, remotes
- 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.
Tuesday, November 4, 2014
Data Frames. Reading in data, etc
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.
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.
Tuesday, November 18, 2014
Plotting. ggplot and the grammar of graphics
Thursday, November 20, 2014
Plotting with ggplot
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
Tuesday, December 2, 2014
String Manipulation and Text Processing in R
Thursday, December 4, 2014
A more formal look at functions. lapply()
Tuesday, December 9, 2014
Plotting on top of maps in R
Thursday, December 11, 2014
NO CLASS. NMFS LAB PARTY
Tuesday, December 9, 2014
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