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About

Amy's course materials for Strategies And Techniques For Analysing Microbial Population Structures (STAMPS) at the Marine Biological Laboratory, 2017

This folder mostly contains materials related to the R tutorial, but some other materials as well

For Students

Before STAMPS/Monday night

Ensure that you have R and RStudio installed on your computer, and that you know how to load a package from both CRAN and github.

See here for instructions on how to do this

Time permitting, we will have a brief lecture introducing R. Otherwise, we will do this between the statistics talk and the lab tomorrow.

Tuesday morning

We will have a lecture on statistical principles for microbiome, before transitioning into the R lab. You have 4 options for choosing a tutorial

  • Option A: Welcome to R! A good introduction/overview for those relatively new to R
  • Option B: R Trainee! Introducing some more complex topics and to give you more exposure. We hope that newcomers to R will have worked through Options A and B by the end of Tuesday night.
  • Option C: R Ninja! To introduce some more advanced concepts
  • Option D: R Guru! Help the your classmates and the TAs as they do their rounds!

Tuesday night

Continue working through up to the end of Option B. Once you've done this, go back and finish the USEARCH lab (if you haven't already). Do not worry about finishing Option C unless you have nothing else to do!

For TAs

For STAMPS TAs who use R regularly

  1. Please work through Option A tutorial, Option B tutorial and Option B solutions. Critically review the material and think about any missing explanations. Note that some code is deliberately erroneous to force the students to practice correcting their own errors.
  2. If you would like to see something included or changed, please fork the repository and submit your changes
  3. Optional but greatly appreciated: I'm trying to think about how to engage some of the more advanced students, so am filling out an Option C tutorial. Please help me by contributing an example or some new functionality along with a description of how to use it. Currently
  • reshape: cast, melt...

  • plyr

  • ddply

  • parallelisation

  • Markdown

mini tutorials need to be filled out. Feel free to contribute to these or include your own! Other options include S4 classes, ?, ?... Because this is for advanced users, I'm not planning to write solutions for exercises here, and the structure of a tutorial can be as simple as pointing them to an existing tutorial on the internet and then asking them to apply the concept to our OTU data.

Because I imagine that many students will be relatively new to R (and programming in general), I'm trying to keep all explanations relatively accessible. For example, a function in R is actually just a type of object, but I'm going to talk about functions and objects as if they are different beasts to avoid confusing anyone. Feel free to ignore technicalities like this for the purposes of getting as many students as possible up and running with confidence in R.

I really, really appreciate your help and time! The STAMPS participants always come eager to learn, so any time you have to help will be both worth it and appreciated by both the students and me!

For STAMPS TAs who know some R

  1. I'll assume that you already have R on your computer, but please also install RStudio
  2. Please work through the Option A tutorial
  • No need to go through in excruciating detail or do the exercises, just enough to know what's happening so you can help students on the day
  1. Have a quick read through the Option B tutorial and the solutions

If you think an important explanation is missing, feel free to fork the repository and submit your changes, or email me!

For STAMPS TAs who don't know R

  1. Please install R and RStudio onto your computer, and read through the instructions on installing R so that you have enough familiarity to help students who encounter difficulties
  2. Please attend the Monday night session to help with installation.
  3. If possible, please also attend the Tuesday morning session to help students where you can

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Course materials for STAMPS @ MBL

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