Repository for introductory R training being run in the Department of Biochemistry on Feb 22 and 23, 2016.
Location: Biochemistry Seminar Room (231 - used to be 228).
Etherpad link: https://public.etherpad-mozilla.org/p/2016-02-22_Otago_Biochem
Pre-workshop survey link: https://docs.google.com/forms/d/10-ZO8zuR0pJ6FQroQauUticrcsJYtEH5ySgGBIey7mE/viewform?c=0&w=1&usp=mail_form_link
Post-workshop survey link: https://docs.google.com/forms/d/1HFO8WYkg4QvyQnV79h_8exPo6Lve1SHJjKSMLNCBeT8/viewform?c=0&w=1&usp=mail_form_link
Monday:
- Session 1 - 9:30am-12:30pm - R/RStudio overview, data organisation, basic data import (Mik/James)
- Mik's slides: https://rawgit.com/mikblacklab/Biochem_R_training/master/01_Session1_data_organisation.html
- James's slides: https://rawgit.com/mikblacklab/Biochem_R_training/master/01_Session2_excel_and_import.html
- Data carpentry lesson for spreadsheets: http://www.datacarpentry.org/spreadsheet-ecology-lesson/
- Session 2 - 1:30pm-4:30pm - Introduction to R (Murray/Tanya/Tom)
- Data carpentry lesson sourced from: https://github.com/datacarpentry/R-ecology
- Extra content from https://github.com/murraycadzow/R_tutorials/blob/master/Intro_R.Rmd
- Data carpentry materials available here http://www.datacarpentry.org/R-ecology/
Tuesday:
- Session 3 - 9:30am-12:30pm - Data manipulation & visualisation (Murray/Elizabeth/Tanya)
- Data capentry lesson for dplyr and visualisation: https://github.com/datacarpentry/R-ecology
- Data carpentry materials available here http://www.datacarpentry.org/R-ecology/
- Session 4 - 1:30pm-4:30pm - Reproducible research with Rmarkdown (Mik/James)
- Slides for Rmarkdown intro: https://github.com/Reproducible-Science-Curriculum/rr-literate-programming/raw/master/slides/lit-prog-slides/lit-prog-slides.pdf
- Markdown tutorial: http://markdowntutorial.com/
- Rmarkdown activity: https://github.com/mikblacklab/Biochem_R_training/blob/master/04_Session4_rmarkdown_activity.md
- Project organization: https://github.com/Reproducible-Science-Curriculum/rr-init
This will be a hands-on workshop, so you will need to bring your own laptop (we will have plenty of power strips), and it needs to be able to connect to the university wifi (we will generate some spare user accounts just in case your login doesn’t work).
In preparation for the workshop, you will need to have some sort of spreadsheet program installed on your laptop. For many of you this will be Microsoft Excel, but if you need to install one, LibreOffice provides a free option for Mac, Windows and Linux:
You will also need to have R and RStudio installed. Instructions for installing R are here:
http://cran.stat.auckland.ac.nz/
Instructions for installing RStudio are here:
https://www.rstudio.com/products/rstudio/download/
If you have problems installing the software, please let us know - if you come along a bit earlier on Monday we should be able to help you get set up.
We will also be using the dplyr, ggplot packages for R - we will provide instructions on how to install these during the workshop (or you can do it in advance if you already know how).