plan.md

Lesson plans

Guidelines

Each lesson must be stored in its own separate repository with a gh-pages branch. The lesson template repository can be found here: https://github.com/swcarpentry/lesson-template

Lesson

See: https://github.com/swcarpentry/lesson-template/blob/gh-pages/LAYOUT.md

A lesson has:

• prerequisites
• a series of topics (10-15 minute lessons followed by exercises)
• Motivation slides
• A reference guide
• A page of general discussions
• An instructor guide

Schedule

4 x 90 minute blocks gives time for 24 x 15 minute topics or 6 lessons with 4 topics each. or 8 lessons with 3 topics each.

Topic: Introduction to RStudio and Reproducible workflows

• Explain and show the various panes in R.

• Principles for reproducibility (Separation of style and content). -- See: http://resbaz.github.io/2014-r-materials/lessons/20-projects/

• Introduce Projects in R

  • install packrat
    • explain libraries
  • Create a new project for the bootcamp
  • Show packrat/ folder
  • explain packrat::bundle() -- we'll use this at the end to bundle up the whole course.
  • install ProjectTemplate, initialise project with both.

• Explain what just happened

  • Open README
  • explain folders
  • show packrat::status()
  • modify .gitignore to ignore data/ and munge/ directories

• Upload gapminder data set

• Run load.project, explain what happened

• Show config

• add packrat to libraries

• set load_libraries to TRUE

• Run load.project

• Install missing libraries

• run packrat::status()

• Show git integration.

Topic: Introduction to R

• http://resbaz.github.io/2014-r-materials/lessons/01-intro_r/r-basics.html
• merged with http://swcarpentry.github.io/r-novice-inflammation/01-starting-with-data.html
• Reading tabular data

Topic: Seeking help

• Show helpfile for read.table
• http://resbaz.github.io/2014-r-materials/lessons/01-intro_r/seeking-help.html
• Stackoverflow
• CRAN Task views

Topic: Data Structures in R

• http://resbaz.github.io/2014-r-materials/lessons/01-intro_r/data-structures.html
• Needs exercises

Topic: Subsetting Data

• http://resbaz.github.io/2014-r-materials/lessons/01-intro_r/subsetting.html

Topic: Vectorisation

• http://resbaz.github.io/2014-r-materials/lessons/01-intro_r/vectorisation.html

Topic: Functions:

• http://swcarpentry.github.io/r-novice-inflammation/02-func-R.html
• merge with http://resbaz.github.io/2014-r-materials/lessons/10-functions/