skills.md

Reproducible Research requires fou4 sets of skills:

1. Data Management
2. Graph Production
3. Statistical Modeling
4. Dynamic Reporting

You can review my discussion of toolbox and skillset of reproducible research in slides and videoes here

Skill sets

Links grouped by the skillset.

Data Management

• Introduction to data cleaning in R, a discussion paper by Edwin de Jonge and Mark van der Loo.

Graph Production

• Winston Chang's R Graphics Cookbook is a perfect book to get you started with producing graphs with RStudio.
• ggplots for publication.
• working with multiple plots examples

Statistical Modeling

• regressing "x on y" or "x on y"?
  • Doug Bates on statistical modeling with Julia(video

Package support

Package dplyr::

• Introduction to dplyr the official vignette of the package.
• Tutorials for the dplyr package in R by Kevin Markham
• A work-along scripts following Wickham's Tidy data paper, but re-doing it in dplyr.

Package stats::

Function stats::lm()

Function stats::glm()

• Comparing functions stats::lm() vs stats::glm()

Package lme4::

• lme4::lmer()

Package nlme::

Function nlme::gls()

Function nlme::lme()

• Comparing functions nlme::gls() vs. nlme::lme()

Dynamic Reporting

Git and GitHub

• GitHub cheat sheet by Kevin Markham. All issues have screen-shots. More resources in the README after the link.
• Git quick reference for beginners by Kevin Markham

Markdown

• in-browser markdown simulator, created in javascript by Jeroen Ooms. Great for playing with markdown formatting and doing simple tasks and demonstrations in R without installation.

• markdown in R : a blog entry on getting started with rmarkdown - a version of markdown enhanced for the use with RStudio. By Jeromy Anglim.

• markdown guide : a well-written "breaking into" guide. Gives ample verbal description. Recommended for newbies. By John Gruber.

• markdown cheat-sheet : brief, simple, parallel view of what the code is doing. By Mashery group.

• another markdown simulator with a different feel. You can't run R script in here, but it's good for understanding the formatting. Give a link to a decent cheatsheet on markdown.

• MultiMarkdown allows for mathematical formulas and other features

Rmarkdown

• see the official documentation by RStudio, best starting point IMHO

Slides

• RStudio provides a native format for creating presentations - .Rpres, availible in the "New file" option. For a quick start with .Rpres see this article

Stat Graphing for the Web

• Highcharts point and click implementation for sharing interactive graphs.