2016-01-20
Follow a schedule for the 3 hour class with the following elements per module:
Lecture to introduce: watch presentation
Demo to show: watch instructor use RStudio to get overall idea
Exercise to learn: do it yourself, individually, with given material
Group to apply: apply new technique to your group project (ie specific data and question)
Technology changes rapidly
Yes, you're learning about tools and libraries specific to R, but the concepts are applicable to most any programming language
The real skill learned here is critical thinking / problem solving / googling to figure out how to get your science done!
Teacher's role: "Sage on the Stage" -> "Guide on the Side"
Inspired by Data Carpentry for Biologists, created by Knewton
Gandrud (2013) Reproducible Research with R and Rstudio
Rmarkdown = R + markdown
In RStudio, menu File > New File > Rmarkdown… Document, HTML. Knit HMTL button to render the right.
"easy" HTML
Github renders (with flavor), eg README.md
Surround code with 3 backticks with {r} in first line
Surround code in single backticks
pi=`r pi` evaluates to "pi=3.1415927"
Uses Latex markup language for equations as input. Outputs using MathJax JavaScript library for HTML output, native for PDF.
$$
\frac{1}{n} \sum_{i=i}^{n} x_{i}
$$
\[ \frac{1}{n} \sum_{i=i}^{n} x_{i} \]
The Arithmetic mean is equal to $\frac{1}{n} \sum_{i=i}^{n} x_{i}$, or the summation of n numbers divided by n.
The Arithmetic mean is equal to \(\frac{1}{n} \sum_{i=i}^{n} x_{i}\), or the summation of n numbers divided by n.
Rmarkdown (*.Rmd) renders as markdown (*.md)
easy to see change in simple text files (vs binary / proprietary formats)
Rstudio: menu File > New File > Rmarkdown… Document, HTML. Knit HMTL button.