Why?

• Do you ever work through an analysis example in class with code and then never get around to typing it up nicely?
• Do you ever get students copy-pasting assignments from their classmates?
• Do you ever type up a piece of analysis by copy-pasting graph after graph or table after table, only to realise there’s a problem with the data and you have to redo everything?
• Do you ever need to include code from one or more languages and struggle to get the syntax highlighted nicely?
• Have you ever been asked by a reviewer to make your work more reproducible?

What?

• Notebooks are all the rage
• Instead of micro-managing your document, you use codes to indicate headings, links, or emphasis
• You type your document and code in a single editor
• In the end you press a button and it compiles your document for you, running the code and embedding the output along the way
• It’s the modern workflow
• Markdown is the popular notebook format
• R Markdown is what I use
• Everything discussed here applies to other popular packages too

How?

• I’m going to focus on RStudio
• Click File -> New File -> R Markdown
• Choose whether you want a Word document, a website, a pdf, a slideshow, etc.
• Save
• Click Knit

Where?

• I use it and nothing else for ALL my consultation projects
• I use it when I teach my classes
• I teach it to the students to use for their assignments and tests
  • with markdown there cannot be a disconnect between code, output, and discussion
• I use it for research projects
• I use it for myself
• And yes, this presentation was made in RStudio

Assignments

• To enable good assessment, students must be able to answer with code, maths, graphs, and written explanations interspersed
• Thus we need submissions in a modern shareable and mark-able format such as .pdf or .docx
• Until recently that meant that students would:
  • Make a Word document
  • Search how to do the thing they were supposed to study
  • Copy their code to the document
  • Run their code and realise there’s a problem, fix the problem and run again
  • Copy the output (text and graphs) to the document
  • Forget to copy the changed code, creating inconsistencies, and so on…

How to reduce copying

• To reduce copying I give each student different data
• This is not more work (usually)
• I generate data randomly based on some properties I need them to learn about
• And repeat for each student number
• How does markdown factor into this?
  • it doesn’t, markdown comes in with the memo
  • R Markdown allows for document parameters (like student number) to be entered when compiling to create a unique document just for the relevant student
  • I include marking guidance in the markdown file and give it to a competent marking assistant

Data generating example

• In this example I generate regression data with 1 significant variable and 1 insignficant variable to see if the students can differentiate

library(openxlsx)
students <- c(2001234567,2012345678,2000000123)
nStudents <- length(students)
n <- 100
datasets <- vector('list',nStudents)
for (i in 1:nStudents) {
  x1 <- rnorm(n,4,1)
  x2 <- rgamma(n,4,2)
  y <- 20 + 2*x1 + rnorm(n)
  datasets[[i]] <- data.frame(y,x1,x2)
}
names(datasets) <- paste0('St',students)
write.xlsx(datasets, file = "Practical1data.xlsx")

Memo example

• Will be shown in RStudio
• Available for download here: