Embedding R code


This session will cover embedding R code in qmd.

Session Details

  • Date: [Day of week], [Month] [Day], [Year]
  • Time: [Start time]–[End time] ([morning/afternoon/evening] session)
  • Location: [Venue or virtual platform]
  • Instructor: [Instructor Name]

Embedding R code into the website

The quarto markdown .qmd is essentially a successor to RMarkdown, mostly backward compatible and following similar syntax.

Code chunks

library(ape)
library(phangorn)

tree1 <- ape::read.tree(text='(((A,B),C),D);')
tree2 <- ape::read.tree(text='(((A,C),B),D);')

dist <- phangorn::RF.dist(tree1, tree2)

dist
[1] 2

Library loading

Here we are loading the libraries used throughout this document.

library(ape)
library(phangorn)

Cross reference figures

You can add special tags to be able to create links to figures. See Figure 1 for details.

Code 
tree1 <- ape::read.tree(text='(((A,B),C),D);')

plot(tree1)
Figure 1: You can link to this figure

Reading external datasets

We can also read in files that are provided in a relative location to this document.

my.trees <- ape::read.nexus('../data/example.trees')

phangorn::RF.dist(my.trees)
           STATE_0 STATE_2000
STATE_2000      26           
STATE_4000      28         16