Pete Phillips

NHS lab-rat & pianist.

Blog posts with rmarkdown on Jekyll with servr and knitr

2 minute read

So I’m trying to set up my jekyll system to allow me to edit rmarkdown files and insert them into the jekyll system.

This is one way, but I couldn’t get this to work (too impatient), and in the end I found this post with a neat script which I have edited. My edits are mainly to fix the issue that my jekyll instance runs in a /blog/ subdirectory, and also to allow rebuilding of a page by removing the previously generated ../fig/xxx directory from a previous run of the script. I’m sure that there will be easier ways to accomplish this (without the hard coding of the /blog) but I’m too much of a novice with jekyll.

#!/usr/bin/env Rscript

input <- commandArgs(trailingOnly = TRUE)
#KnitPost <- function(input, base.url = "/") {
KnitPost <- function(input, base.url = "/blog/") {
    require(knitr)
    opts_knit$set(base.url = base.url)
# fig.path <- paste0("../figs/", sub(".Rmd$", "", basename(input)), "/")
    fig.path <- paste0("figs/", sub(".Rmd$", "", basename(input)), "/")
    opts_chunk$set(fig.path = fig.path)
    opts_chunk$set(fig.cap = "center")
    render_jekyll()
    print(paste0("../_posts/", sub(".Rmd$", "", basename(input)), ".mkd"))
    knit(input, output = paste0("../_posts/", sub(".Rmd$", "", basename(input)), ".mkd"), envir = parent.frame())
# now move the fig file 
# 1 but remove existing directory first
    rm.command<-paste0("rm -r ","../figs/", sub(".Rmd$", "", basename(input)), "/") 
# 2 - create a system command to move from the subdir to the parent directory,
    mv.command<-paste0("mv ","figs/", sub(".Rmd$", "", basename(input)), "/", " ../figs/") 
# 3 - now run it
    system(rm.command)
    system(mv.command)
}

KnitPost(input)

So let’s try some R…

install.packages(c('servr', 'knitr'), repos = 'http://cran.rstudio.com')

R code chunks

Following is from here

Now we write some R code chunks in this post. For example,

options(digits = 3)
cat("hello world!")
## hello world!
set.seed(123)
(x = rnorm(40) + 10)
##  [1]  9.44  9.77 11.56 10.07 10.13 11.72 10.46  8.73  9.31  9.55 11.22
## [12] 10.36 10.40 10.11  9.44 11.79 10.50  8.03 10.70  9.53  8.93  9.78
## [23]  8.97  9.27  9.37  8.31 10.84 10.15  8.86 11.25 10.43  9.70 10.90
## [34] 10.88 10.82 10.69 10.55  9.94  9.69  9.62
# generate a table
knitr::kable(head(mtcars))
  mpg cyl disp hp drat wt qsec vs am gear carb
Mazda RX4 21.0 6 160 110 3.90 2.62 16.5 0 1 4 4
Mazda RX4 Wag 21.0 6 160 110 3.90 2.88 17.0 0 1 4 4
Datsun 710 22.8 4 108 93 3.85 2.32 18.6 1 1 4 1
Hornet 4 Drive 21.4 6 258 110 3.08 3.21 19.4 1 0 3 1
Hornet Sportabout 18.7 8 360 175 3.15 3.44 17.0 0 0 3 2
Valiant 18.1 6 225 105 2.76 3.46 20.2 1 0 3 1 
(function() {
  if (TRUE) 1 + 1  # a boring comment
})()
## [1] 2
names(formals(servr::jekyll))  # arguments of the jekyll() function
## [1] "dir"     "input"   "output"  "script"  "serve"   "command" "..."

Just to test inline R expressions1 in knitr, we know the first element in x (created in the code chunk above) is 9.44. You can certainly draw some graphs as well:

par(mar = c(4, 4, .1, .1))
plot(cars, pch = 19, col = 'red')  # a scatterplot

A scatterplot of the cars data

Other ways to do this

* http://rmarkdown.rstudio.com/rmarkdown_websites.html

  1. The syntax in R Markdown for inline expressions is ` r code`, where code is the R expression that you want to evaluate, e.g. x[1]. ↩

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