Blog with RStudio, R, RMarkdown, Jekyll and Github

浅浅的花香味﹌ 2022-07-16 01:23 213阅读 0赞

In the first post of this new blog I’ll outline how I’ve set the blog up.

*  writing posts in `Rmarkdown`
 *  converting posts to markdown from R
 *  push to Github where Jekyll renders the markdown
 *  organising all as an RStudio project

## What I wanted ##

I wanted to be able to write about R related things without having to copy and paste code, figures or files. I had used [Rmarkdown][]and [knitr][] before so wanted to use them. I have a wordpress site elsewhere that someone helped me set up a couple of years ago with a blog that I’ve never used. Initially I tried seeing if I could create posts using `RMarkdown` and put them into that wordpress blog. A brief search revealed that was not straightforward and that Jekyll was the way to go.

## What I’ve got ##

Now I have this blog set up so that I can write all of the posts (including this one) in RMarkdown (`.Rmd`) and run an R function to convert them to markdown (`.md`). The blog is hosted for free on[Github][] (you get one free personal site). The site is created using[Jekyll][] on Github, so I didn’t need to install Jekyll or Ruby. I simply edit files locally, then commit and push to Github. I manage the site as an [RStudio][] project, enabling me to edit text, keep track of files and interact with Git all from one interface.

## How I got here (steps) ##

### creating Jekyll site on Github ###

I used Barry Clarks amazing [Jekyll-Now repository][] which you can fork directly from Github and start editing to customize. He gives excellent instructions. What attarcted me to it was that it takes a matter of minutes to set up initially and if you decide you don’t like it you can just delete.

Thanks to Jan Gorecki whose answer on [stackoverflow][] pointed me in this direction and I’ve copied some extra features like the Links and Index pages from his [site][].

### enabling editing of the site from RStudio ###

I cloned the Github repository for my site using RStudio :

*  File, New project, Version control, Clone git
 *  Repo URL : https://github.com/AndySouth/andysouth.github.io
 *  Project directory name : andysouth.github.io

### setting up so that I can write the posts in RMarkdown ###

This was the tricky bit for me. I followed inspiration from [Jason Bryer][]and [Jon Zelner][]. I had to tweak them both, the relative paths of figures was my main stumbling block. This was partly because I’m running windows and I couldn’t run the shell scripts that they created. Instead I just run an R function [rmd2md][] which is much the same as Jason’s with some edits to paths and jekyll rendering.

Jason’s function searches a folder that you specify for `.Rmd` files and then puts `.md` files into another folder. I set this up so that any plots are put into a third folder. Thus in the root of my site includes these 3 folders.

<table style="border-collapse:collapse; border-spacing:0px; margin:1em 0px; color:rgb(68,68,68); font-family:STHeiti; font-size:14px; orphans:2; widows:2"> 
 <thead> 
  <tr> 
   <th style="font-family:&quot;Trebuchet MS&quot;,Verdana,Arial,Helvetica,sans-serif; font-weight:normal; background:rgb(238,238,238); border:1px solid rgb(204,204,204); text-transform:uppercase; padding:6px"> FOLDER</th> 
   <th style="font-family:&quot;Trebuchet MS&quot;,Verdana,Arial,Helvetica,sans-serif; font-weight:normal; background:rgb(238,238,238); border:1px solid rgb(204,204,204); text-transform:uppercase; padding:6px"> &nbsp;</th> 
   <th style="font-family:&quot;Trebuchet MS&quot;,Verdana,Arial,Helvetica,sans-serif; font-weight:normal; background:rgb(238,238,238); border:1px solid rgb(204,204,204); text-transform:uppercase; padding:6px"> CONTENTS</th> 
  </tr> 
 </thead> 
 <tbody> 
  <tr> 
   <td style="border:1px solid rgb(204,204,204); padding:6px">_Rmd</td> 
   <td style="border:1px solid rgb(204,204,204); padding:6px">&nbsp;</td> 
   <td style="border:1px solid rgb(204,204,204); padding:6px">RMarkdown files that I edit</td> 
  </tr> 
  <tr> 
   <td style="border:1px solid rgb(204,204,204); padding:6px">_md</td> 
   <td style="border:1px solid rgb(204,204,204); padding:6px">&nbsp;</td> 
   <td style="border:1px solid rgb(204,204,204); padding:6px">md files created by RMarkdown</td> 
  </tr> 
  <tr> 
   <td style="border:1px solid rgb(204,204,204); padding:6px">figures</td> 
   <td style="border:1px solid rgb(204,204,204); padding:6px">&nbsp;</td> 
   <td style="border:1px solid rgb(204,204,204); padding:6px">plots created by any chunks of R code</td> 
  </tr> 
 </tbody> 
</table>

This then means that any R plot is automatically generated, saved as a png and it’s address is written into the md document so that the plot is displayed in the blog. This is shown in a simple example below that queries the WHO API to get the number of cases of one of the forms of sleeping sickness in 2013.

code <- "NTD_4"
    year <- 2013
    url <- paste0('http://apps.who.int/gho/athena/api/GHO/',code,'.csv?filter=COUNTRY:*;YEAR:',year)
    #read query result into dataframe
    dF <- read.csv(url,as.is=TRUE)
    library(rworldmap)
    sPDF <- joinCountryData2Map(dF, nameJoinColumn="COUNTRY", joinCode="ISO3")

## 24 codes from your data successfully matched countries in the map
    ## 0 codes from your data failed to match with a country code in the map
    ## 220 codes from the map weren't represented in your data

mapCountryData(sPDF,nameColumnToPlot="Numeric",catMethod="fixedWidth",mapRegion="africa", mapTitle="Gambian sleeping sickness cases in 2013")

![plot of chunk 14-12-10-rworldmap][]

The code syntax highlighting and dark grey background for both code and R text outputs are what come as the default with Jekyll-Now. I’m a little unsure about them. They seem to be specified in[\_highlights.scss][highlights.scss], perhaps I’ll look at modifying later.

If you’d like to look here is the [entire source code][] for the blog and for this [individual page][].

[Rmarkdown]: http://rmarkdown.rstudio.com/
[knitr]: http://yihui.name/knitr/
[Github]: https://github.com/
[Jekyll]: http://jekyllrb.com/
[RStudio]: http://www.rstudio.com/products/RStudio
[Jekyll-Now repository]: https://github.com/barryclark/jekyll-now
[stackoverflow]: http://stackoverflow.com/a/26703757/1718356
[site]: https://github.com/jangorecki/jangorecki.github.io
[Jason Bryer]: http://jason.bryer.org/posts/2012-12-10/Markdown_Jekyll_R_for_Blogging.html
[Jon Zelner]: http://www.jonzelner.net/jekyll/knitr/r/2014/07/02/autogen-knitr/
[rmd2md]: https://github.com/AndySouth/andysouth.github.io/blob/master/rmd2md.r
[plot of chunk 14-12-10-rworldmap]: /images/20220716/79add9ab940c4cc08908a6ec15c47c54.png
[highlights.scss]: https://github.com/AndySouth/andysouth.github.io/blob/master/_scss/_highlights.scss
[entire source code]: https://github.com/AndySouth/andysouth.github.io/
[individual page]: https://github.com/AndySouth/andysouth.github.io/blob/master/_rmd/2014-12-10-blog-setup.Rmd