I reasoned that there were two general approaches to solving this problem: I suppose I could do that manually for all my Markdown files every time I knit, but the whole point of blogging with R Markdown/knitr/jekyll/GitHub is supposed to be the convenient workflow, and having to edit all the figure paths in my Markdown files after knitting them is not my idea of convenience. Then GitHub/jekyll would leave my paths alone and produce proper html tags linking to my figures. After creating my caRds.Rmd file, I added it to my website’s projects folder, and then ran knit like so: Locally, my website lives in the directory /Users/nunnlab/Desktop/GitHub//. What I AM going to do is explain what exactly I did that seemed to cause the problem, and how I fixed it with a few lines of R code. I am not going to attempt to figure out what sorcery caused this extra slash to appear in my html- I’m sure there is a good reason why GitHub/jekyll behave this way. Apparently the offending slash was being added when my *.md files were rendered into *.html by GitHub/jekyll.
#Rmarkdown github display plots code
I checked the html source code for the page and discovered the immediate problem: the file paths to the figures had an extra forward slash appended to the beginning of the path, e.g., rather than. But when I went to view the live site, I was horrified to see that all of the R figures were missing! How could this be? I then built and previewed my site locally on my machine, and when I saw that everything was beautiful, I pushed it to GitHub. I added my first *.Rmd-> *.md page with R figures (my silly cards page). Sit back and relax as GitHub pages automatically builds and serves your site, rendering your *.md and dependent files into an attractive *.html page with syntax highlighting for your code and R output displayed.Add the *.md file and output to the GitHub repository for your site.Use knitr to “knit” the *.Rmd file, which produces a simple Markdown *.md file and output files, including any figures produced by your R code.Write your page in an R Markdown document, including chunks of R code.I read several blog posts on using R Markdown and knitr to create pages for your jekyll/GitHub site (e.g., here and here). Not bad for a day’s work.īut the smooth sailing ended the next day when I started trying to incorporate R Markdown documents with R code and graphical output. I added some basic content (About Me, publications, etc), and by nightfall I was happy enough with my new site to go live on GitHub Pages. Next, I started pulling and modifying files from the hyde theme until I had the basic look I wanted (a minimalist black-and-white theme with a permanent sidebar and blog). Thanks largely to this awesome blog post, it took me less than an hour to set up a local jekyll site on my machine and familiarize myself with the structure. Back to blog Figure path mess with R Markdown/knitr/jekyll/GitHub
0 kommentar(er)
