How to display images in Markdown on github generated from knitr without using external image hosting? - r

Question

I like uploading repositories to github that include multiple R Markdown and Markdown files.
Here is an example of such a markdown file on github. And here's a screen grab.
The problem is that images do not display. You can click on the image, and you will go to where the file is stored.
The file referenced is:
https://github.com/... /blob/.../myfigure.png
whereas I presume it needs to reference
https://github.com/... /raw/.../myfigure.png
Things I considered:
imgur: I could use external image hosting (e.g., see this example) by adding the following code:
```{r setup}
opts_knit$set(upload.fun = imgur_upload) # upload all images to imgur.com
````
However, for various reasons I don't want to do this (I have trouble uploading when behind a firewall; it's slow; it creates an unnecessary dependency)
Rpubs: There's also RPubs which is quite cool. However, at time of posting it seems more suited to single markdown documents rather than multiple R markdown documents. And it doesn't provide such a close link between source R Markdown and the Markdown document.
Question
Is there a workflow for using R Markdown and knitr to produce Markdown files which when uploaded to github permit the Markdown file to display images stored in the github repository?

Answer 1

This used to be part of the minimal example, use
opts_knit$set(base.url='https://github.com/.../raw/.../')
See the changes here and here.
Also see http://yihui.name/knitr/options.
EDIT [with update to restore base.url to former value
Regarding switching, you could define a function as
create_gitpath <- function(user, repo, branch = 'master'){
paste0(paste('https://github.com', user, repo, 'raw', branch, sep = '/'),'/')
}
my_repo <- create_gitpath(user, repo)
knit.github <- function(..., git_url ){
old_url <- opts_knit$get('base.url')
on.exit(opts_knit$set(base.url = old_url))
opts_knit$set(base.url = git_url)
knit(..., envir = parent.frame())
}
Run with knit until you want to push to github then run knit.github(..., git_url = my_repo)

Answer 2

What about the following code at the beginning of your markdown file?
``` {r setup,echo=FALSE,message=FALSE}
gitsubdir <- paste(tail(strsplit(getwd(),"/")[[1]],1),"/",sep="")
gitrep <- "https://github.com/mpiktas/myliuduomenis.lt"
gitbranch <- "master"
opts_knit$set(base.url=paste(gitrep,"raw",gitbranch,gitsubdir,sep="/"))
```
It is possible to tweak it so that gitrep and gitbranch will be reported by git. Here I assumed that I am one directory level below the main git repository directory. Again this might be tweaked to accommodate more complicated scenarios.
I've tested on github, here is the Rmd file and corresponding md file.