Rmarkdown: different output folders, shared libs

pandoc, r, r-markdown, rstudio, yaml

Solution

I solved my immediate problem by passing some of the front matter in the render call:

rmarkdown::render("file1.Rmd", 
                   output_dir=file.path(uddannelse),
                   output_file=paste("file1", uddannelse,".html", sep="_"),
                   output_options=list(html_document = 
                     list(self_contained = FALSE, 
                          lib_dir = file.path(uddannelse, "lib"),
                          css = paste("lib", "custom_css", "custom.css",
                                      sep="/"),
                          include = list(
                            after_body = file.path(uddannelse,
                                                  "footer_w_index.html")))),
                   encoding="UTF-8")

Notice that `lib_dir` has to be relative to the `Rmd`file and `css` has to be relative to the output-file.

For some reason - regardless of whether I use `paste` or `file.path(fsep="/", ...)` the `css` path in the output file is linked with windows separator ("\") - and thus not usable in e.g. Firefox.

Problem

I have an `.R` file wherein I for each unique value in a list, render a number of different `.Rmd` files. Something like this: ``` for (uddannelse in unique(c("Monkey","Horse"))) { rmarkdown::render("file1.Rmd", output_dir=file.path(getwd(), uddannelse) ,output_file=paste("file1", uddannelse,".html", sep="_"), encoding="UTF-8") rmarkdown::render("file2.Rmd", output_dir=file.path(getwd(), uddannelse), output_file=paste("file2", uddannelse,".html", sep="_"), encoding="UTF-8") } ``` As evident by the render parameters, the html-output should go into a separate folder for each value in the list, in the above example: folder: "Monkey" and folder "Horse". Each `.Rmd` file has the following front matter (the files go to a static html website and needs to have `self_contained: false`: ``` --- output: html_document: theme: readable self_contained: false lib_dir: pub/libs css: pub/libs/custom_css/custom.css date: "`r format(Sys.time(), '%d %B, %Y')`" --- ``` However: When I call the render functions I recieve this error: Error in relativeTo(basepath, dir) : The path C:/Users/ac/Dropbox/2014_07_WIP/pub/libs/jquery-1.11.0 does not appear to be a descendant of C:/Users/ac/Dropbox/2014_07_WIP/Monkey/ So I guess the `rmarkdwown::render` first creates the lib directories relative to the Rmd file, yet expect the files to be placed relative to the output files. How can I get around this, so that I can have a set of common Rmd input files in one folder, and have output in different folders, yet share a common lib? I tried to place something like this in the fronmatter. ``` --- output: html_document: theme: readable self_contained: false lib_dir: "`r file.path(uddannelse, "libs")`" css: "`r file.path(uddannelse, "libs", "custom_css", "custom.css")`" date: "`r format(Sys.time(), '%d %B, %Y')`" --- ``` And I got this error: ``` Error in yaml::yaml.load(front_matter) : Parser error: while parsing a block mapping at line 3, column 5did not find expected key at line 5, column 50 ```

Original source