CODEWITHSUNDEEP
rr-markdown
gdol
gdol

Reputation: 185

R-Markdown: input and output with relative pathes

I am working on a project which is developed by our team. We share the codes in a repository. Every team member is using his/her own machine with his/her own working directories. That is why we use relative paths in our projects. Usually we use something like

setwd("MyUser/MyProject/MyWD/myCodesDir") # local
...
MyReportingPath <- "../ReportsDir" # in repository

Now I try to render a markdown report to this directory:

rmarkdown::render(input = "relevantPath/ReportingHTML.Rmd",
                output_file = paste0(MyReportingPath, "/ReportingHTML.html"))

This doesn't work. It only works if I type in the full path of the output file ("/home/User/..../ReportingHTML.html") This is one of the issues I would like to clarify: is there any possibility to use relative paths in any way for Markdown?

Second issue is that if I type in an non-existing directory in the output_file, pandoc throws me an error instead of creating this directory with my output file. Is there any possibility to do a dynamic output directory creation? (except for doing system(paste0("mkdir ", reportPath), intern = T) before rendering)

P.S. It is important for me to render the markdown document in a separate R function, where I create the whole environment which is inherited by my Markdown document.

Upvotes: 4

Views: 1894

Answers (2)

Jesse
Jesse

Reputation: 172

I just ran into this myself, and as it turns out, there's one additional complication here: You really do need to use an absolute path for the output if your input file being rendered isn't in your current working directory. You also need to use absolute paths for anything else during rendering, for example images like ![](path.png).

This looks to be because rmarkdown::render temporarily sets your working directory to the directory containing the input file, so it interprets a relative directory as relative to that path, not your initial working directory. (EDIT: There's currently an open issue for this on github.)

For example if you have this setup:

subdir/test.Rmd
outdir

And you do this:

rmarkdown::render(
  input = "subdir/test.Rmd",
  output_file = "outdir/out.html")

You get the error:

Error: The directory 'outdir' does not not exist.
Execution halted

Instead, you could do:

output_path <- file.path(normalizePath("."), "outdir/out.html")
rmarkdown::render(
  input = "subdir/test.Rmd",
  output_file = output_path)

...and that should work.

You might think you could just use normalizePath("outdir/out.html"), but you can't, because that function only works when the path already exists. You also might think you could do this:

rmarkdown::render(
  input = "subdir/test.Rmd",
  output_file = file.path(normalizePath("."), "outdir/out.html"))

but you can't, because R only gets around to interpreting the value of output_file once the working directory has already been changed.

Upvotes: 1

DonJ
DonJ

Reputation: 963

Trivial issue - since you're using paste0 you need to provide the / delimiter between your output directory and output file.

You wrote:

rmarkdown::render(input = "relevantPath/ReportingHTML.Rmd",
            output_file = paste0(MyReportingPath, "ReportingHTML.html"))

Instead, try:

rmarkdown::render(input = "relevantPath/ReportingHTML.Rmd",
            output_file = paste0(MyReportingPath, "/", "ReportingHTML.html"))

More broadly:

For your first issue (settting the path for the input file) - I also suggest using here::here(). If you need to navigate up from your working directory you can break down the path as follows:

parent_dir <- paste(head(unlist(strsplit(here::here(), "/", fixed = TRUE)), -1), collapse = "/")
grandparent_dir <- paste(head(unlist(strsplit(here::here(), "/", fixed = TRUE)), -2), collapse = "/")

However - it might be easier to set the working directory to a higher level, then build up your code and results directories, for example:

project_dir <- here::here()
codefile <- paste(project_dir, "code", "myreport.Rmd", sep = "/")
outfile <- paste(project_dir, "results", "myreport.html", sep = "/")
rmarkdown::render(input = codefile,
            output_file = outfile))

For your second issue (creating the directory for output) - using dir.create("MyReportingPath", recursive = TRUE) will create the output directory and any intermediate levels. You will get a warning if the directory exists which can be suppressed using showWarnings = FALSE.

Upvotes: 2

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