Using packrat libraries with knitr and the rstudio compile PDF button

Question

As explained by Yihui Xie in this post, when one uses the Compile PDF button of the RStudio IDE to produce a PDF from a .Rnw file, knit() uses the globalenv() of a new R session. Is there a way that this new R session would use the packrat libraries of my project (even the version of knitr included in my packrat libraries) instead of my personal user libraries to ensure a maximum level of reproducibility? I guess that the new R session would have to be linked to the project itself, but I don't know how to do this efficiently.

I know I could directly use the knit() function instead of the Compile PDF button and, that way, knit() would use my current globalenv(), but I don't like this solution since it's less reproducible.

Answer 1

I think I got the problem myself, but I want to share with others who could confirm I'm right, and possibly help improve my solution.

My specific problem is that my .Rnw file is in a sub-directory of my whole project. When the Compile PDF button creates a new R session, it is created in this sub-directory, thus not finding the .Rprofile file that would initialize packrat. I think the easiest solution would be to create a .Rprofile file in my subdirectory which contains

temp <- getwd()
setwd("..")
source("packrat/init.R")
setwd(temp)
rm(temp)

I have to change the working directory at the project level before source("packrat/init.R") because the file itself refers to the directory...

Anybody can see a better solution?

Answer 2

P.,

I don't know if this solution works for even the knitr package, but I am 99% sure it works for all other packages as it seems to for me.

(I believe) I have a very similar problem. I have my project folder, but my working directory has always been the sub folder where my .rnw file is located, in a subdirectory of my project folder.

The link to Yihiu Xie's answer was very helpful.

Originally I wanted a project folder such as:

project-a/
               working/
                        data/
                                  datas.csv
                        analysis/
                                  library.R
                                  rscripts.R
                        rnw/
                                  report.rnw
                        child/
                                  preamble.rnw
                        packrat/

But I'm not sure if that is possible with packrat when my R library() calls are not in the working directory and packrat cannot parse the .rnw file (I call the library.R file from a chunck using source() in my .rnw file). A few notes:

• I wanted to use a .Rproj file to open the project and have project-a/working as the working directory
  • If this was true then packrat can find the library.R script
  • But the .rnw file still defaults to its own working directory when compiling
• I thought an .Rprofile with knitr::opts_knit$set(root.dir = "..") would work but I don't think it works for latex commands like input\, it defaults back to the directory containing the .rnw file
  • I thought this was insufficient because then you have two working directories, one for your r chunks and one for your latex!

Since .rnw always sets the working directory, I put my library.R script in the same directory as my .rnw file which creates the packrat folder in project-a/working/rnw. I am 99% sure this works because when I created the packrat folder in the project-a/working/rnw folder WITHOUT relocating the library.R file it received an error that no packages could be found and I could not compile the .rnw file.

project-a/
               working/
                        data/
                                  datas.csv
                        analysis/
                                  rscripts.R
                        rnw/
                                  report.rnw
                                  library.R
                                  packrat/
                        child/
                                  preamble.rnw

Again, unless I am overlooking something or misunderstanding which packages are being used, this seems to have worked for me. Disclaimer here that I am relatively new to packrat.