Ideas for R and RMD

[jaseeverett]

Hiya
I had hassles trying to do basic R Markdown due to having many global environment variables and Knit not finding them. I found this info and it worked a treat:
Instead of using the Knit HTML button, type rmarkdown::render("your_doc.Rmd") at the R console. This will knit in the current session instead of a background session.
Save your global environment to an .Rdata file prior to rendering (use R's save function), and load it in your document.
Used option 1 and it saved me a world of grief!

Caching is obviously an option too.. but I found this quick and easy for what I needed.

thanks
Rose

[PhDyellow]

On the other hand, an Rmd document that only knits if you already have variables and functions in your global environment is not reproducible. Saving key variables to rds or rdata files and loading at the top of the file is fine.

[PhDyellow]

The knit HTML button becomes a test: "Does my Rmd file depend on things in my global environment or is it self-contained?"