How to use objects from global environment in Rstudio Markdown

I've seen similar questions on Stack Overflow but virtually no conclusive answers, and certainly no answer that worked for me.

What is the easiest way to access and use objects (regression fits, data frames, other objects) that are located in the global R environment in the Markdown (Rstudio) script.

I find it surprising that there is no easy solution to this, given the tendency of the RStudio team to make things comfortable and effective.

Thanks in advance.

Solution 1:

For better or worse, this omission is intentional. Relying on objects created outside the document makes your document less reproducible--that is, if your document needs data in the global environment, you can't just give someone (or yourself in two years) the document and data files and let them recreate it themselves.

For this reason, and in order to perform the render in the background, RStudio actually creates a separate R session to render the document. That background R session cannot see any of the environments in the interactive R session you see in RStudio.

The best way around this problem is to take the code you used to create the contents of your global environment and move it inside your document (you can use echo = FALSE if you don't want it to show up in the document). This makes your document self-contained and reproducible.

If you can't do that, there are a few approaches you can take to use the data in the global environment directly:

1. 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. Alternatively:

2. Save your global environment to an .Rdata file prior to rendering (use R's save function), and load it in your document.

Solution 2:

Going to RStudio´s 'Tools' and 'Global options' and visiting the 'R Markdown' tab, you can make a selection in 'Evaluate chunks in directory', there select the option 'Documents' and the R Markdown knitting engine will be accessing the global environment as plain R code does. Hope this helps those who search this info!

Solution 3:

Well, in my case i found the following solution:

(1) Save your Global Environmental in a .Rdata file inside the same folder where you have your .Rmd file. (You just need click at disquet picture that is on "Global Environmental" panel)

(2) Write the following code in your script of Rmarkdown:

load(file = "filename.RData") #  it load the file that you saved before

and stop suffering.

Solution 4:

I have the same problem myself. Some stuff is pretty time consuming to reproduce every time.

I think there could be another answer. What if you save your environment with the save.image() function to a different file than the standard .Rdata one. Then, bring it back with load().

To be sure you are using the same data, use the md5sum() from tools.

Cheers, Cord

Solution 5:

I think I solved this problem by referring to the package explicitly in the code that is being knitted. Using the yarrr package, for example, I loaded the dataframe "pirates" using data(pirates). This worked fine at the console and within an Rstudio code chunk, but with knitr it failed following the pattern in the question above. If, however, I loaded the data into memory by creating an object using pirates <- yarrr::pirates, the document then knitted cleanly to HTML.