R in Python
Sometimes you need the best of both worlds, using R and Python together.
Here is one approach, without using elaborate libraries, to write and then run R scripts within python. (It even works in Colab!)
An Approach to run R scripts inside Python scripts, to get the best of both worlds.
Goals
1. Run an R-script from python (Simple call)
2. Get the output of a function (run in R) back into python (Two Way Communication)
Spirit of Approach
- small is good
- fewer libraries and dependencies are better
- cross-system compatibility is good
- less special environment configuration is good
Approach:
The strategy is to use python to make and then call R scripts.
R in Colab:
Amazingly, most of this works in Colab (so Colab includes R as well as Python…wow…)
Summary 1. Run an R-script from python (Simple call)
There are only 2 lines of code to be run in R
df <- readRDS("{doc_name}.rds")
write.csv(df, "{doc_name}.csv")The challenge is to automate the R code. The automation and file management is easier in Python (and in some cases the required code-stack is python, not R)
What we need is the ability to call an R script inside Python:
We can do this with this one line (not including the import), which wonderfully does not require any special installs or pip-installed libraries, just ‘subprocess’ which comes standard:
import subprocess
subprocess.call(['/usr/bin/Rscript','convert.r'])
or
subprocess.call([ where R is on your computer , the r script])Script Factory
With python we can make and remake and run R scripts very easily as we need them. This may be a little verbose, but it is not fragile, OS dependent, or a black box.
Summary 2. Output from R back into Python (Two Way Communication)
Just two lines of R code will direct the output into a file (rather than a console print). The function needed is sink().
A “Sink Sandwich”:
Sandwich your code between two calls to the sink() function, and the output is then readable to python (in the file you name in that call).
e.g.
sink(file = "ouput_file_name.txt")
funtion_with_ouput()
sink(file = NULL)
