How to pass integer arguments to R-script from python

Question

i have the below posted R-code and i want to pass the parameter nfrom python code and display the results. that is, if i passed 4 then 16 must be printed out on the screen. please let me know how to pass argumnets to R-script from python

R-Code:

Square <- function(n) {
return(n^2)
}

Python-code:

command ='Rscript'
path2Func1Script ='/var/www/aw/Rcodes/func-1.R'
args = [3]
cmd = [command, path2Func1Script]

output = None
try:
    x = subprocess.call(cmd + args, shell=True)
    print("x: ", x)
except subprocess.CalledProcessError as e:
    output = e.output
    print("output: ", output)

Can you add to the question the python version you are using? — Jorge Verdeguer Gómez
– Jorge Verdeguer Gómez, Commented Jul 16, 2021 at 9:00
Hi @Letsamrit, I have conducted further testing and research and have made sure my answer answers everything, and I hope it helps — TERMINATOR
– TERMINATOR, Commented Jul 19, 2021 at 7:56

TERMINATOR · Accepted Answer · 2021-07-19 08:11:52Z

1

+50

Solution:

I see you are doing this manually may I suggest you use an awesome python library built for this called rpy2. Rpy2 provides a lot of functionality to use R libraries and functions from python itself without having to manually call the r script in a command line argument from python using subprocess, and this not only makes it easier to code but is more efficient.

The most important thing to note is that to parse a python integer list to an r function you need to convert it to an r IntVector like so robjects.vectors.IntVector().Another thing to mention is you need to set your R_HOME environment variable to the path of your R installation if you are using windows

Firstly install rpy2 by using conda(pip only works on linux with this package):

conda install -c conda-forge rpy2

Here is the code python code:

import rpy2.robjects as robjects


# Defining the R script and loading the instance in Python
r = robjects.r
r['source']('func-1.R')

# Loading the function we have defined in R.
square_func = robjects.globalenv['Square']

# defining the args
args = robjects.vectors.IntVector([3])

#Invoking the R function and getting the result
result_r = square_func(args)

#printing it.
print('x: ' , result_r)

Output:

x: [1] 9

edited Jul 19, 2021 at 8:11

answered Jul 16, 2021 at 9:04

TERMINATOR

1,2871 gold badge14 silver badges24 bronze badges

Sign up to request clarification or add additional context in comments.

2 Comments

Amrmsmb Over a year ago

would you please show me how to adapt the code to pass array of integers ?

lgautier Over a year ago

You can also encapsulate the code in the R source file in a namespace. See rpy2.github.io/doc/v3.4.x/html/…

Collectives™ on Stack Overflow

How to pass integer arguments to R-script from python

1 Answer 1

Solution:

2 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

Solution:

2 Comments

Your Answer

Sign up or log in

Post as a guest

Related