calling a R function from python code with passing arguments

Question

rtest = function(input ,output) {
  a <- input
  b <- output 
  outpath <- a+b
  print(a+b)
  return(outpath)
}

I have just return this R code for as a function for getting sum of two numbers. I tried to run this function from my python code using subprocess by passing 2 numbers as arguments. But it does not return sum value as return output. Do you know any method for implement this in python3 by passing function arguments.

my python code using subprocess is:

args=['3','10'] # (i tried to pass aruments like this) 
command="Rscript" 
path2script = '/...path/rtest.R' 
cmd = [command, path2script] +args 
x = subprocess.check_output(cmd, universal_newlines=True) 
print(x)

but x return ' ' null value

Please show your actual code for both your python subprocess call and your R script. It is not a problem to run a R script from python using subprocess. The problem is probably with your subprocess call. What are you actually calling? This code you provide is just an R function. When you call the R script, does it run this function and return the output? Or does it just define the function and do nothing? — divibisan
– divibisan, Commented May 29, 2018 at 13:17

9113303 · Accepted Answer · 2018-06-26 10:51:49Z

6

This could be easily done by rpy2 library in python.

    import rpy2.robjects as ro
    path="specify/path to/ R file"

        def function1(input,output):
            r=ro.r
            r.source(path+"rtest.R")
            p=r.rtest(input,output)
            return p


  a=function1(12,12)   # calling the function with passing arguments

Thanks.

edited Jun 26, 2018 at 10:51

answered Jun 22, 2018 at 9:47

9113303

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