Pass variable into python script from R using system2()

Question

I have seen various versions of this question, but have not been able to figure out how to pass numeric variables into Python from R using system2()

For example suppose I have the following python script as Test.py.

a = 1
b = 2
def add(a,b):
    print a + b

I can run this in R with

pypath = './Test.py'
system2('python', args=(sprintf('"%1$s"',pypath)))

but what if I wanted to pass the values of a and b in, and have the values returned within R to an R object? Something like,

a = 1
b = 2
d = system2('python',args = (sprintf('"%1$s" "%2$s" "%3$s"',pypath,a,b)))

I have tried a variety of ways of doing this, but have failed. I know the above is wrong, I just can't figure out how to pass in a and b, much less return a value

My questions are (1) is it possible? and (2) how do you do it?

Yes it's possible. But before you start with this, I think it would benefit to take a look at IPython, which was built pretty much for such integration purposes — inspectorG4dget
– inspectorG4dget, Commented May 20, 2015 at 19:05
Passing a and b is easy. You don't even need to use sptintf as you are doing right now. args argument takes in an array of characters so it you just to system2('python', args = c('./Test.py', as.character(a), as.character(b))). To write into a file, as a workaround you can use > to direct the output to a temp file and read from the file with R. It'll be slower but it'll work — OganM
– OganM, Commented May 20, 2015 at 19:09
Thanks @OganM. That is exactly what I was looking for. How do I use > to direct the output to a file using system2()? I have seen it used it with system, but not system2(). — user44796
– user44796, Commented May 20, 2015 at 19:26
just add it as another argument. system2('yourcommand',c('ARG1', 'ARG2', '>/targetDir/targetFile')) — OganM
– OganM, Commented May 20, 2015 at 19:49

OganM · Accepted Answer · 2015-05-21 01:35:53Z

3

System2 takes in an array of characters. So instead of trying to feed an entire string, you can just do

system2('python', args = c('./Test.py', as.character(a), as.character(b)))

One way of transferring the output to R is to use ">" to write it to a file then reading the file from R. (I'm sure this isn't the most efficient way to do this).

system2('python',args = c('/Test.py', as.character(a), as.character(b), '>/targetDir/targetFile'))

answered May 21, 2015 at 1:35

OganM

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cory · Accepted Answer · 2015-05-20 19:07:23Z

1

I've always just concatenated my whole string together...

a <- "/path/to/python"
b <- "script_to_call.py"
c <- 1

system(paste0(a, " ", b, " ", c))

answered May 20, 2015 at 19:07

cory

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