I am learning Python and R and am having an issue passing parameters from Python to an R function named "Contours". The below works.....
Python (testr.py)
import rpy2.robjects as robjects
robjects.r('''
source('Wrapper.R')
''')
r_myfunc = robjects.globalenv['Contours']
r_myfunc()
R (Wrapper.R)
source ('./DrawCompRecVark.R')
imageDirectory="./tmp/"
Contours <- function()
{
k=c(0,1)
sens=c(0.8, 0.9, 0.95, 0.995)
spec=0.8
prev=0.001
N=1
uniqueId=1
#graph
prepareSaveGraph(imageDirectory, "PPVkSensSpec-", uniqueId)
DrawSensSpec(k, sens, spec, prev, N)
dev.off()
#save the cNPV graph
prepareSaveGraph(imageDirectory, "cNPVkSensSpec-", uniqueId)
DrawVarcSpec(k, sens, spec, prev, N)
dev.off()
}
So as you can tell, my hard coding of the values in the R code works fine, it's the passing from Python to R that throws me. I tried this....
R function
Contours <- function(k, sens, spec, prev, N, uniqueId)
and trying to pass from Python like this....
r_myfunc( c(0,1), c(0.8, 0.9, 0.95, 0.995), 0.8, 0.001, 1, 986)
and
r_myfunc( "c(0,1)", "c(0.8, 0.9, 0.95, 0.995)", 0.8, 0.001, 1, 986)
Neither of which work. Has anyone encountered this before? Any pointers in the right direction would be greatly appreciated. JW
You can import an R source as if it was a package (see http://rpy.sourceforge.net/rpy2/doc-2.5/html/robjects_rpackages.html#importing-arbitrary-r-code-as-a-package)
import os
from rpy2.robjects.packages import SignatureTranslatedAnonymousPackage
with open('Wrapper.R') as fh:
rcode = os.linesep.join(fh.readlines())
wrapper = SignatureTranslatedAnonymousPackage(rcode, "wrapper")
Now to call the function Contours present in that namespace, you'll just use wrapper.Contours but you'll have to use Python syntax. In R scalars are vectors of length 1, but in Python scalars and sequences are quite different.
If you want to use R's c():
from rpy2.robjects.packages import importr
base = importr("base")
wrapper.Contours(base.c(0,1),
base.c(0.8, 0.9, 0.95, 0.995),
0.8, 0.001, 1, 986)
Otherwise:
from rpy2.robjects.vectors import IntVector, FloatVector
wrapper.Contours(IntVector((0,1)),
FloatVector((0.8, 0.9, 0.95, 0.995)),
0.8, 0.001, 1, 986)
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