Calling R functions from Python using rpy2

Question

I have been following the instructions on Working with R's OOPS in the rpy2 documentation here: https://rpy2.readthedocs.io/en/version_2.8.x/robjects_oop.html. I am trying to create a Python class to call the function rfsrc in the R package randomForestSRC.

Under what conditions does this work? Does rpy2 have a fixed list of packages that it allows you to access and if so is randomForestSRC on this list?

When I run the code below from a Jupyter Notebook (Python 3, R 3.5.1), I get the error: Error in (function (f, signature = character(), where = topenv(parent.frame()), : no generic function found for 'rfsrc'

import rpy2.robjects.packages as rpackages
from rpy2.robjects.vectors import StrVector

utils = rpackages.importr('utils')
utils.chooseCRANmirror(ind=1) # select the first mirror in the list
packnames = ('randomForestSRC', 'survival', 'tidyverse', 'magrittr', 'ggRandomForests', 'mlr')
utils.install_packages(StrVector(packnames))

from rpy2.robjects.packages import importr
randomForestSRC = importr('randomForestSRC')
from rpy2.robjects.methods import RS4Auto_Type
import six

class rfsrc(six.with_metaclass(RS4Auto_Type)):
    __rname__ = 'rfsrc'
    __rpackagename__ = 'randomForestSRC'

What else do I need to do to get this to work?

I also tried the manual method as shown below and got the same error.

import rpy2.robjects as robjects
import rpy2.rinterface as rinterface
from rpy2.robjects.packages import importr

lme4 = importr("randomForestSRC")
getmethod = robjects.baseenv.get("getMethod")

StrVector = robjects.StrVector

class rfsrc(robjects.methods.RS4):

    _coef = getmethod("rfsrc", 
                  signature = StrVector(["rfsrc", ]),
                  where = "package:randomForestSRC")

    def _call_get(self):
        return self.do_slot("call")
    def _call_set(self, value):
        return self.do_slot("call", value)
    call = property(_call_get, _call_set, None, "Get or set the RS4 slot      'call'.")

    def coef(self):
        """ fitted coefficients """
        return self._coef(self)

lgautier · Accepted Answer · 2018-11-10 18:08:09Z

1

There are several questions. I picked the one that might be the origin of all others.

Does rpy2 have a fixed list of packages that it allows you to access and if so is randomForestSRC on this list?

rpy2 is only able to use the R packages available with your R installation. The documentation has something about installing R packages from Python (also, note the URL for the documentation of rpy2-2.9.x): https://rpy2.github.io/doc/v2.9.x/html/robjects_rpackages.html#installing-removing-r-packages

Edit:

The question was edited to now focus on the error message no generic function found for 'rfsrc'. The error is coming from R because no generic function called "rfsrc" was found.

I think that rfsrc is just a regular R function (not a generic, see https://github.com/cran/randomForestSRC/blob/master/R/rfsrc.R ). Also, I am not the packages randomForest uses S4 much, and the rpy2 features you are trying to use are specifically designed for R's S4 OOP system.

edited Nov 10, 2018 at 18:08

answered Nov 8, 2018 at 4:21

lgautier

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3 Comments

panda Over a year ago

Thanks. I have edited the code above to add the installation of packages, but I am still getting the error "Error in get0(cname, where, inherits = inherits) : invalid 'envir' argument". The packages were already installed in my copy of R and I had been loading them with R library calls, using the R Magic operator %%R.

panda Over a year ago

Thanks @lgautier. I have edited the question again as I am now getting the same error using both methods: Error in (function (f, signature = character(), where = topenv(parent.frame()), : no generic function found for 'rfsrc'. So my main question now is: does this error mean it is not possible to use this method to call the function rfsrc in the package randomForestSRC?

lgautier Over a year ago

Answered as an addendum to the existing answer.

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