rpy_classic

This module provides an API similar to the one in RPy-1.x (rpy).

Warning

The implementation of the RPy-1.x characteristics is incomplete. This is likely not due to limitations in the low-level interface rpy2.rinterface but due to limited time from this author, and from limited contributions to get it improved.

To match examples and documentation for rpy, we load the module as:

>>> import rpy2.rpy_classic as rpy

Conversion

Although the proposed high-level interface in rpy2.robjects does not need explicit conversion settings, the conversion system existing in rpy is provided, and the default mode can be set with set_default_mode():

>>> rpy.set_default_mode(rpy.NO_CONVERSION)
>>> rpy.set_default_mode(rpy.BASIC_CONVERSION)

R instance

The r instance of class R behaves like before:

>>> rpy.r.help

‘dots’ in the R name are translated to underscores:

>>> rpy.r.wilcox_test

>>> rpy.r.wilcox_test([1,2,3], [4,5,6])

>>> x = rpy.r.seq(1, 3, by=0.5)
>>> rpy.r.plot(x)

An example:

degrees = 4
grid = rpy.r.seq(0, 10, length=100)
values = [rpy.r.dchisq(x, degrees) for x in grid]
rpy.r.par(ann=0)
rpy.r.plot(grid, values, type='l')

rpy.r.library('splines')

type(rpy.r.seq)

Functions

As in RPy-1.x, all R objects are callable:

>>> callable(rpy.r.seq)
True
>>> callable(rpy.r.pi)
True
>>>

If an object is not a R function, a RuntimeError is thrown by R whenever called:

>>> rpy.r.pi()

The function are called like regular Python functions:

>>> rpy.r.seq(1, 3)
>>> rpy.r.seq(1, 3, by=0.5)
>>> rpy.r['options'](show_coef_Pvalues=0)
>>>

>>> m = rpy.r.matrix(r.rnorm(100), 20, 5)
>>> pca = rpy.r.princomp(m)
>>> rpy.r.plot(pca, main = "PCA")
>>>

Partial use of rpy_classic

The use of rpy_classic does not need to be exclusive of the other interface(s) proposed in rpy2.

Chaining code designed for either of the interfaces is rather easy and, among other possible use-cases, should make the inclusion of legacy rpy code into newly written rpy2 code a simple take.

The link between rpy_classic and the rest of rpy2 is the property RObj.sexp, that give the representation of the underlying R object in the low-level rpy2.rinterface definition. This representation can then be used in function calls with rpy2.rinterface and rpy2.robjects. With rpy2.robjects, a conversion using rpy2.robjects.default_ri2py() can be considered.

Note

Obviously, that property sexp is not part of the original Robj in rpy.

An example:

import rpy2.robjects as ro
import rpy2.rpy_classic as rpy
rpy.set_default_mode(rpy.NO_CONVERSION)


def legacy_paste(v):
    # legacy rpy code
    res = rpy.r.paste(v, collapse = '-')
    return res


rletters = ro.r['letters']

# the legaxy code is called using an rpy2.robjects object
alphabet_rpy = legacy_paste(rletters)

# convert the resulting rpy2.rpy_classic object to
# an rpy2.robjects object
alphabet = ro.default_ri2py(alphabet_rpy.sexp)