Environments

R environments can be described to the Python user as an hybrid of a dictionary and a scope.

The first of all environments is called the Global Environment, that can also be referred to as the R workspace.

An R environment in RPy2 can be seen as a kind of Python dictionnary.

Assigning a value to a symbol in an environment has been made as simple as assigning a value to a key in a Python dictionary:

>>> robjects.r.ls(globalenv)
>>> robjects.globalenv["a"] = 123
>>> print(robjects.r.ls(globalenv))

Care must be taken when assigning objects into an environment such as the Global Environment, as this can hide other objects with an identical name. The following example should make one measure that this can mean trouble if no care is taken:

>>> globalenv["pi"] = 123
>>> print(robjects.r.pi)
[1] 123
>>>
>>> robjects.r.rm("pi")
>>> print(robjects.r.pi)
[1] 3.1415926535897931

The class inherits from the class rpy2.rinterface.SexpEnvironment.

An environment is also iter-able, returning all the symbols (keys) it contains:

>>> env = robjects.r.baseenv()
>>> [x for x in env]
<a long list returned>

Note

Although there is a natural link between environment and R packages, one should consider using the convenience wrapper dedicated to model R packages (see R packages).

class rpy2.robjects.Environment(o=None)

Bases: RObjectMixin, SexpEnvironment

An R environement, implementing Python’s mapping interface.

clear() → None.  Remove all items from D.

find(item: str, wantfun: bool = False)

Find an item, starting with this R environment.

Raises a KeyError if the key cannot be found.

This method is called find because it is somewhat different from the method get() in Python mappings such dict. This is looking for a key across enclosing environments, returning the first key found.

Parameters:

item – string (name/symbol)

Return type:

object (as returned by conversion.converter.rpy2py())

items() → Generator[Tuple[str, Sexp], None, None]

Iterate through the symbols and associated objects in this R environment.

keys() → Generator[str, None, None]

Return an iterator over keys in the environment.

pop(k[, d]) → v, remove the specified key

and return the corresponding value. If the key is not found, d is returned if given, otherwise KeyError is raised.

popitem() -> (k, v), remove and return some (key, value)

pair as a 2-tuple; but raise KeyError if E is empty.

values() → Generator[Sexp, None, None]

Iterate through the objects in this R environment.

Environments as (temporary) local contexts

Environments are like nested boxes, each with an arbritrary number of symbols (the objects names) bound to objects (the actual code or data associated with the symbol). The topmost environment is globalenv (.GlobalEnv in R).

When looking for a symbol, R will normally start looking for it in a starting environment, and if it does not find it it will look for it the enclosing (parent) environment. This is will repeat until the symbol is found or globalenv is reached and there is no more environment to search.

The evaluation of R code can be given a starting environment, and this can be an alternative from cluttering globalenv.

To illustrate this, we have an R code that adds one to a value y it has to find somewhere in its evaluation context.

>>> res = robjects.r('y + 1')
RRuntimeError: Error in (function (expr, envir = parent.frame(), enclos = if (is.list(envir) ||  :
  object 'y' not found

Evaluating that code when no y can be found results in an error message.

Adding a y to globalenv solves the issue:

>>> robjects.globalenv['y'] = 2
>>> res = robjects.r('y + 1')
>>> print(res)
[1] 3

This is happening because globalenv is the environment where our function was defined (its closure).

However, we could also an other environment.

There as several mechanisms to do that, and one them is to use rpy2.robjects.environments.local_context() (also available as rpy2.robjects.local_context()). It provides an easy way to temporarily set evaluation contexts.

rsrc = 'y + 1'
if 'y' in robjects.globalenv:
    del(robjects.globalenv['y'])
with robjects.local_context() as lc_a:
    lc_a['y'] = 2
    print('In local context a:')
    print(robjects.r(rsrc))
    with robjects.local_context() as lc_b:
        lc_b['y'] = 3
        print('In local context b (masking a):')
        print(robjects.r(rsrc))
    print('Back to local context a:')
    print(robjects.r(rsrc))

The result is:

In local context a:
[1] 3

In local context b (masking a):
[1] 4

Back to local context a:
[1] 3

Being able to do this is particularly helpful with R functions that like to report the full data content when anonymous objects are used. This is the case for a lot of the statistical modeling code in R’s standard library. A local context can help with binding the object to a symbol while R code is evaluated.

Note

The function rpy2.robjects.rl() will turn a string into an unevaluated R language object. To know more, see Section R language.

from rpy2.robjects.packages import importr
from rpy2.robjects import rl

stats = importr('stats')
mtcars = robjects.r('mtcars')
with robjects.local_context() as lc:
    lc['mtcars'] = mtcars
    fit = stats.lm('mpg ~ gear', data=rl('mtcars'))