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)  123 >>> >>> robjects.r.rm("pi") >>> print(robjects.r.pi)  3.1415926535897931
The class inherits from the class
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>
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)¶
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.
item – string (name/symbol)
- Return type:
object (as returned by
- items() Generator[Tuple[str, Sexp], None, None] ¶
Iterate through the symbols and associated objects in this R 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.
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)  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
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:  3 In local context b (masking a):  4 Back to local context a:  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.
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'))