Dear all,
I have been a long time rpy user. rpy is *very simple* to use in that
you essentially only need to remember two things:
1. Call a R function using r.func(). The only exception is to use _
for . in case that there is a dot in the function name (r.R_Version()
for R.Version() and r.dev_off() for dev.off()).
2. Call a R function or a long script using r('blah blah').
Because rpy2 is said to be replacing rpy. I had a quick look at the
rpy2 manual (I admit that I am positively impressed) and tried to use
rpy2 today. In one of my scripts, the first call is to a R.Version
function to determine its revision number. This is where the nightmare
began.
Using rpy, this is simply int(r.R_Version()['svn rev']). Please allow
me to quote and comment on what I have done. Note that this is using
Python 2.4.3, rpy2.0.3 on a Redhat RHEL5 system.
% python
Python 2.4.3 (#1, Sep 17 2008, 16:07:08)
[GCC 4.1.2 20071124 (Red Hat 4.1.2-41)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from rpy2.robjects import *
>>> r.R_Version()
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib64/python2.4/site-packages/rpy2/robjects/__init__.py",
line 511, in __getattribute__
raise orig_ae
AttributeError: 'R' object has no attribute 'R_Version'
>>> r.R.Version()
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib64/python2.4/site-packages/rpy2/robjects/__init__.py",
line 511, in __getattribute__
raise orig_ae
AttributeError: 'R' object has no attribute 'R'
The _ to . conversion is gone! Then I read
http://rpy.sourceforge.net/rpy2/doc/html/robjects.html and notice
that, to use such functions, I have to use rpy_classic.
>>> from rpy2.rpy_classic import *
>>> r.R_Version()
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib64/python2.4/site-packages/rpy2/rpy_classic.py", line
254, in __getattr__
res = self.__getitem__(name)
File "/usr/lib64/python2.4/site-packages/rpy2/rpy_classic.py", line
261, in __getitem__
res = rpy2py(res)
File "/usr/lib64/python2.4/site-packages/rpy2/rpy_classic.py", line
176, in rpy2py
raise ValueError("Invalid default mode.")
ValueError: Invalid default mode.
Well, I remember there was a mode thing in rpy, but BASIC_CONVERSION
was set by default. Anyway,
>>> set_default_mode(BASIC_CONVERSION)
>>> r.R_Version()
[['x86_64-redhat-linux-gnu'], ['x86_64'], ['linux-gnu'], ['x86_64,
linux-gnu'], [''], ['2'], ['7.1'], ['2008'], ['06'], ['23'],
['45970'], ['R'], ['R version 2.7.1 (2008-06-23)']]
But where is the 'svn rev' key?
In R, this function returns something like
> R.Version()
$platform
[1] "x86_64-redhat-linux-gnu"
$arch
[1] "x86_64"
$os
[1] "linux-gnu"
and rpy returns a dictionary, as expected.
>>> r.R_Version()
{'status': '', 'major': '2', 'version.string': 'R version 2.7.1
(2008-06-23)', 'language': 'R', 'os': 'linux-gnu', 'svn rev': '45970',
'system': 'x86_64, linux-gnu', 'month': '06', 'platform':
'x86_64-redhat-linux-gnu', 'year': '2008', 'arch': 'x86_64', 'day':
'23', 'minor': '7.1'}
Maybe the raw R object has more information?
>>> set_default_mode(NO_CONVERSION)
>>> r.R_Version()
<rpy2.rpy_classic.Robj object at 0x2b3f5bda4810>
>>> r.R_Version()[0]
<rpy2.rpy_classic.Robj object at 0x2b3f5bda4b90>
What is this? I admit that I am completely lost and do not know how to proceed.
Now, what about the old faithful r('R.Version()')? In rpy, I could do
>>> r('R.Version()')
{'status': '', 'major': '2', 'version.string': 'R version 2.7.1
(2008-06-23)', 'language': 'R', 'os': 'linux-gnu', 'svn rev': '45970',
'system': 'x86_64, linux-gnu', 'month': '06', 'platform':
'x86_64-redhat-linux-gnu', 'year': '2008', 'arch': 'x86_64', 'day':
'23', 'minor': '7.1'}
In rpy2,
>>> from rpy2.rpy_classic import *
>>> set_default_mode(NO_CONVERSION)
>>> r('R.Version()')
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib64/python2.4/site-packages/rpy2/rpy_classic.py", line
265, in __call__
return self.eval(self.parse(text=s))
File "/usr/lib64/python2.4/site-packages/rpy2/rpy_classic.py", line
199, in __call__
a = a.getSexp()
AttributeError: 'Robj' object has no attribute 'getSexp'
What about the robject mode?
>>> from rpy2.robjects import *
>>> r('R.Version()')
<RVector - Python:0x2b74072e0830 / R:0x20256eb8>
>>> r('R.Version()')[0]
<RVector - Python:0x2b740af211b8 / R:0x20a4db48>
>>> r('R.Version()')[0][0]
'x86_64-redhat-linux-gnu'
Looks better, it is a vector, but why the first element is [0][0], not [0]?
>>> print r('R.Version()')
$platform
[1] "x86_64-redhat-linux-gnu"
..
Great, the information is there, but how can I get 'svn rev'???
>>> print r('R.Version()').getnames()
[1] "platform" "arch" "os" "system"
[5] "status" "major" "minor" "year"
[9] "month" "day" "svn rev" "language"
[13] "version.string"
>>> print r('R.Version()')['svn rev']
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib64/python2.4/site-packages/rpy2/robjects/__init__.py",
line 266, in __getitem__
res = super(RVector, self).__getitem__(i)
TypeError: an integer is required
Finally, I found the subset function,
>>> r('R.Version()').subset('svn rev')
<RVector - Python:0x2b740af231b8 / R:0x20556ec8>
>>> print r('R.Version()').subset('svn rev')
$`svn rev`
[1] "45970"
but the only way to get the revision number seems to be
>>> r('R.Version()').subset('svn rev')[0][0]
'45970'
If the correct answer is r('R.Version()').subset('svn rev')[0][0], I
have to say that rpy2 is not for me. I can see that a lot of energy
has been devoted to make Python and R integrate better, but I do not
see any benefit from such an effort. In summary,
1. rpy_classic is not the same as rpy.
2. The R vector etc are too complicated to use, and I do not see any
benefit of using them.
3. The rpy_object stuff is almost useless without support for the . to
_ conversion, because there are so many functions in R with .
(dev.off(), as.xxxx()...).
I apologize if all these were due to my incorrect use of rpy2.
Bo
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