Revision: 662
http://rpy.svn.sourceforge.net/rpy/?rev=662&view=rev
Author: lgautier
Date: 2008-10-25 17:26:39 +0000 (Sat, 25 Oct 2008)
Log Message:
-----------
- Added check in constructor for robjects.RDataFrame
- Edits in the doc regarding data frames
Modified Paths:
--------------
branches/rpy_nextgen/NEWS
branches/rpy_nextgen/doc/source/robjects.rst
branches/rpy_nextgen/rpy/robjects/__init__.py
branches/rpy_nextgen/rpy/robjects/tests/testRDataFrame.py
Modified: branches/rpy_nextgen/NEWS
===================================================================
--- branches/rpy_nextgen/NEWS 2008-10-20 18:37:54 UTC (rev 661)
+++ branches/rpy_nextgen/NEWS 2008-10-25 17:26:39 UTC (rev 662)
@@ -1,6 +1,13 @@
SVN
===
+Changes
+-------
+
+:mod:`rpy2.robjects`:
+
+- Constructor for :class:`rpy2.robjects.RDataFrame` checks that R lists are
data.frames (not all lists are data.frame)
+
Bugs fixed
----------
@@ -32,7 +39,7 @@
:mod:`rpy2.robjects`:
-- constructor for RDataFrame now now accepts either
:class:`rlike.container.TaggedList` or :class:`rinterface.SexpEnvironment`
+- constructor for RDataFrame now now accepts either
:class:`rlike.container.TaggedList` or :class:`rinterface.SexpVector`
:mod:`rpy2.rinterface`:
Modified: branches/rpy_nextgen/doc/source/robjects.rst
===================================================================
--- branches/rpy_nextgen/doc/source/robjects.rst 2008-10-20 18:37:54 UTC
(rev 661)
+++ branches/rpy_nextgen/doc/source/robjects.rst 2008-10-25 17:26:39 UTC
(rev 662)
@@ -286,18 +286,56 @@
A :class:`RMatrix` is a special case of :class:`RArray`.
-:class:`RDataFrame`
--------------------
+Data frames
+-----------
-A :class:`RDataFrame` represents the `R` class `data.frame`.
-Currently, the constructor is flagged as experimental.
-It accepts either a :class:`rinterface.SexpVector`
-(with :attr:`typeof` equal to *VECSXP*)
+Data frames are important data structures in R, as they are used to
+represent a data to analyze in a study in a relatively
+large nunmber of cases.
+
+A data frame can be thought of as a tabular representation of data,
+with one variable per column, and one data point per row. Each column
+is an R vector, which implies one type for all elements
+in one given column, and which allows for possibly different types across
+different columns.
+
+
+In :mod:`rpy2.robjects`,
+:class:`RDataFrame` represents the `R` class `data.frame`.
+
+Creating an :class:`RDataFrame` can be done by:
+
+* Using the constructor for the class
+
+* Create the data.frame through R
+
+The constructor for :class:`RDataFrame` accepts either a
+:class:`rinterface.SexpVector`
+(with :attr:`typeof` equal to *VECSXP*, that is an R `list`)
or an instance of class :class:`rpy2.rlike.container.TaggedList`.
>>> robjects.RDataFrame()
+
+Creating the data.frame in R can be achieved in numerous ways,
+as many R functions do return a data.frame.
+In this example, will use the R function `data.frame()`, that
+constructs a data.frame from named arguments
+
+>>> import array
+>>> d = {'value': robjects.IntSexpVector((1,2,3)),
+ 'letter': robjects.StrSexpVector(('x', 'y', 'z'))}
+>>> dataf = robjects.r['data.frame'](**d)
+>>> dataf.colnames()
+c("letter", "value")
+
+.. note::
+ The order of the columns `value` and `letter` cannot be conserved,
+ since we are using a Python dictionnary. This difference between
+ R and Python can be resolved by using TaggedList instances
+ (XXX add material about that).
+
.. autoclass:: rpy2.robjects.RDataFrame
:show-inheritance:
:members:
Modified: branches/rpy_nextgen/rpy/robjects/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/__init__.py 2008-10-20 18:37:54 UTC
(rev 661)
+++ branches/rpy_nextgen/rpy/robjects/__init__.py 2008-10-25 17:26:39 UTC
(rev 662)
@@ -330,7 +330,7 @@
def __init__(self, tlist):
""" Create a new data frame.
- :param tlist: TaggedList
+ :param tlist: rpy2.rlike.container.TaggedList or
rpy2.rinterface.SexpVector (and of class 'data.frame' for R)
"""
if isinstance(tlist, rlc.TaggedList):
df = baseNameSpaceEnv["data.frame"].rcall(tlist.items())
@@ -338,6 +338,8 @@
elif isinstance(tlist, rinterface.SexpVector):
if tlist.typeof != rinterface.VECSXP:
raise ValueError("tlist should of typeof VECSXP")
+ if not r['inherits'](tlist, 'data.frame')[0]:
+ raise ValueError('tlist should of R class "data.frame"')
super(RDataFrame, self).__init__(tlist)
else:
raise ValueError("tlist can be either"+
Modified: branches/rpy_nextgen/rpy/robjects/tests/testRDataFrame.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/tests/testRDataFrame.py 2008-10-20
18:37:54 UTC (rev 661)
+++ branches/rpy_nextgen/rpy/robjects/tests/testRDataFrame.py 2008-10-25
17:26:39 UTC (rev 662)
@@ -15,6 +15,17 @@
self.assertEquals("data.frame", df.rclass()[0])
+ def testNewFromRObject(self):
+ numbers = robjects.r('1:5')
+ self.assertRaises(ValueError, robjects.RDataFrame, numbers)
+
+ rlist = robjects.r('list(a=1, b=2, c=3)')
+ self.assertRaises(ValueError, robjects.RDataFrame, rlist)
+
+ rdataf = robjects.r('data.frame(a=1:2, b=c("a", "b"))')
+ dataf = robjects.RDataFrame(rdataf)
+
+
def testDim(self):
letters = robjects.r.letters
numbers = robjects.r('1:26')
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