Revision: 725
http://rpy.svn.sourceforge.net/rpy/?rev=725&view=rev
Author: lgautier
Date: 2008-12-20 10:49:58 +0000 (Sat, 20 Dec 2008)
Log Message:
-----------
- Edits to the doc
rlike:
- pop() for TaggedList now returns the "popped" element
robjects:
- rclass is now a property (and the original rclass moved to getrclass())
- names is now a property
Modified Paths:
--------------
rpy2/branches/version_2.0.x/NEWS
rpy2/branches/version_2.0.x/doc/source/conf.py
rpy2/branches/version_2.0.x/doc/source/introduction.rst
rpy2/branches/version_2.0.x/doc/source/overview.rst
rpy2/branches/version_2.0.x/doc/source/rlike.rst
rpy2/branches/version_2.0.x/doc/source/robjects.rst
rpy2/branches/version_2.0.x/rpy/rlike/container.py
rpy2/branches/version_2.0.x/rpy/rlike/tests/test_container.py
rpy2/branches/version_2.0.x/rpy/robjects/__init__.py
rpy2/branches/version_2.0.x/rpy/robjects/tests/testRDataFrame.py
rpy2/branches/version_2.0.x/rpy/robjects/tests/testRFormula.py
rpy2/branches/version_2.0.x/rpy/robjects/tests/testRObject.py
Modified: rpy2/branches/version_2.0.x/NEWS
===================================================================
--- rpy2/branches/version_2.0.x/NEWS 2008-12-19 21:53:06 UTC (rev 724)
+++ rpy2/branches/version_2.0.x/NEWS 2008-12-20 10:49:58 UTC (rev 725)
@@ -2,6 +2,23 @@
Release 2.0.1
=============
+New features
+------------
+
+:mod:`rpy2.robjects`:
+
+- Property `names` for the :class:`RVector` methods :meth:`getnames`
+ and :meth:`setnames` (this was likely forgotten for Release 2.0.0).
+
+- Property `rclass` for :class:`RObjectMixin`
+
+Changes
+-------
+
+:mod:`rpy2.robjects`:
+
+- :meth:`rclass` becomes :meth:`getrclass`
+
Bugs fixed
----------
@@ -11,6 +28,14 @@
- Setup.py has no longer a (possibly outdated) static hardcoded version number
for rpy2
+- Testing no longer stops with an error in the absence of the third-party
+ module :mod:`numpy`
+
+- :meth:`rpy2.rlike.container.TaggedList.pop` is now returning the element
+ matching the given index
+
+
+
Release 2.0.0
=============
Modified: rpy2/branches/version_2.0.x/doc/source/conf.py
===================================================================
--- rpy2/branches/version_2.0.x/doc/source/conf.py 2008-12-19 21:53:06 UTC
(rev 724)
+++ rpy2/branches/version_2.0.x/doc/source/conf.py 2008-12-20 10:49:58 UTC
(rev 725)
@@ -45,7 +45,7 @@
# The short X.Y version.
version = '2.0'
# The full version, including alpha/beta/rc tags.
-release = '2.0.0'
+release = '2.0.1'
releaselevel = ''
# There are two options for replacing |today|: either, you set today to some
Modified: rpy2/branches/version_2.0.x/doc/source/introduction.rst
===================================================================
--- rpy2/branches/version_2.0.x/doc/source/introduction.rst 2008-12-19
21:53:06 UTC (rev 724)
+++ rpy2/branches/version_2.0.x/doc/source/introduction.rst 2008-12-20
10:49:58 UTC (rev 725)
@@ -50,8 +50,14 @@
>>> robjects.r['pi']
3.14159265358979
+.. note::
+ Under the hood, the variable `pi` is gotten by default from the
+ R *base* package, unless an other variable with the name `pi` was
+ created in the `globalEnv`. The Section :ref:`robjects-environments`
+ tells more about that.
+
Evaluating R code
-----------------
@@ -106,7 +112,14 @@
`f`. That function `f` is present in the R `Global Environement`, and can
be accessed with the `__getitem__` mechanism outlined above:
+>>> robjects.globalEnv['f']
+function (r)
+{
+ 2 * pi * r
+}
+or
+
>>> robjects.r['f']
function (r)
{
@@ -207,7 +220,7 @@
By default, calling R functions will return R objects.
-More information on functions is in Section :ref:`robjects-functions`
+More information on functions is in Section :ref:`robjects-functions`.
Examples
@@ -234,12 +247,18 @@
r.layout(r.matrix(robjects.IntVector([1,2,3,2]), nrow=2, ncol=2))
r.plot(r.runif(10), y, xlab="runif", ylab="foo/bar", col="red")
+Setting dynamically the number of arguments in a function call can be
+done the usual way in python
+
+.. code-block:: python
+
+ args = [x, y]
kwargs = {'ylab':"foo/bar", 'type':"b", 'col':"blue", 'log':"x"}
- r.plot(x, y, **kwargs)
+ r.plot(*args, **kwargs)
.. note::
Since the named parameters are a Python :class:`dict`,
- the order of the parameters is lost.
+ the order of the parameters is lost for `**kwargs` arguments.
Linear models
@@ -279,8 +298,37 @@
lm_D90 = r.lm("weight ~ group - 1")
print(r.summary(lm_D90))
+Q:
+ Now how extract data from the resulting objects ?
+
+A:
+ The same, never it is. On the R object all depends.
+
+When taking the results from the code above, one could go like:
+
+>>> print(lm_D9.rclass)
+[1] "lm"
+
+Here the resulting object is a list structure, as either inspecting
+the data structure or reading the R man pages for `lm` would tell us.
+Checking its element names is then trivial:
+
+>>> print(lm_D9.names)
+ [1] "coefficients" "residuals" "effects" "rank"
+ [5] "fitted.values" "assign" "qr" "df.residual"
+ [9] "contrasts" "xlevels" "call" "terms"
+[13] "model"
+
+And so is extracting a particular element:
+
+>>> print(lm_D9.r['coefficients'])
+$coefficients
+(Intercept) groupTrt
+ 5.032 -0.371
+
+More about extracting elements from vectors is available
+at :ref:`robjects-vectors-indexing`.
-
Principal component analysis
----------------------------
Modified: rpy2/branches/version_2.0.x/doc/source/overview.rst
===================================================================
--- rpy2/branches/version_2.0.x/doc/source/overview.rst 2008-12-19 21:53:06 UTC
(rev 724)
+++ rpy2/branches/version_2.0.x/doc/source/overview.rst 2008-12-20 10:49:58 UTC
(rev 725)
@@ -159,8 +159,13 @@
matter most. Here the programmer gets close(r) to R's C-level
API.
+:mod:`rpy2.rlike`
+^^^^^^^^^^^^^^^^^
+Data structures and functions to mimic some of R's features and specificities
+
+
Design notes
------------
Modified: rpy2/branches/version_2.0.x/doc/source/rlike.rst
===================================================================
--- rpy2/branches/version_2.0.x/doc/source/rlike.rst 2008-12-19 21:53:06 UTC
(rev 724)
+++ rpy2/branches/version_2.0.x/doc/source/rlike.rst 2008-12-20 10:49:58 UTC
(rev 725)
@@ -119,13 +119,11 @@
(although more flexibility can be achieved using their
method :meth:`iterontags`):
-
>>> import rpy2.rlike.container as rlc
>>> tl = rlc.TaggedList([1, 2, 3], tags = ('a', 'b', 'a'))
>>> rlf.tapply(tl, tl.tags(), sum)
[('a', 4), ('b', 2)]
-
.. module:: rpy2.rlike.indexing
Indexing
@@ -133,16 +131,18 @@
Much of the R-style indexing can be achieved with Python's list comprehension:
->>> x = ('a', 'b', 'c')
->>> x_i = (0, 2)
->>> [x[i] for i in x_i]
+>>> l = ('a', 'b', 'c')
+>>> l_i = (0, 2)
+>>> [l[i] for i in l_i]
['a', 'c']
In `R`, negative indexes mean that values should be excluded. Again,
-list comprehension can be used:
+list comprehension can be used (although this is not the most efficient way):
->>> x = ('a', 'b', 'c')
->>> x_i = (0, 2)
+>>> l = ('a', 'b', 'c')
+>>> l_i = (-1, -2)
+>>> [x for i, x in enumerate(l) if -i not in l_i]
+['a']
.. function:: order(seq, cmp = default_cmp, reverse = False)
@@ -161,4 +161,4 @@
>>> o
[0, 2, 1]
>>> [x[i] for i in o]
-['a', 'b', 'c']
\ No newline at end of file
+['a', 'b', 'c']
Modified: rpy2/branches/version_2.0.x/doc/source/robjects.rst
===================================================================
--- rpy2/branches/version_2.0.x/doc/source/robjects.rst 2008-12-19 21:53:06 UTC
(rev 724)
+++ rpy2/branches/version_2.0.x/doc/source/robjects.rst 2008-12-20 10:49:58 UTC
(rev 725)
@@ -220,6 +220,8 @@
.. index::
pair: RVector;indexing
+.. _robjects-vectors-indexing:
+
Indexing
--------
@@ -393,6 +395,8 @@
:members:
+.. _robjects-environments:
+
Environments
============
Modified: rpy2/branches/version_2.0.x/rpy/rlike/container.py
===================================================================
--- rpy2/branches/version_2.0.x/rpy/rlike/container.py 2008-12-19 21:53:06 UTC
(rev 724)
+++ rpy2/branches/version_2.0.x/rpy/rlike/container.py 2008-12-20 10:49:58 UTC
(rev 725)
@@ -246,13 +246,26 @@
yield tag
def pop(self, index=None):
+ """
+ Pop the item at a given index out of the list
+
+ :param index: integer
+
+ """
if index is None:
index = len(self) - 1
- super(TaggedList, self).pop(index)
+ res = super(TaggedList, self).pop(index)
self.__tags.pop(index)
+ return res
def remove(self, value):
+ """
+ Remove a given value from the list.
+
+ :param value: object
+
+ """
found = False
for i in xrange(len(self)):
if self[i] == value:
@@ -262,6 +275,7 @@
self.pop(i)
def reverse(self):
+ """ Reverse the order of the elements in the list. """
super(TaggedList, self).reverse()
self.__tags.reverse()
Modified: rpy2/branches/version_2.0.x/rpy/rlike/tests/test_container.py
===================================================================
--- rpy2/branches/version_2.0.x/rpy/rlike/tests/test_container.py
2008-12-19 21:53:06 UTC (rev 724)
+++ rpy2/branches/version_2.0.x/rpy/rlike/tests/test_container.py
2008-12-20 10:49:58 UTC (rev 725)
@@ -186,12 +186,14 @@
tv = [1,2,3]
tl = rlc.TaggedList(tv, tags = tn)
self.assertEquals(3, len(tl))
- tl.pop()
+ elt = tl.pop()
+ self.assertEquals(3, elt)
self.assertEquals(2, len(tl))
self.assertEquals(tl.tags(), ('a', 'b'))
self.assertEquals(tuple(tl), (1, 2))
- tl.pop(0)
+ elt = tl.pop(0)
+ self.assertEquals(1, elt)
self.assertEquals(1, len(tl))
self.assertEquals(tl.tags(), ('b', ))
Modified: rpy2/branches/version_2.0.x/rpy/robjects/__init__.py
===================================================================
--- rpy2/branches/version_2.0.x/rpy/robjects/__init__.py 2008-12-19
21:53:06 UTC (rev 724)
+++ rpy2/branches/version_2.0.x/rpy/robjects/__init__.py 2008-12-20
10:49:58 UTC (rev 725)
@@ -144,10 +144,11 @@
"""
return repr_robject(self, linesep='\n')
- def rclass(self):
+ def getrclass(self):
""" Return the name of the R class for the object. """
return baseNameSpaceEnv["class"](self)
+ rclass = property(getrclass)
class RObject(RObjectMixin, rinterface.Sexp):
""" Base class for all R objects. """
@@ -283,6 +284,10 @@
res = r["names<-"](self, value)
return res
+ names = property(getnames, setnames,
+ "Names for the items in the vector.")
+
+
class StrVector(RVector):
""" Vector of string elements """
def __init__(self, obj):
Modified: rpy2/branches/version_2.0.x/rpy/robjects/tests/testRDataFrame.py
===================================================================
--- rpy2/branches/version_2.0.x/rpy/robjects/tests/testRDataFrame.py
2008-12-19 21:53:06 UTC (rev 724)
+++ rpy2/branches/version_2.0.x/rpy/robjects/tests/testRDataFrame.py
2008-12-20 10:49:58 UTC (rev 725)
@@ -13,7 +13,7 @@
df = robjects.RDataFrame(rlc.TaggedList((letters, numbers),
tags = ('letters', 'numbers')))
- self.assertEquals("data.frame", df.rclass()[0])
+ self.assertEquals("data.frame", df.rclass[0])
def testNewFromRObject(self):
numbers = robjects.r('1:5')
Modified: rpy2/branches/version_2.0.x/rpy/robjects/tests/testRFormula.py
===================================================================
--- rpy2/branches/version_2.0.x/rpy/robjects/tests/testRFormula.py
2008-12-19 21:53:06 UTC (rev 724)
+++ rpy2/branches/version_2.0.x/rpy/robjects/tests/testRFormula.py
2008-12-20 10:49:58 UTC (rev 725)
@@ -6,12 +6,12 @@
def testNew(self):
fml = robjects.RFormula("y ~ x")
- self.assertEquals("formula", fml.rclass()[0])
+ self.assertEquals("formula", fml.rclass[0])
def testGetenvironment(self):
fml = robjects.RFormula("y ~ x")
env = fml.getenvironment()
- self.assertEquals("environment", env.rclass()[0])
+ self.assertEquals("environment", env.rclass[0])
def testSetenvironment(self):
fml = robjects.RFormula("y ~ x")
Modified: rpy2/branches/version_2.0.x/rpy/robjects/tests/testRObject.py
===================================================================
--- rpy2/branches/version_2.0.x/rpy/robjects/tests/testRObject.py
2008-12-19 21:53:06 UTC (rev 724)
+++ rpy2/branches/version_2.0.x/rpy/robjects/tests/testRObject.py
2008-12-20 10:49:58 UTC (rev 725)
@@ -32,11 +32,11 @@
def testRclass(self):
self.assertEquals("character",
- robjects.baseNameSpaceEnv["letters"].rclass()[0])
+ robjects.baseNameSpaceEnv["letters"].rclass[0])
self.assertEquals("numeric",
- robjects.baseNameSpaceEnv["pi"].rclass()[0])
+ robjects.baseNameSpaceEnv["pi"].rclass[0])
self.assertEquals("function",
- robjects.globalEnv.get("help").rclass()[0])
+ robjects.globalEnv.get("help").rclass[0])
def testDo_slot(self):
self.assertEquals("A1.4, p. 270",
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