Revision: 669
http://rpy.svn.sourceforge.net/rpy/?rev=669&view=rev
Author: lgautier
Date: 2008-10-30 21:03:28 +0000 (Thu, 30 Oct 2008)
Log Message:
-----------
robjects:
Formerly-new attribute is now gone. The doc points to rpy_classic if for
that kind of things
rinterface:
Fixed test for NA
doc:
Bumped target R-version in the doc to R-2.8
Modified Paths:
--------------
branches/rpy_nextgen/doc/source/introduction.rst
branches/rpy_nextgen/doc/source/overview.rst
branches/rpy_nextgen/doc/source/robjects.rst
branches/rpy_nextgen/doc/source/rpy_classic.rst
branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
branches/rpy_nextgen/rpy/robjects/__init__.py
branches/rpy_nextgen/rpy/robjects/tests/testRobjects.py
Modified: branches/rpy_nextgen/doc/source/introduction.rst
===================================================================
--- branches/rpy_nextgen/doc/source/introduction.rst 2008-10-29 20:39:25 UTC
(rev 668)
+++ branches/rpy_nextgen/doc/source/introduction.rst 2008-10-30 21:03:28 UTC
(rev 669)
@@ -208,3 +208,120 @@
More information on functions is in Section :ref:`robjects-functions`
+
+
+Examples
+========
+
+This section demonstrates some of the features of
+rpy2 by the example. The wiki on the sourceforge website
+will hopefully be used as a cookbook.
+
+
+.. code-block:: python
+
+ import rpy2.robjects as robjects
+ import array
+
+ r = robjects.r
+
+ x = array.array('i', range(10))
+ y = r.rnorm(10)
+
+ r.X11()
+
+ r.layout(r.matrix(array.array('i', [1,2,3,2]), nrow=2, ncol=2))
+ r.plot(r.runif(10), y, xlab="runif", ylab="foo/bar", col="red")
+
+ kwargs = {'ylab':"foo/bar", 'type':"b", 'col':"blue", 'log':"x"}
+ r.plot(x, y, **kwargs)
+
+.. note::
+ Since the named parameters are a Python :class:`dict`,
+ the order of the parameters is lost.
+
+
+Linear models
+-------------
+
+The R code is:
+
+.. code-block:: r
+
+ ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
+ trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
+ group <- gl(2, 10, 20, labels = c("Ctl","Trt"))
+ weight <- c(ctl, trt)
+
+ anova(lm.D9 <- lm(weight ~ group))
+
+ summary(lm.D90 <- lm(weight ~ group - 1))# omitting intercept
+
+One way to achieve the same with :mod:`rpy2.robjects` is
+
+.. code-block:: python
+
+ import rpy2.robjects as robjects
+
+ r = robjects.r
+
+ ctl =
robjects.FloatVector([4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14])
+ trt =
robjects.FloatVector([4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69])
+ group = r.gl(2, 10, 20, labels = ["Ctl","Trt"])
+ weight = ctl + trt
+
+ robjects.globalEnv["weight"] = weight
+ robjects.globalEnv["group"] = group
+ lm_D9 = r.lm("weight ~ group")
+ print(r.anova(lm_D9))
+
+ lm_D90 = r.lm("weight ~ group - 1")
+ print(r.summary(lm_D90))
+
+
+
+Principal component analysis
+----------------------------
+
+The R code is
+
+.. code-block:: r
+
+ m <- matrix(rnorm(100), ncol=5)
+ pca <- princomp(m)
+ plot(pca, main="Eigen values")
+ biplot(pca, main="biplot")
+
+The :mod:`rpy2.robjects` code is
+
+.. testcode::
+
+ import rpy2.robjects as robjects
+
+ r = robjects.r
+
+ m = r.matrix(r.rnorm(100), ncol=5)
+ pca = r.princomp(m)
+ r.plot(pca, main="Eigen values")
+ r.biplot(pca, main="biplot")
+
+
+
+S4 classes
+----------
+
+.. code-block:: python
+
+ import rpy2.robjects as robjects
+ import array
+
+ r = robjects.r
+
+ r.setClass("Track",
+ r.representation(x="numeric", y="numeric"))
+
+ a = r.new("Track", x=0, y=1)
+
+ a.x
+
+
Modified: branches/rpy_nextgen/doc/source/overview.rst
===================================================================
--- branches/rpy_nextgen/doc/source/overview.rst 2008-10-29 20:39:25 UTC
(rev 668)
+++ branches/rpy_nextgen/doc/source/overview.rst 2008-10-30 21:03:28 UTC
(rev 669)
@@ -41,14 +41,12 @@
Python version 2.4 or higher, and R-2.7.0 or higher are required.
-Although the development was done with R-2.7.2 and Python-2.5.2,
-it has also been tested with:
+Although the development was first done with R-2.7.2 (now with R-2.8.0)
+and Python-2.5.2, it has also been tested with:
- * R-2.8.0
-
* Python-2.6.0 (numpy-support not tested)
-Gcc-4.2.3 was used for compiling the C parts.
+Gcc-4.2.3, then gcc-4.2.4 were used for compiling the C parts.
Download
Modified: branches/rpy_nextgen/doc/source/robjects.rst
===================================================================
--- branches/rpy_nextgen/doc/source/robjects.rst 2008-10-29 20:39:25 UTC
(rev 668)
+++ branches/rpy_nextgen/doc/source/robjects.rst 2008-10-30 21:03:28 UTC
(rev 669)
@@ -65,18 +65,19 @@
This approach has limitation as:
- * The actual Python attributes for the object masks the R elements
+* The actual Python attributes for the object masks the R elements
- * '.' (dot) is syntactically valid in names for R objects, but not for
+* '.' (dot) is syntactically valid in names for R objects, but not for
python objects.
-That last limitation can partly be removed by setting the attribute
-:attr:`_dotter` from False to True.
+That last limitation can partly be removed by using :mod:`rpy.rpy_classic` if
+this feature matters most to you.
>>> robjects.r.as_null
# AttributeError raised
->>> robjects.r._dotter = True
->>> robjects.r.as_null
+>>> import rpy2.rpy_classic as rpy
+>>> rpy.set_default_mode(NO_CONVERSION)
+>>> rpy.r.as_null
# R function as.null() returned
.. warning::
@@ -92,11 +93,10 @@
2. Check if the attribute is can be accessed in R, starting from `globalEnv`
- 3. If :attr:`_dotter` is True, turn all `_` into `.` and repeat the step
above
+When safety matters most, or when getting extraordinary funds for a bailout
+is unlikely, we recommed using :meth:`__getitem__` to get
+a given R object (and store it in a python variable if wanted):
-When safety matters most, we recommed using :meth:`__getitem__` to get
-and R object (and store it in a python variable if wanted):
-
>>> as_null = robjects.r['as.null']
@@ -124,7 +124,10 @@
>>> x = robjects.r.rnorm(100)
>>> robjects.r('hist(%s, xlab="x", main="hist(x)")' %repr(x))
+.. warning::
+ Doing this with large objects might not be the best use of
+ your computing power.
.. index::
pair: robjects;RObject
@@ -571,119 +574,3 @@
.. autofunction:: rpy2.robjects.default_py2ro
-Examples
-========
-
-This section demonstrates some of the features of
-rpy2 by the example. The wiki on the sourceforge website
-will hopefully be used as a cookbook.
-
-
-.. code-block:: python
-
- import rpy2.robjects as robjects
- import array
-
- r = robjects.r
-
- x = array.array('i', range(10))
- y = r.rnorm(10)
-
- r.X11()
-
- r.layout(r.matrix(array.array('i', [1,2,3,2]), nrow=2, ncol=2))
- r.plot(r.runif(10), y, xlab="runif", ylab="foo/bar", col="red")
-
- kwargs = {'ylab':"foo/bar", 'type':"b", 'col':"blue", 'log':"x"}
- r.plot(x, y, **kwargs)
-
-.. note::
- Since the named parameters are a Python :class:`dict`,
- the order of the parameters is lost.
- Check :meth:`rpy2.rinterface.SexpClosure.rcall`
- to know how to keep the order of parameters.
-
-Linear models
--------------
-
-The R code is:
-
-.. code-block:: r
-
- ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
- trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
- group <- gl(2, 10, 20, labels = c("Ctl","Trt"))
- weight <- c(ctl, trt)
-
- anova(lm.D9 <- lm(weight ~ group))
-
- summary(lm.D90 <- lm(weight ~ group - 1))# omitting intercept
-
-One way to achieve the same with :mod:`rpy2.robjects` is
-
-.. code-block:: python
-
- import rpy2.robjects as robjects
-
- r = robjects.r
-
- ctl =
robjects.FloatVector([4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14])
- trt =
robjects.FloatVector([4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69])
- group = r.gl(2, 10, 20, labels = ["Ctl","Trt"])
- weight = ctl + trt
-
- robjects.globalEnv["weight"] = weight
- robjects.globalEnv["group"] = group
- lm_D9 = r.lm("weight ~ group")
- print(r.anova(lm_D9))
-
- lm_D90 = r.lm("weight ~ group - 1")
- print(r.summary(lm_D90))
-
-
-
-Principal component analysis
-----------------------------
-
-The R code is
-
-.. code-block:: r
-
- m <- matrix(rnorm(100), ncol=5)
- pca <- princomp(m)
- plot(pca, main="Eigen values")
- biplot(pca, main="biplot")
-
-The :mod:`rpy2.robjects` code is
-
-.. testcode::
-
- import rpy2.robjects as robjects
-
- r = robjects.r
-
- m = r.matrix(r.rnorm(100), ncol=5)
- pca = r.princomp(m)
- r.plot(pca, main="Eigen values")
- r.biplot(pca, main="biplot")
-
-
-
-S4 classes
-----------
-
-.. code-block:: python
-
- import rpy2.robjects as robjects
- import array
-
- r = robjects.r
-
- r.setClass("Track",
- r.representation(x="numeric", y="numeric"))
-
- a = r.new("Track", x=0, y=1)
-
- a.x
-
-
Modified: branches/rpy_nextgen/doc/source/rpy_classic.rst
===================================================================
--- branches/rpy_nextgen/doc/source/rpy_classic.rst 2008-10-29 20:39:25 UTC
(rev 668)
+++ branches/rpy_nextgen/doc/source/rpy_classic.rst 2008-10-30 21:03:28 UTC
(rev 669)
@@ -14,7 +14,7 @@
To match examples and documentation for *rpy*,
we load the module as:
->>> from rpy2.rpy_classic import *
+>>> import rpy2.rpy_classic as rpy
.. index::
single: conversion
@@ -28,36 +28,36 @@
existing in *rpy* is provided, and the default
mode can be set with :func:`set_default_mode`:
->>> set_default_mode(NO_CONVERSION)
->>> set_default_mode(BASIC_CONVERSION)
+>>> rpy.set_default_mode(rpy.NO_CONVERSION)
+>>> rpy.set_default_mode(rpy.BASIC_CONVERSION)
R instance
==========
The ``r`` instance of class :class:`R` behaves like before:
->>> r.help
+>>> rpy.r.help
'dots' in the R name are translated to underscores:
->>> r.wilcox_test
+>>> rpy.r.wilcox_test
->>> r.wilcox_test([1,2,3], [4,5,6])
+>>> rpy.r.wilcox_test([1,2,3], [4,5,6])
->>> x = r.seq(1, 3, by=0.5)
->>> r.plot(x)
+>>> x = rpy.r.seq(1, 3, by=0.5)
+>>> rpy.r.plot(x)
An example::
degrees = 4
- grid = r.seq(0, 10, length=100)
- values = [r.dchisq(x, degrees) for x in grid]
- r.par(ann=0)
- r.plot(grid, values, type='l')
+ grid = rpy.r.seq(0, 10, length=100)
+ values = [rpy.r.dchisq(x, degrees) for x in grid]
+ rpy.r.par(ann=0)
+ rpy.r.plot(grid, values, type='l')
- r.library('splines')
+ rpy.r.library('splines')
- type(r.seq)
+ type(rpy.r.seq)
.. index::
pair: rpy_classic;function
@@ -67,29 +67,29 @@
As in RPy-1.x, all R objects are callable:
->>> callable(r.seq)
+>>> callable(rpy.r.seq)
True
->>> callable(r.pi)
+>>> callable(rpy.r.pi)
True
>>>
If an object is not a R function, a :class:`RuntimeError`
is thrown by R whenever called:
->>> r.pi()
+>>> rpy.r.pi()
The function are called like regular Python functions:
->>> r.seq(1, 3)
->>> r.seq(1, 3, by=0.5)
->>> r['options'](show_coef_Pvalues=0)
+>>> rpy.r.seq(1, 3)
+>>> rpy.r.seq(1, 3, by=0.5)
+>>> rpy.r['options'](show_coef_Pvalues=0)
>>>
->>> m = r.matrix(r.rnorm(100), 20, 5)
->>> pca = r.princomp(m)
->>> r.plot(pca, main = "PCA")
+>>> m = rpy.r.matrix(r.rnorm(100), 20, 5)
+>>> pca = rpy.r.princomp(m)
+>>> rpy.r.plot(pca, main = "PCA")
>>>
Modified: branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
2008-10-29 20:39:25 UTC (rev 668)
+++ branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
2008-10-30 21:03:28 UTC (rev 669)
@@ -98,7 +98,7 @@
ok = isCharacter(sexp)[0]
self.assertTrue(ok)
- ri.NA_STRING[0]
+ self.assertRaises(ValueError, ri.NA_STRING.__getitem__, 0)
def testNewUnicode(self):
sexp = ri.SexpVector([u'abc', ], ri.STRSXP)
Modified: branches/rpy_nextgen/rpy/robjects/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/__init__.py 2008-10-29 20:39:25 UTC
(rev 668)
+++ branches/rpy_nextgen/rpy/robjects/__init__.py 2008-10-30 21:03:28 UTC
(rev 669)
@@ -473,7 +473,6 @@
class R(object):
_instance = None
- _dotter = False
def __init__(self):
if R._instance is None:
@@ -492,17 +491,8 @@
try:
return self[attr]
except LookupError, le:
- pass
+ raise orig_ae
- if self._dotter:
- attr = attr.replace('_', '.')
- try:
- return self[attr]
- except LookupError, le:
- pass
-
- raise orig_ae
-
def __getitem__(self, item):
res = rinterface.globalEnv.get(item)
Modified: branches/rpy_nextgen/rpy/robjects/tests/testRobjects.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/tests/testRobjects.py 2008-10-29
20:39:25 UTC (rev 668)
+++ branches/rpy_nextgen/rpy/robjects/tests/testRobjects.py 2008-10-30
21:03:28 UTC (rev 669)
@@ -27,13 +27,6 @@
for i, li in enumerate(myList):
self.assertEquals(i, myList[i][0])
-
- def testGetAttr(self):
- robjects.r._dotter = True
- self.assertRaises(LookupError, robjects.r.__getitem__, 'as_null')
- res = robjects.r.as_null
- self.assertTrue(isinstance(res, rinterface.SexpClosure))
-
def testEval(self):
# vector long enough to span across more than one line
x = robjects.baseNameSpaceEnv['seq'](1, 50, 2)
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