Revision: 663
http://rpy.svn.sourceforge.net/rpy/?rev=663&view=rev
Author: lgautier
Date: 2008-10-26 14:09:49 +0000 (Sun, 26 Oct 2008)
Log Message:
-----------
doc:
- Added short introduction
rpy2:
- added __version__
rpy2.rinterface:
- Added class BoolSexpVector
rpy2.robjects:
- Added classes BoolVector, IntVector, FloatVector, StrVector
Modified Paths:
--------------
branches/rpy_nextgen/NEWS
branches/rpy_nextgen/doc/source/index.rst
branches/rpy_nextgen/doc/source/robjects.rst
branches/rpy_nextgen/rpy/__init__.py
branches/rpy_nextgen/rpy/rinterface/__init__.py
branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
branches/rpy_nextgen/rpy/robjects/__init__.py
branches/rpy_nextgen/rpy/robjects/tests/testRVector.py
Added Paths:
-----------
branches/rpy_nextgen/doc/source/introduction.rst
Modified: branches/rpy_nextgen/NEWS
===================================================================
--- branches/rpy_nextgen/NEWS 2008-10-25 17:26:39 UTC (rev 662)
+++ branches/rpy_nextgen/NEWS 2008-10-26 14:09:49 UTC (rev 663)
@@ -8,6 +8,27 @@
- Constructor for :class:`rpy2.robjects.RDataFrame` checks that R lists are
data.frames (not all lists are data.frame)
+New features
+------------
+
+- added :data:`__version__` to rpy2/__init__.py
+
+:mod:`rpy2.robjects`:
+
+- added classes :class:`StrVector`, :class:`IntVector`, :class:`FloatVector`,
:class:`BoolVector`
+
+:mod:`rpy2.rinterface`:
+
+- added missing class :class:`BoolSexpVector`.
+
+
+Changes
+-------
+
+:mod:`rpy2.robjects`:
+
+- does not alias :class:`rinterface.StrSexpVector`,
:class:`rinterface.IntSexpVector`, :class:`rinterface.FloatSexpVector` anymore
+
Bugs fixed
----------
@@ -61,7 +82,7 @@
- setup.py: link to external lapack or blas library when relevant
-- added a MANIFEST.in ensuring that headers get included in the source
distribution
+- added a MANIFEST.in ensuring that headers get included in the source
distribution #missing headers reported by Nicholas Lewin-Koh
- :func:`rinterface.str_typeint` was causing segfault when called with 99
Modified: branches/rpy_nextgen/doc/source/index.rst
===================================================================
--- branches/rpy_nextgen/doc/source/index.rst 2008-10-25 17:26:39 UTC (rev
662)
+++ branches/rpy_nextgen/doc/source/index.rst 2008-10-26 14:09:49 UTC (rev
663)
@@ -6,6 +6,7 @@
:maxdepth: 2
overview
+ introduction
robjects
rinterface
rpy_classic
Added: branches/rpy_nextgen/doc/source/introduction.rst
===================================================================
--- branches/rpy_nextgen/doc/source/introduction.rst
(rev 0)
+++ branches/rpy_nextgen/doc/source/introduction.rst 2008-10-26 14:09:49 UTC
(rev 663)
@@ -0,0 +1,118 @@
+********************
+Introduction to rpy2
+********************
+
+
+This introduction aims at being a gentle start to rpy2,
+either when coming from R to Python/rpy2, from Python to rpy2/R,
+or from elsewhere to Python/rpy2/R.
+
+
+Getting started
+===============
+
+It is assumed here that the rpy2 package was properly installed.
+In python, making a package or module available is achieved by
+importing it.
+
+.. code-block:: python
+
+ import rpy2.robjects as robjects
+
+
+The `r` instance
+================
+
+The object :data:`r` in :mod:`rpy2.robjects` represents the running embedded
+`R` process.
+
+If familiar with R and the R console, :data:`r` is a little like your window
+to R from Python.
+
+
+The method :meth:`__getitem__` functions like calling a variable from the
+R console.
+
+Example in R:
+
+.. code-block:: r
+
+ pi
+
+With :mod:`rpy2`:
+
+>>> robjects.r['pi']
+3.14159265358979
+
+
+
+The :data:`r` object is also callable, and the string passed to it evaluated
+as `R` code:
+
+Example in R:
+
+.. code-block:: r
+
+ pi
+
+With :mod:`rpy2`:
+
+>>> robjects.r('pi')
+3.14159265358979
+
+
+The evaluation is performed in what is know to R users as the
+`Global Environment`, that is the place one starts at when starting
+the R console. Whenever the `R` code creates variables, those
+variables will be "located" in that `Global Environment` by default.
+
+
+Example:
+
+.. code-block:: r
+
+ robjects.r('''
+ f <- function(r) { 2 * pi * r }
+ f(3)
+ ''')
+
+
+The expression above will return the value 18.85, but also create an R function
+`f`. That function `f` is present in the R `Global Environement`, and can
+be accessed with the `__getitem__` mechanism outlined above:
+
+
+>>> robjects.r['f']
+function (r)
+{
+ 2 * pi * r
+}
+
+
+R vectors
+=========
+
+In `R`, data are mostly represented by vectors, even when looking
+like scalars.
+
+When looking closely at the R object `pi` used previously,
+we can observe that this is in fact a vector of length 1.
+
+>>> len(robjects.r['pi'])
+1
+
+
+Creating R vectors can be achieved simply:
+
+>>> robjects.StrVector(['abc', 'def'])
+c("abc", "def")
+>>> robjects.IntVector([1, 2, 3])
+1:3
+>>> robjects.FloatVector([1.1, 2.2, 3.3])
+c(1.1, 2.2, 3.3)
+
+
+R matrixes and arrays are just vector with a `dim` attribute.
+
+
+
\ No newline at end of file
Modified: branches/rpy_nextgen/doc/source/robjects.rst
===================================================================
--- branches/rpy_nextgen/doc/source/robjects.rst 2008-10-25 17:26:39 UTC
(rev 662)
+++ branches/rpy_nextgen/doc/source/robjects.rst 2008-10-26 14:09:49 UTC
(rev 663)
@@ -159,6 +159,20 @@
:class:`rpy2.rinterface.VectorSexp`.
+Creating vectors
+----------------
+
+Creating vectors can be achieved either from R or from Python.
+
+When the vectors are created from R, one should not worry much
+as they will be exposed as they should by :mod:`rpy2.robjects`.
+
+When one wants to create a vector from Python, either the
+class :class:`RVector` or the convenience classes
+:class:`IntVector`, :class:`FloatVector`, :class:`BoolVector`,
:class:`StrVector` can
+used.
+
+
.. index::
pair: RVector;indexing
Modified: branches/rpy_nextgen/rpy/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/__init__.py 2008-10-25 17:26:39 UTC (rev
662)
+++ branches/rpy_nextgen/rpy/__init__.py 2008-10-26 14:09:49 UTC (rev
663)
@@ -0,0 +1 @@
+__version__ = '2.0.0b1'
Modified: branches/rpy_nextgen/rpy/rinterface/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/__init__.py 2008-10-25 17:26:39 UTC
(rev 662)
+++ branches/rpy_nextgen/rpy/rinterface/__init__.py 2008-10-26 14:09:49 UTC
(rev 663)
@@ -58,7 +58,14 @@
def __init__(self, v):
super(FloatSexpVector, self).__init__(v, REALSXP)
+class BoolSexpVector(SexpVector):
+ """
+ Vector of floats.
+ """
+ def __init__(self, v):
+ super(BoolSexpVector, self).__init__(v, LGLSXP)
+
# wrapper because print is strangely not a function
# Python prior to version 3.0
def consolePrint(x):
Modified: branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
===================================================================
--- branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
2008-10-25 17:26:39 UTC (rev 662)
+++ branches/rpy_nextgen/rpy/rinterface/tests/test_SexpVector.py
2008-10-26 14:09:49 UTC (rev 663)
@@ -27,6 +27,12 @@
ok = isStr(sexp)[0]
self.assertTrue(ok)
+ def testBool(self):
+ sexp = ri.BoolSexpVector([True, ])
+ isBool = ri.globalEnv.get("is.logical")
+ ok = isBool(sexp)[0]
+ self.assertTrue(ok)
+
class SexpVectorTestCase(unittest.TestCase):
def testMissinfType(self):
Modified: branches/rpy_nextgen/rpy/robjects/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/__init__.py 2008-10-25 17:26:39 UTC
(rev 662)
+++ branches/rpy_nextgen/rpy/robjects/__init__.py 2008-10-26 14:09:49 UTC
(rev 663)
@@ -12,11 +12,6 @@
import rpy2.rinterface as rinterface
import rpy2.rlike.container as rlc
-StrSexpVector = rinterface.StrSexpVector
-IntSexpVector = rinterface.IntSexpVector
-FloatSexpVector = rinterface.FloatSexpVector
-
-
#FIXME: close everything when leaving (check RPy for that).
def default_ri2py(o):
@@ -278,6 +273,27 @@
res = r["names<-"](self, value)
return res
+class StrVector(RVector):
+ def __init__(self, obj):
+ obj = rinterface.StrSexpVector(obj)
+ super(StrVector, self).__init__(obj)
+
+class IntVector(RVector):
+ def __init__(self, obj):
+ obj = rinterface.IntSexpVector(obj)
+ super(IntVector, self).__init__(obj)
+
+class BoolVector(RVector):
+ def __init__(self, obj):
+ obj = rinterface.BoolSexpVector(obj)
+ super(BoolVector, self).__init__(obj)
+
+class FloatVector(RVector):
+ def __init__(self, obj):
+ obj = rinterface.FloatSexpVector(obj)
+ super(FloatVector, self).__init__(obj)
+
+
class RArray(RVector):
""" An R array """
def __init__(self, o):
@@ -428,9 +444,9 @@
def __init__(self, formula, environment = rinterface.globalEnv):
inpackage = rinterface.baseNameSpaceEnv["::"]
- asformula = inpackage(StrSexpVector(['stats', ]),
- StrSexpVector(['as.formula', ]))
- formula = rinterface.SexpVector(StrSexpVector([formula, ]))
+ asformula = inpackage(rinterface.StrSexpVector(['stats', ]),
+ rinterface.StrSexpVector(['as.formula', ]))
+ formula = rinterface.SexpVector(rinterface.StrSexpVector([formula, ]))
robj = asformula(formula,
env = environment)
super(RFormula, self).__init__(robj)
Modified: branches/rpy_nextgen/rpy/robjects/tests/testRVector.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/tests/testRVector.py 2008-10-25
17:26:39 UTC (rev 662)
+++ branches/rpy_nextgen/rpy/robjects/tests/testRVector.py 2008-10-26
14:09:49 UTC (rev 663)
@@ -22,6 +22,30 @@
del(ri_v)
self.assertEquals(ri.INTSXP, ro_v.typeof)
+ def testNewStrVector(self):
+ vec = robjects.StrVector(['abc', 'def'])
+ self.assertEquals('abc', vec[0])
+ self.assertEquals('def', vec[1])
+ self.assertEquals(2, len(vec))
+
+ def testNewIntVector(self):
+ vec = robjects.IntVector([123, 456])
+ self.assertEquals(123, vec[0])
+ self.assertEquals(456, vec[1])
+ self.assertEquals(2, len(vec))
+
+ def testNewFloatVector(self):
+ vec = robjects.FloatVector([123.0, 456.0])
+ self.assertEquals(123.0, vec[0])
+ self.assertEquals(456.0, vec[1])
+ self.assertEquals(2, len(vec))
+
+ def testNewBoolVector(self):
+ vec = robjects.BoolVector([True, False])
+ self.assertEquals(True, vec[0])
+ self.assertEquals(False, vec[1])
+ self.assertEquals(2, len(vec))
+
def testAddOperators(self):
seq_R = robjects.r["seq"]
mySeqA = seq_R(0, 3)
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