Revision: 571
http://rpy.svn.sourceforge.net/rpy/?rev=571&view=rev
Author: lgautier
Date: 2008-07-05 07:43:41 -0700 (Sat, 05 Jul 2008)
Log Message:
-----------
doc:
- many fixes and little additions
- transferred content of preface.rst to the index / main page.
Modified Paths:
--------------
branches/rpy_nextgen/doc/source/index.rst
branches/rpy_nextgen/doc/source/overview.rst
branches/rpy_nextgen/doc/source/rinterface.rst
branches/rpy_nextgen/doc/source/robjects.rst
Removed Paths:
-------------
branches/rpy_nextgen/doc/source/preface.rst
Modified: branches/rpy_nextgen/doc/source/index.rst
===================================================================
--- branches/rpy_nextgen/doc/source/index.rst 2008-07-04 13:59:57 UTC (rev
570)
+++ branches/rpy_nextgen/doc/source/index.rst 2008-07-05 14:43:41 UTC (rev
571)
@@ -5,12 +5,23 @@
Documentation for rpy2
======================
+
+This document describes RPy2, a rewrite of
+the RPy package.
+
+It is developped for R-2.7 (and is not expected to work
+with a previous version), together with Python 2.5. Compatibility
+with Python 2.4 is expected but it was observed to segfault at rare occasions
+(and the cause is not yet identified).
+
+
+
+
Contents:
.. toctree::
:maxdepth: 2
- preface
overview
robjects
rinterface
Modified: branches/rpy_nextgen/doc/source/overview.rst
===================================================================
--- branches/rpy_nextgen/doc/source/overview.rst 2008-07-04 13:59:57 UTC
(rev 570)
+++ branches/rpy_nextgen/doc/source/overview.rst 2008-07-05 14:43:41 UTC
(rev 571)
@@ -45,9 +45,8 @@
^^^^^^^^
Source Python packages, as well as pre-compiled binaries for Microsoft's
Windows are available
-on the Sourceforge page.
+on the `Sourceforge page <http://downloads.sourceforge.net/rpy>`_.
-
.. note::
MacOSX binaries may appear in the future (contributions to build them are
welcome)
@@ -119,3 +118,15 @@
demonstrate how to extend :mod:`rpy2.rinterface` with an alternative
to inheritance.
+
+Acknowledgements
+----------------
+
+Acknowledgements go to:
+
+Walter Moreira, and Gregory Warnes
+ For the original RPy and its maintainance through the years.
+
+Alexander Belopolsky.
+ His code contribution to RPy is acknowledged. I have found great
+ inspiration in reading that code.
Deleted: branches/rpy_nextgen/doc/source/preface.rst
===================================================================
--- branches/rpy_nextgen/doc/source/preface.rst 2008-07-04 13:59:57 UTC (rev
570)
+++ branches/rpy_nextgen/doc/source/preface.rst 2008-07-05 14:43:41 UTC (rev
571)
@@ -1,20 +0,0 @@
-Preface
-=======
-
-This presentation describes RPy2, a rewrite of
-the RPy package.
-
-It is developped for R-2.7 (and is not expected to work
-with a previous version), together with Python 2.5. Compatibility
-with Python 2.4 is expected but not tested when writing
-those lines.
-
-Acknowledgements go to:
-
-Walter Moreira, and Gregory Warnes
- For the original RPy and its maintainance through the years.
-
-Alexander Belopolsky.
- The contributed code of Alexander Belopolsky, who contributed
- a first rewrite to RPy is acknowledged. I have found great
- inspiration in reading that code.
Modified: branches/rpy_nextgen/doc/source/rinterface.rst
===================================================================
--- branches/rpy_nextgen/doc/source/rinterface.rst 2008-07-04 13:59:57 UTC
(rev 570)
+++ branches/rpy_nextgen/doc/source/rinterface.rst 2008-07-05 14:43:41 UTC
(rev 571)
@@ -32,9 +32,9 @@
>>> rinterface.initEmbeddedR()
-Initialization should only be performed once and in the case
-of a second call to :func:`initEmbeddedR`, to avoid unpredictable results
-when using the embedded R, an exception is be fired.
+Initialization should only be performed once. In the unfortunate event
+of a second call to :func:`initEmbeddedR`, and to avoid unpredictable results
+when using the embedded R, an exception will be fired.
Parameters for the initialization are in the module variable
`initOptions`.
@@ -254,6 +254,7 @@
The functions *array* and *asarray* is all that is needed:
+
>>> import numpy
>>> rx = rinterface.SexpVector([1,2,3,4], rinterface.INTSXP)
>>> nx = numpy.array(rx)
@@ -263,6 +264,8 @@
.. note::
when using :meth:`asarray`, the data are not copied.
+>>> rx[2]
+3
>>> nx_nc[2] = 42
>>> rx[2]
42
Modified: branches/rpy_nextgen/doc/source/robjects.rst
===================================================================
--- branches/rpy_nextgen/doc/source/robjects.rst 2008-07-04 13:59:57 UTC
(rev 570)
+++ branches/rpy_nextgen/doc/source/robjects.rst 2008-07-05 14:43:41 UTC
(rev 571)
@@ -83,7 +83,7 @@
The astute reader will quickly realize that R objects named
by python variables can
-be plugged into code by their string representation:
+be plugged into code through their string representation:
>>> x = robjects.r.rnorm(100)
>>> robjects.r('hist(%s, xlab="x", main="hist(x)")' %repr(x))
@@ -155,7 +155,7 @@
>>> x.r[1]
1L
-The two next examples demonstrate features of `R` regarding indexing,
+The two next examples demonstrate some of `R`'s features regarding indexing,
respectively element exclusion and recycling rule:
>>> x.r[-1]
@@ -174,7 +174,7 @@
are performed element-wise in R, recycling the shortest vector if, and
as much as, necessary.
-The delegating attribute mention in the Indexing section can also
+The delegating attribute mentioned in the Indexing section can also
be used with the following operators:
+----------+---------+
@@ -232,6 +232,14 @@
A :class:`RMatrix` is a special case of :class:`RArray`.
+:class:`RDataFrame`
+-------------------
+
+A :class:`RDataFrame` represents the `R` class `data.frame'.
+
+Currently, the constructor is flagged as experimental. It accepts either a
:class:`rinterface.SexpVector`
+or a dictonnary which elements will be the columns of the `data.frame`.
+
R environments
==============
@@ -350,29 +358,54 @@
Mapping between rpy2 objects and other python objects
=====================================================
-The conversion, as often needed with RPy-1.x, is no longer
+The conversion, often present when working with RPy-1.x, is no longer
necessary as the R objects can be either passed on to R functions
-or used in Python. T
+or used in Python.
-There is a low-level mapping between `R` and `Python` objects
-performed behind the (Python-level) scene.
+However, there is a low-level mapping between `R` and `Python` objects
+performed behind the (Python-level) scene, done by the :mod:`rpy2.rinterface`,
+while an higher-level mapping is done between low-level objects and
+higher-level objects using the functions:
-The mapping between low-level objects and higher-level objects
-is performed by the functions.
-
:meth:`ri2py`
- :mod:`rpy2.rinterface` to Python
+ :mod:`rpy2.rinterface` to Python. By default, this function
+ is just an alias for the function :meth:`default_ri2py`.
:meth:`py2ri`
- Python to :mod:`rpy2.rinterface`
+ Python to :mod:`rpy2.rinterface`. By default, this function
+ is just an alias for the function :meth:`default_py2ri`.
:meth:`py2ro`
Python to :mod:`rpy2.robjects`. That one function
- is merely a call to py2ri followed by a call to ri2py.
+ is merely a call to :meth:`py2ri` followed by a call to :meth:`ri2py`.
-Those functions can be modifyied to satisfy all requirements.
+Those functions can be modifyied to satisfy all requirements, with
+the easiest option being to write a custom function calling itself
+the default function.
+As an example, let's assume that one want to return atomic values
+whenever an R numerical vector is of length one. This is only a matter
+of writing a new function `ri2py` that handles this, as shown below:
+.. code-block:: python
+ import rpy2.robjects as robjects
+
+ def my_ri2py(obj):
+ res = robjects.default_ri2py(obj)
+ if isinstance(res, robjects.RVector) and (len(res) == 1):
+ res = res[0]
+ return res
+
+ robjects.ri2py = my_ri2py
+
+Once this is done, we can verify immediately that this is working with:
+
+>>> pi = robjects.r.pi
+>> type(pi)
+<type 'float'>
+>>>
+
+
Examples
========
@@ -381,7 +414,8 @@
will hopefully be used as a cookbook.
-.. testcode:: robjects
+.. code-block:: python
+
import rpy2.robjects as robjects
import array
@@ -434,7 +468,7 @@
print(r.anova(lm_D9))
lm_D90 = r.lm("weight ~ group - 1")
- r.summary(lm_D90)
+ print(r.summary(lm_D90))
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