Revision: 608
http://rpy.svn.sourceforge.net/rpy/?rev=608&view=rev
Author: lgautier
Date: 2008-08-03 09:16:24 +0000 (Sun, 03 Aug 2008)
Log Message:
-----------
work on the documentation
Modified Paths:
--------------
branches/rpy_nextgen/doc/source/conf.py
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/rlike.rst
branches/rpy_nextgen/doc/source/robjects.rst
Modified: branches/rpy_nextgen/doc/source/conf.py
===================================================================
--- branches/rpy_nextgen/doc/source/conf.py 2008-08-03 09:15:45 UTC (rev
607)
+++ branches/rpy_nextgen/doc/source/conf.py 2008-08-03 09:16:24 UTC (rev
608)
@@ -24,7 +24,7 @@
# Add any Sphinx extension module names here, as strings. They can be
extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.doctest', ]
+extensions = ['sphinx.ext.doctest', 'sphinx.ext.autodoc']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -46,6 +46,7 @@
version = '2.0'
# The full version, including alpha/beta/rc tags.
release = '2.0.0a2'
+releaselevel = 'alpha'
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
Modified: branches/rpy_nextgen/doc/source/index.rst
===================================================================
--- branches/rpy_nextgen/doc/source/index.rst 2008-08-03 09:15:45 UTC (rev
607)
+++ branches/rpy_nextgen/doc/source/index.rst 2008-08-03 09:16:24 UTC (rev
608)
@@ -1,24 +1,7 @@
-.. rpy2 documentation master file, created by sphinx-quickstart on Fri May 23
22:16:57 2008.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
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 on rare occasions
-(and the cause is not yet identified).
-
-
-
-
-Contents:
-
.. toctree::
:maxdepth: 2
Modified: branches/rpy_nextgen/doc/source/overview.rst
===================================================================
--- branches/rpy_nextgen/doc/source/overview.rst 2008-08-03 09:15:45 UTC
(rev 607)
+++ branches/rpy_nextgen/doc/source/overview.rst 2008-08-03 09:16:24 UTC
(rev 608)
@@ -27,10 +27,16 @@
.. _Omegahat project: http://www.omegahat.org/RSPython
-The present documentation covers RPy2, an evolution of RPy-1.x.
+The present documentation describes RPy2, an evolution of RPy-1.x.
Naturally RPy2 is inspired by RPy, but also by A. Belopolskys's contributions
that were waiting to be included into RPy.
+This effort can be seen as a rewrite of the RPy package.
+It is developped for R-2.7 (and it will not work
+with a previous version), together with Python 2.5. Compatibility
+with Python 2.4 is expected but it was observed to segfault on rare occasions
+(and the cause is not yet identified).
+
Installation
@@ -86,7 +92,7 @@
Test an installation
^^^^^^^^^^^^^^^^^^^^
-An installation can be tested as follows:
+At any time, an installation can be tested as follows:
.. code-block:: python
@@ -108,7 +114,7 @@
^^^^^^^^^^^^^^^^^^^^^^^
Higher-level interface similar to the one in RPy-1.x.
-This is provided for compatibility reasons, and facilitate the migration
+This is provided for compatibility reasons, as well as to facilitate the
migration
to RPy2.
Modified: branches/rpy_nextgen/doc/source/rinterface.rst
===================================================================
--- branches/rpy_nextgen/doc/source/rinterface.rst 2008-08-03 09:15:45 UTC
(rev 607)
+++ branches/rpy_nextgen/doc/source/rinterface.rst 2008-08-03 09:16:24 UTC
(rev 608)
@@ -1,3 +1,9 @@
+.. module:: rpy2.rinterface
+ :platform: Unix, Windows
+ :synopsis: Low-level interface with R
+
+
+
**********
rinterface
**********
@@ -2,7 +8,3 @@
-.. module:: rpy2.rinterface
- :platform: Unix, Windows
- :synopsis: Low-level interface with R
-
Overview
@@ -19,17 +21,23 @@
>>> import rpy2.rinterface as rinterface
+
.. index::
- single: initEmbeddedR
- single: initialize
+ single: initialization
-:func:`initEmbeddedR`
----------------------
+Initialization
+--------------
One has to initialize R before much can be done.
The function :func:`initEmbeddedR` lets one initialize
-the embedded R:
+the embedded R.
+This is done with the function :meth:`initEmbeddedR`.
+
+
+.. autofunction:: initEmbeddedR()
+
+
>>> rinterface.initEmbeddedR()
Initialization should only be performed once. In the unfortunate event
@@ -48,6 +56,7 @@
your path (:envvar:`PATH` on unix-alikes, or :envvar:`Path` on Microsoft
Windows) or
have the environment variable :envvar:`R_HOME` defined.
+
R space and Python space
------------------------
@@ -108,74 +117,77 @@
# output from the R console will now be appended to the list 'buf'
rinterface.setWriteConsole(f)
+.. autofunction:: setWriteConsole(function)
+ :param function: function
-:class:`Sexp`
-=============
+Classes
+=======
-Methods:
+Sexp
+----
-typeof()
- Type of the object
+The class :class:`Sexp` is the base class for all R objects.
-do_slot([name])
- Access attribute *name* for the object
-.. index::
- single: Sexp; typeof
+.. class:: Sexp
-:meth:`typeof`
---------------
+ .. method:: typeof()
-The internal R type in which an object is stored can be
-accessed with the method :meth:`typeof`.
+ The internal R type in which an object is stored can be
+ accessed with the method :meth:`typeof`.
->>> letters.typeof()
+ :rtype: integer
-FIXME: talk about the all the types.
-.. index::
- single: Sexp; do_slot
+ .. doctest::
-:meth:`do_slot`
----------------
+ >>> letters.typeof()
+ 16
-R objects can be given attributes. In R the function
-*attr* lets one access attribute, while called :meth:`do_slot`
-in the C interface to R.
+ .. method:: do_slot(name)
->>> matrix = rinterface.globalEnv.get("matrix")
->>> letters = rinterface.globalEnv.get("letters")
->>> ncol = rinterface.SexpVector([2, ], rinterface.INTSXP)
->>> m = matrix(letters, ncol = ncol)
->>> [x for x in m.do_slot("dim")]
-[13, 2]
->>>
+ R objects can be given attributes. In R the function
+ *attr* lets one access attribute, while called :meth:`do_slot`
+ in the C interface to R.
-.. index::
- single: Sexp; named
+ :param name: string
+ :rtype: Sexp (or Sexp-inheriting) object
-:meth:`named`
----------------
+ >>> matrix = rinterface.globalEnv.get("matrix")
+ >>> letters = rinterface.globalEnv.get("letters")
+ >>> ncol = rinterface.SexpVector([2, ], rinterface.INTSXP)
+ >>> m = matrix(letters, ncol = ncol)
+ >>> [x for x in m.do_slot("dim")]
+ [13, 2]
+ >>>
-`R` does not count references for its object. This method
-returns the `NAMED` value (see the R-extensions manual).
+ .. method:: named()
+ `R` does not count references for its object. This method
+ returns the `NAMED` value (see the R-extensions manual).
+ :rtype: integer
+.. .. autoclass:: rpy2.rinterface.Sexp
+.. :members:
+
+
+
.. index::
single: SexpVector
single: rinterface; SexpVector
+
:class:`SexpVector`
-===================
+-------------------
Overview
---------
+^^^^^^^^
In R all scalars are in fact vectors.
Anything like a one-value variable is a vector of
@@ -204,7 +216,7 @@
pair: rinterface;indexing
Indexing
---------
+^^^^^^^^
The indexing is working like it would on regular `Python`
tuples or lists.
@@ -220,14 +232,14 @@
Common attributes
------------------
+^^^^^^^^^^^^^^^^^
.. index::
single: names;rinterface
-Names
-^^^^^
+.. rubric:: Names
+
In R, vectors can be named, that is each value in the vector
can be given a name (that is be associated a string).
The names are added to the other as an attribute (conveniently
@@ -245,8 +257,7 @@
single: dimnames
-Dim and dimnames
-^^^^^^^^^^^^^^^^
+.. rubric:: Dim and dimnames
In the case of an `array`, the names across the
respective dimensions of the object are accessible
@@ -258,7 +269,7 @@
pair: SexpVector; numpy
Numpy
------
+^^^^^
The :class:`SexpVector` objects are made to behave like arrays as defined
in the Python package :mod:`numpy`.
@@ -282,16 +293,21 @@
42
>>>
+.. .. autoclass:: rpy2.rinterface.SexpVector
+.. :members:
+
+
+
.. index::
single: SexpEnvironment
single: rinterface; SexpEnvironment
:class:`SexpEnvironment`
-========================
+------------------------
:meth:`get`
------------
+^^^^^^^^^^^
Whenever a search for a symbol is performed, the whole
search path is considered: the environments in the list
@@ -305,7 +321,7 @@
:meth:`__getitem__` / :meth:`__setitem__`
------------------------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The *[* operator will only look for a symbol in the environment
(FIXME: first in the list then ?),
@@ -333,7 +349,7 @@
a copy of the R object is made in the R space.
:meth:`__iter__`
-----------------
+^^^^^^^^^^^^^^^^
The object is made iter-able.
@@ -358,10 +374,9 @@
pair: rinterface; function
:class:`SexpClosure`
-====================
+--------------------
-A function with a context
--------------------------
+.. rubric:: A function with a context
In R terminology, a closure is a function (with its enclosing
environment). That enclosing environment can be thought of as
@@ -375,6 +390,9 @@
>>>
+.. index::
+ single: rcall
+
.. rubric:: Order for named parameters
One point where function calls in R can differ from the ones in
@@ -382,7 +400,8 @@
all parameters in R are passed in the order they are in the call
(no matter whether the parameter is named or not),
while in Python only parameters without a name are passed in order.
-Using the class :class:`ArgsDict` in the module :mod:`rpy2.rlike.container`
+Using the class :class:`ArgsDict` in the module :mod:`rpy2.rlike.container`,
+together with the method :meth:`rcall`,
permits calling a function the same way it would in R. For example::
import rpy2.rlike.container as rpc
@@ -396,9 +415,12 @@
>>> [x for x in rl.do_slot("names")]
['x', '', 'y']
-closureEnv
-----------
+.. index::
+ single: closureEnv
+
+.. rubric:: closureEnv
+
In the example below, we inspect the environment for the
function *plot*, that is the namespace for the
package *graphics*.
@@ -410,9 +432,6 @@
>>>
-
-
-
Misc. variables
===============
Modified: branches/rpy_nextgen/doc/source/rlike.rst
===================================================================
--- branches/rpy_nextgen/doc/source/rlike.rst 2008-08-03 09:15:45 UTC (rev
607)
+++ branches/rpy_nextgen/doc/source/rlike.rst 2008-08-03 09:16:24 UTC (rev
608)
@@ -21,6 +21,10 @@
>>> import rpy2.rlike.container as rlc
+
+.. index::
+ single: ArgsDict
+
ArgsDict
--------
@@ -47,11 +51,35 @@
>>> nl[None] = 'no name'
+.. index::
+ single: TaggedList
-
TaggedList
----------
-A :class:`TaggedList` is a Python list in which each item has
-an associated tag.
+A :class:`TaggedList` is a Python :class:`list` in which each item has
+an associated `tag`.
This is similar to `named` vectors in R.
+
+>>> tl = rlc.TaggedList([1,2,3])
+>>> tl
+[1, 2, 3]
+>>> tl.tags()
+(None, None, None)
+>>> tl.settag(0, 'a')
+>>> tl.tags()
+('a', None, None)
+
+
+>>> tl = rlc.TaggedList([1,2,3], tags=('a', 'b', 'c'))
+>>> tl
+[1, 2, 3]
+>>> tl.tags()
+('a', 'b', 'c')
+>>> tl.settag(0, 'c')
+>>> tl.tags()
+('c', 'b', 'c')
+>>> it = tl.iterontag('c')
+>>> [x for x in it]
+[1, 3]
+
Modified: branches/rpy_nextgen/doc/source/robjects.rst
===================================================================
--- branches/rpy_nextgen/doc/source/robjects.rst 2008-08-03 09:15:45 UTC
(rev 607)
+++ branches/rpy_nextgen/doc/source/robjects.rst 2008-08-03 09:16:24 UTC
(rev 608)
@@ -7,8 +7,6 @@
:platform: Unix, Windows
:synopsis: High-level interface with R
-.. testsetup:: robjects
- import rpy2.robjects as robjects
Overview
========
@@ -107,8 +105,8 @@
.. index::
pair: robjects;RVector
-R vectors
-=========
+Vectors
+=======
Beside functions, and environemnts, most of the objects
an R user is interacting with are vector-like.
@@ -255,8 +253,8 @@
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
-==============
+Environments
+============
R environments can be described to the Python user as
an hybrid of a dictionary and a scope.
@@ -307,8 +305,8 @@
pair: robjects; RFunction
pair: robjects; function
-R functions
-===========
+Functions
+=========
>>> plot = robjects.r.plot
>>> rnorm = robjects.r.rnorm
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