Revision: 598
http://rpy.svn.sourceforge.net/rpy/?rev=598&view=rev
Author: lgautier
Date: 2008-07-27 14:44:27 +0000 (Sun, 27 Jul 2008)
Log Message:
-----------
(Many) changes to the documentation (edition, additions).
The documentation now refers to 2.0.0a2 (as the next alpha, possibly the last
one,
is getting closer).
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/robjects.rst
branches/rpy_nextgen/doc/source/rpy_classic.rst
branches/rpy_nextgen/doc/source/rpy_logo_header.png
Added Paths:
-----------
branches/rpy_nextgen/doc/source/rlike.rst
Modified: branches/rpy_nextgen/doc/source/conf.py
===================================================================
--- branches/rpy_nextgen/doc/source/conf.py 2008-07-27 14:31:56 UTC (rev
597)
+++ branches/rpy_nextgen/doc/source/conf.py 2008-07-27 14:44:27 UTC (rev
598)
@@ -45,7 +45,7 @@
# The short X.Y version.
version = '2.0'
# The full version, including alpha/beta/rc tags.
-release = '2.0a1'
+release = '2.0.0a2'
# 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 2008-07-27 14:31:56 UTC (rev
597)
+++ branches/rpy_nextgen/doc/source/index.rst 2008-07-27 14:44:27 UTC (rev
598)
@@ -31,10 +31,3 @@
changes
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
Modified: branches/rpy_nextgen/doc/source/overview.rst
===================================================================
--- branches/rpy_nextgen/doc/source/overview.rst 2008-07-27 14:31:56 UTC
(rev 597)
+++ branches/rpy_nextgen/doc/source/overview.rst 2008-07-27 14:44:27 UTC
(rev 598)
@@ -31,6 +31,8 @@
Naturally RPy2 is inspired by RPy, but also by A. Belopolskys's contributions
that were waiting to be included into RPy.
+
+
Installation
------------
@@ -48,15 +50,24 @@
on the `Sourceforge page <http://downloads.sourceforge.net/rpy>`_.
.. note::
- MacOSX binaries may appear in the future (contributions to build them are
welcome)
+ Choose files from the `rpy2` package, not `rpy`.
+.. note::
+ MacOSX binaries may appear in the future (contributions to build them are
welcome)
+
+.. index::
+ single: install;win32
+
+
Microsoft's Windows precompiled binaries
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-The executable can be ran; they will install the package in the default Python
installation
+The executable can be ran; it will install the package in the default Python
installation
on the system.
+.. index::
+ single: install;source
Install from source
^^^^^^^^^^^^^^^^^^^
@@ -69,7 +80,25 @@
cd <rpy_package>
python setup.py install
+.. index::
+ single: test;whole installation
+Test an installation
+^^^^^^^^^^^^^^^^^^^^
+
+An installation can be tested as follows:
+
+.. code-block:: python
+
+ import rpy2.tests
+ import unittest
+
+ # the verbosity level can be increased if needed
+ tr = unittest.TextTestRunner(verbosity = 1)
+ suite = rpy2.tests.suite()
+ tr.run(suite)
+
+
Contents
--------
@@ -101,6 +130,15 @@
Design notes
------------
+
+When designing ryp2, attention was given to make:
+
+- the use of the module simple from both a Python or R user's perspective
+
+- minimize the need for knowledge about R, and the need for tricks are
workaround.
+- the possibility to customize a lot only with Python (without having to go to
C-level).
+
+
:mod:`rpy2.robjects` implements an extension to the interface in
:mod:`rpy2.rinterface` by extending the classes for R
objects defined there with child classes.
Modified: branches/rpy_nextgen/doc/source/rinterface.rst
===================================================================
--- branches/rpy_nextgen/doc/source/rinterface.rst 2008-07-27 14:31:56 UTC
(rev 597)
+++ branches/rpy_nextgen/doc/source/rinterface.rst 2008-07-27 14:44:27 UTC
(rev 598)
@@ -157,6 +157,17 @@
>>>
.. index::
+ single: Sexp; named
+
+:meth:`named`
+---------------
+
+`R` does not count references for its object. This method
+returns the `NAMED` value (see the R-extensions manual).
+
+
+
+.. index::
single: SexpVector
single: rinterface; SexpVector
@@ -204,7 +215,7 @@
The *__getitem__* operator *[*
is returning a Python scalar. Casting
an *SexpVector* into a list is only a matter
- either iterating through it, or simply calling
+ of either iterating through it, or simply calling
the constructor :func:`list`.
@@ -212,7 +223,7 @@
-----------------
.. index::
- single: names
+ single: names;rinterface
Names
^^^^^
@@ -363,6 +374,28 @@
6
>>>
+
+.. rubric:: Order for named parameters
+
+One point where function calls in R can differ from the ones in
+Python is that
+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`
+permits calling a function the same way it would in R. For example::
+
+ import rpy2.rlike.container as rpc
+ args = rpc.ArgsDict()
+ args['x'] = rinterface.SexpVector([1,2,3], rinterface.INTSXP)
+ args[None] = rinterface.SexpVector([4,5], rinterface.INTSXP)
+ args['y'] = rinterface.SexpVector([6, ], rinterface.INTSXP)
+ rlist = rinterface.baseNameSpaceEnv['list']
+ rl = rlist.rcall(args.items())
+
+>>> [x for x in rl.do_slot("names")]
+['x', '', 'y']
+
closureEnv
----------
Added: branches/rpy_nextgen/doc/source/rlike.rst
===================================================================
--- branches/rpy_nextgen/doc/source/rlike.rst (rev 0)
+++ branches/rpy_nextgen/doc/source/rlike.rst 2008-07-27 14:44:27 UTC (rev
598)
@@ -0,0 +1,57 @@
+*****
+rlike
+*****
+
+.. module:: rpy2.rlike
+ :platform: Unix, Windows
+ :synopsis: Operate (a bit) like in R
+
+
+Overview
+========
+
+The package proposes R features for a pure Python
+context, that is without an embedded R running.
+
+
+
+Containers
+==========
+.. module:: rpy2.rlike.container
+
+>>> import rpy2.rlike.container as rlc
+
+ArgsDict
+--------
+
+The :class:`ArgsDict` proposes an implementation of what is
+sometimes referred to in Python as an ordered dictionnary, with a
+particularity: a key ``None`` means that, although an item has a rank
+and can be retrieved from that rank, it has no "name".
+
+In the hope of simplifying its usage, the API for an ordered dictionnary
+in :pep:`372` was implemented. An example of usage is:
+
+>>> x = (('a', 123), ('b', 456), ('c', 789))
+>>> nl = rlc.ArgsDict(x)
+
+
+>>> nl['a']
+123
+>>> nl.index('a')
+0
+
+Not all elements have to be named, and specifying a key value equal
+to `None` indicates a value for which no name is associated.
+
+
+>>> nl[None] = 'no name'
+
+
+
+TaggedList
+----------
+
+A :class:`TaggedList` is a Python list in which each item has
+an associated tag.
+This is similar to `named` vectors in R.
Modified: branches/rpy_nextgen/doc/source/robjects.rst
===================================================================
--- branches/rpy_nextgen/doc/source/robjects.rst 2008-07-27 14:31:56 UTC
(rev 597)
+++ branches/rpy_nextgen/doc/source/robjects.rst 2008-07-27 14:44:27 UTC
(rev 598)
@@ -28,7 +28,7 @@
Visible differences with RPy-1.x are:
-- no CONVERSION mode in :mod:`rpy2`, the design has made this unnecessary
+- no ``CONVERSION`` mode in :mod:`rpy2`, the design has made this unnecessary
- easy to modify or rewrite with an all-Python implementation
@@ -199,7 +199,22 @@
>>> x.r + 1
2:11
+
+.. note::
+ In Python, the operator ``+`` concatenate sequence object, and this behavior
+ has been conserved.
+
.. index::
+ single: names; robjects
+
+Names
+-----
+
+``R`` vectors can have a name given to all or some of the items.
+The method :meth:`getnames` retrieve those names.
+
+
+.. index::
pair: RVector; numpy
Numpy
@@ -408,7 +423,7 @@
Examples
========
-The following section demonstrates some of the features of
+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.
@@ -431,6 +446,11 @@
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.rcall`
+ to know how to keep the order of parameters.
+
Linear models
-------------
Modified: branches/rpy_nextgen/doc/source/rpy_classic.rst
===================================================================
--- branches/rpy_nextgen/doc/source/rpy_classic.rst 2008-07-27 14:31:56 UTC
(rev 597)
+++ branches/rpy_nextgen/doc/source/rpy_classic.rst 2008-07-27 14:44:27 UTC
(rev 598)
@@ -3,7 +3,7 @@
rpy_classic
***********
-.. module:: rpy2.rpy_classix
+.. module:: rpy2.rpy_classic
:platform: Unix, Windows
:synopsis: Emulate the orignal rpy
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