Revision: 618
http://rpy.svn.sourceforge.net/rpy/?rev=618&view=rev
Author: lgautier
Date: 2008-08-05 11:00:11 +0000 (Tue, 05 Aug 2008)
Log Message:
-----------
refactored a bit the documentation
Modified Paths:
--------------
branches/rpy_nextgen/doc/source/conf.py
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 2008-08-05 10:57:00 UTC (rev
617)
+++ branches/rpy_nextgen/doc/source/conf.py 2008-08-05 11:00:11 UTC (rev
618)
@@ -94,7 +94,7 @@
-html_favicon = 'rpy.ico'
+html_favicon = 'rpy_fav.ico'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
Modified: branches/rpy_nextgen/doc/source/overview.rst
===================================================================
--- branches/rpy_nextgen/doc/source/overview.rst 2008-08-05 10:57:00 UTC
(rev 617)
+++ branches/rpy_nextgen/doc/source/overview.rst 2008-08-05 11:00:11 UTC
(rev 618)
@@ -58,7 +58,7 @@
Choose files from the `rpy2` package, not `rpy`.
.. note::
- MacOSX binaries may appear in the future (contributions to build them are
welcome)
+ MacOSX binaries may appear in the future (help to build them is welcome)
.. index::
@@ -173,3 +173,4 @@
Alexander Belopolsky.
His code contribution 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 2008-08-05 10:57:00 UTC
(rev 617)
+++ branches/rpy_nextgen/doc/source/rinterface.rst 2008-08-05 11:00:11 UTC
(rev 618)
@@ -4,18 +4,18 @@
-**********
-rinterface
-**********
+*******************
+Low-level interface
+*******************
Overview
========
-A lower-level interface is provided for situations where
-the use-cases addressed by :mod:`robjects` are not covered,
-and for the cases where the layer in :mod:`robjects`
-has an excessive cost in term of performances.
+The package :mod:`rinterface` is provided as a lower-level interface,
+for situations where either the use-cases addressed by :mod:`robjects`
+are not covered, or for the cases where the layer in :mod:`robjects`
+has an excessive cost in terms of performances.
The package can be imported with:
@@ -40,9 +40,9 @@
>>> rinterface.initEmbeddedR()
-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.
+Initialization should only be performed once.
+To avoid unpredictable results when using the embedded R,
+subsequent calls to :func:`initEmbeddedR` will not have any effect.
Parameters for the initialization are in the module variable
`initOptions`.
@@ -65,12 +65,32 @@
The :class:`Sexp_Type` objects can be considered as Python enveloppes pointing
to data stored and administered in the R space.
+R variables are existing within an embedded R workspace, and can be accessed
+from Python through their python object representations.
+
+We distinguish two kind of R objects: named objects and anonymous objects.
+Named objects have an associated symbol in the R workspace.
+
+Named objects
+^^^^^^^^^^^^^
+
+For example, the following R code is creating two objects, named `x` and `hyp`
+respectively, in the `global environment`.
+Those two objects could be accessed from Python using their names.
+
+.. code-block:: r
+
+ x <- c(1,2,3)
+
+ hyp <- function(x, y) sqrt(x^2 + y^2)
+
+Two environments are provided as :class:`rpy2.rinterface.SexpEnvironment`
+
.. index::
single: globalEnv
single: SexpEnvironment; globalEnv
-globalEnv
----------
+.. rubric:: globalEnv
The global environment can be seen as the root (or topmost) environment,
and is in fact a list, that is a sequence, of environments.
@@ -87,26 +107,52 @@
pair: rinterface; baseNamespaceEnv
single: SexpEnvironment; baseNamespaceEnv
-baseNamespaceEnv
-----------------
+.. rubric:: baseNamespaceEnv
The base package has a namespace, that can be accessed as an environment.
.. note::
Depending on what is in `globalEnv` and on the attached packages, base
- objects can be masked when starting the search from `globalEnv`. Use this
- environment when you want to be sure to access a function you know to be
+ objects can be masked when starting the search from `globalEnv`.
+ Use `baseNamespaceEnv`
+ when you want to be sure to access a function you know to be
in the base namespace.
-.. index::
- single: Sexp
-Ouput from the R console
-------------------------
+Anonymous objects
+^^^^^^^^^^^^^^^^^
+Anonymous R objects do not have an associated symbol, yet are protected
+from garbage collection.
+
+Such objects can be created when using the constructor for an `Sexp*` class.
+
+
+
+Interacting with the R console
+------------------------------
+
+Two functions can be used to set callbacks.
+
+.. autofunction:: setWriteConsole(function)
+
+ :param function: function
+
+.. autofunction:: setReadConsole(function)
+
+ :param function: function
+
+
+Output from the console
+^^^^^^^^^^^^^^^^^^^^^^^
+
The function :meth:`setWriteConsole` let one specify what do with
output from the R console with a callback function.
+The callback function should accept one argument of type string
+(that is the string output to the console)
+
+
An example should make it obvious::
buf = []
@@ -117,12 +163,22 @@
# output from the R console will now be appended to the list 'buf'
rinterface.setWriteConsole(f)
-.. autofunction:: setWriteConsole(function)
+ rprint = rinterface.baseNamespaceEnv['print']
+ rprint(rinterface.baseNamespaceEnv['date'])
- :param function: function
+ # restore default function
+ rinterface.setWriteConsole(rinterface.consolePrint)
+Input to the console
+^^^^^^^^^^^^^^^^^^^^
+User input to the console can be can be customized the very same way.
+
+The callback function should accept one argument of type string (that is the
+prompt string), and return a string (what was returned by the user).
+
+
Classes
=======
@@ -297,7 +353,20 @@
.. :members:
+Convenience classes are provided to create vectors of a given type:
+.. autoclass:: rpy2.rinterface.StrSexpVector
+ :show-inheritance:
+ :members:
+
+.. autoclass:: rpy2.rinterface.IntSexpVector
+ :show-inheritance:
+ :members:
+
+.. autoclass:: rpy2.rinterface.FloatSexpVector
+ :show-inheritance:
+ :members:
+
.. index::
single: SexpEnvironment
single: rinterface; SexpEnvironment
Modified: branches/rpy_nextgen/doc/source/rlike.rst
===================================================================
--- branches/rpy_nextgen/doc/source/rlike.rst 2008-08-05 10:57:00 UTC (rev
617)
+++ branches/rpy_nextgen/doc/source/rlike.rst 2008-08-05 11:00:11 UTC (rev
618)
@@ -17,6 +17,7 @@
Containers
==========
+
.. module:: rpy2.rlike.container
>>> import rpy2.rlike.container as rlc
@@ -83,3 +84,8 @@
>>> [x for x in it]
[1, 3]
+
+The Python docstring for the class is:
+
+.. autoclass:: rpy2.rlike.container.TaggedList
+ :members:
\ No newline at end of file
Modified: branches/rpy_nextgen/doc/source/robjects.rst
===================================================================
--- branches/rpy_nextgen/doc/source/robjects.rst 2008-08-05 10:57:00 UTC
(rev 617)
+++ branches/rpy_nextgen/doc/source/robjects.rst 2008-08-05 11:00:11 UTC
(rev 618)
@@ -1,7 +1,7 @@
-*************
-rpy2.robjects
-*************
+********************
+High-level interface
+********************
.. module:: rpy2.robjects
:platform: Unix, Windows
@@ -33,7 +33,7 @@
`r`: the instance of `R`
-==============================
+========================
This class is currently a singleton, with
its one representation instanciated when the
@@ -335,7 +335,8 @@
fit <- lm(y ~ x)
-In the call to `lm`, the argument is a `formula`.
+In the call to `lm`, the argument is a `formula`, and it can read like
+*model y using x*.
A formula is a `R` language object, and the terms in the formula
are evaluated in the environment it was defined in. Without further
specification, that environment is the environment in which the
@@ -418,6 +419,13 @@
>>>
+The docstrings for :meth:`default_ri2py`, :meth:`default_py2ri`, and
:meth:`ri2py` are:
+
+.. autofunction:: rpy2.robjects.default_ri2py
+.. autofunction:: rpy2.robjects.default_py2ri
+.. autofunction:: rpy2.robjects.default_py2ro
+
+
Examples
========
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