[Rcpp-commits] r2148 - papers/rjournal
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Sep 24 01:04:10 CEST 2010
Author: edd
Date: 2010-09-24 01:04:10 +0200 (Fri, 24 Sep 2010)
New Revision: 2148
Modified:
papers/rjournal/EddelbuettelFrancois.tex
Log:
one more round -- acknowledging all your changes which were great
I think we need to attempt the one or two new write-ups you mention,
redo the the benchmark part and are otherwise there
Modified: papers/rjournal/EddelbuettelFrancois.tex
===================================================================
--- papers/rjournal/EddelbuettelFrancois.tex 2010-09-23 15:48:59 UTC (rev 2147)
+++ papers/rjournal/EddelbuettelFrancois.tex 2010-09-23 23:04:10 UTC (rev 2148)
@@ -37,6 +37,7 @@
% please see the next paragraph where I now talk about classic
% but also note deprecated and link to the recommended new API
% [romain] : alright
+% [dirk] : great, will remove discussion in next revision
%The current version of
The \pkg{Rcpp} package combines two distinct
@@ -63,7 +64,8 @@
in early 2006. Several releases (all by Samperi) followed in quick succession
under the name \pkg{Rcpp}. The package was then renamed to
\pkg{RcppTemplate}; several more releases followed during 2006 under the new
-name. However, no new releases were made during 2007 or 2008.
+name. However, no new releases were made during 2007 or 2008. It briefly
+reappeared and the end of 2009 only to be withdrawn yet again.
Given the continued use of the package, Eddelbuettel decided to revitalize it. New
releases, using the initial name \pkg{Rcpp}, started in November 2008. These
@@ -93,6 +95,7 @@
% [ minutes later ]
% ok, one 'new' is gone above as the corresponding section title is gone
% [romain] fine
+% [dirk] good, will clean out discussion here too
\subsection{Comparison}
@@ -125,9 +128,10 @@
\cite{templelang09:rgcctranslationunit} who uses compiler output for
references on the code in order to add bindings and wrappers.
%
-The \pkg{cxxPack} package \citep{cran:cxxPack} builds on top of
-\pkg{Rcpp} and adds a small collection of diverse functions.
+% The \pkg{cxxPack} package \citep{cran:cxxPack} builds on top of
+% \pkg{Rcpp} and adds a small collection of diverse functions.
% [romain] So what ? Is this the mention you want to remove ? Go right ahead !
+% [dirk] Done!!
%DE: Removed per editor
%A critical comparison of these packages that addresses relevant aspects such
@@ -166,7 +170,12 @@
% TODO: Wrap this this so that it ties in better with what follows
% [romain] : should this section be merged with the next one. It looks odd on its own.
+% [dirk] : yes but 'Rcpp Use Cases' is the end of the Introduction, whereas
+% what follows is a new section. But if you can find a nice way
+% to combine them ... go for it.
+
+
\section{The \pkg{Rcpp} API}
\label{sec:new_rcpp}
@@ -195,7 +204,7 @@
for (int j = 0; j < n_xb; j++)
xab[i + j] += xa[i] * xb[j];
- return xab ;
+ return xab;
}
\end{example}
@@ -213,6 +222,7 @@
% the length reported by the programmer.
% [romain] : hmmm. There is no need for extra parameters if you use .Call
% with the R API. I don't think the point is valid.
+% [dirk] Nice catch ctach
and with the use of the
\verb|operator[]| to extract and set individual elements of the vector.
Fifth, the computation itself is
@@ -314,7 +324,7 @@
Using the \code{Rcpp::NumericVector} class, the code can be rewritten:
\begin{example}
-Rcpp::NumericVector ab(2) ;
+Rcpp::NumericVector ab(2);
ab[0] = 123.45;
ab[1] = 67.89;
\end{example}
@@ -337,6 +347,7 @@
% [romain] I'm trading this for the use of create, as this always works
% so that we don't confuse readers because if you have gcc 4.4
% you don't get this automatically, you have to enable it, etc ...
+% [dirk] Nicely done!
The snippet can also be written more concisely using the \code{create}
static member function of the \code{NumericVector} class:
@@ -349,6 +360,7 @@
It should be noted that although the copy constructor of the
\code{NumericVector} class is used, it does not imply copies of the
underlying array, only the \code{SEXP} is copied.
+% [dirk] Huh? But so there is a copy?
\subsection{Character vectors}
@@ -421,7 +433,8 @@
Wrappability of an object type is resolved at compile time using
modern techniques of template meta programming and class traits. The
\code{Rcpp-extending} vignette discusses in depth how to extend \code{wrap}
-to third party types and the \pkg{RcppArmadillo} features several examples.
+to third-party types. The \pkg{RcppArmadillo} package
+\citep{cran:rcpparmadillo} features several examples.
The following code snippet illustrates that the design allows
composition:
@@ -453,7 +466,7 @@
\code{Rcpp::as} template whose signature is:
\begin{example}
template <typename T>
-T as(SEXP x) throw(not_compatible) ;
+T as(SEXP x) throw(not_compatible);
\end{example}
It offers less flexibility and currently
@@ -542,8 +555,8 @@
\ \ \ \ \ \ CONS(ScalarReal(100.0),R_NilValue))));
SET_TAG( CDDR(call), install("sd") );
SEXP res = PROTECT(eval(call, R_GlobalEnv));
-UNPROTECT(4) ;
-return res ;
+UNPROTECT(4);
+return res;
\end{example}
\end{minipage}
@@ -592,8 +605,9 @@
This example illustrates that the \pkg{Rcpp} API permits us to work with code
that is easier to read, write and maintain. More examples are available as
part of the documentation included in the \pkg{Rcpp} package, as well as
-among its over one hundred and ninety unit tests.
+among its over seven hundred and seventy unit tests.
% TODO: bump this up to the current test count
+% [dirk] done, good catch
\section{Using code `inline'}
\label{sec:inline}
@@ -667,6 +681,7 @@
% [romain] hmmmm. we do now have sapply and lapply. I think we should mention
% them here.
+% [dirk] sure, what to give it a go?
% This is taken from :
% http://www.cplusplus.com/reference/algorithm/
@@ -705,7 +720,7 @@
We can use this to calculate a summary of each
column of the \code{faithful} dataset included with R.
-% [Romain] Does this need a reference or is this common knowledge
+% [romain] Does this need a reference or is this common knowledge
% ?faithful has a reference
\begin{example}
@@ -730,10 +745,10 @@
\subsection{C++ exceptions in R}
The internals of the R condition mechanism and the implementation of
-C++ exceptions are both based on a layer above posix jumps. These layers
+C++ exceptions are both based on a layer above POSIX jumps. These layers
both assume total control over the call stack and should not be used together
without extra precaution. \pkg{Rcpp} contains facilities to combine both systems
-so that a C++ exception is caught and recycled into the R condition
+so that C++ exceptions are caught and recycled into the R condition
mechanism.
\pkg{Rcpp} defines the \code{BEGIN\_RCPP} and \code{END\_RCPP} macros that should
@@ -744,8 +759,8 @@
BEGIN_RCPP
int dx = Rcpp::as<int>(x);
if( dx > 10 )
- throw std::range_error("too big") ;
- return Rcpp::wrap( dx * dx) ;
+ throw std::range_error("too big");
+ return Rcpp::wrap( dx * dx);
END_RCPP
\}
\end{example}
@@ -758,12 +773,13 @@
try\{
int dx = Rcpp::as<int>(x);
if( dx > 10 )
- throw std::range_error("too big") ;
- return Rcpp::wrap( dx * dx) ;
+ throw std::range_error("too big");
+ return Rcpp::wrap( dx * dx);
\} catch( std::exception& __ex__ )\{
- forward_exception_to_r( __ex__ ) ;
+ forward_exception_to_r( __ex__ );
\} catch(...)\{
- ::Rf_error( "c++ exception (unknown reason)" ) ;
+ ::Rf_error( "c++ exception "
+ "(unknown reason)" );
\}
\}
\end{example}
@@ -883,6 +899,11 @@
\end{center}
\end{table}
+% [dirk] so what do we want to show here? I like our new table, I
+% particularly like the difference between R API "naive" (which does
+% pretty badly !!) and the highly optimised one. We do look good.
+% So we toss Classic, and I guess we also toss Sugar for now?
+
The first implementation, using the traditional R API, unsurprisingly
appears to be the most efficient. It takes advantage of pointer
arithmetics and does not pay the price of object encapsulation. This provides
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