[Rprotobuf-commits] r823 - papers/jss
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jan 23 00:39:33 CET 2014
Author: murray
Date: 2014-01-23 00:39:33 +0100 (Thu, 23 Jan 2014)
New Revision: 823
Modified:
papers/jss/article.Rnw
Log:
Use \proglang and \pkg in Keywords list for proper typesetting, add Rcpp
keyword.
Improve the table float placement significantly in section 4 by
letting latex do its own thing with [tbp] instead of trying to place
them [h] which never works. With the default [tbp] it gets most of
the floats placed inside section 4 so section 5 is much more readable
now without being interspersed with floats from the previous section.
Improve the histogram / mr example slightly.
Modified: papers/jss/article.Rnw
===================================================================
--- papers/jss/article.Rnw 2014-01-22 22:30:33 UTC (rev 822)
+++ papers/jss/article.Rnw 2014-01-22 23:39:33 UTC (rev 823)
@@ -41,8 +41,8 @@
% particulary well suited for data-driven applications and numerical
% computing.
}
-\Keywords{r, protocol buffers, serialization, cross-platform}
-\Plainkeywords{r, protocol buffers, serialization, cross-platform} %% without formatting
+\Keywords{\proglang{R}, \pkg{Rcpp}, protocol buffers, serialization, cross-platform}
+\Plainkeywords{r, Rcpp, protocol buffers, serialization, cross-platform} %% without formatting
%% at least one keyword must be supplied
%% publication information
@@ -716,6 +716,29 @@
glue code between the R language classes and the underlying C++
classes.
+% MS: I think this looks better at the bottom of the page.
+% so it appears after the new section starts where it is referenced.
+\begin{table}[bp]
+\centering
+\begin{tabular}{lccl}
+\toprule
+\textbf{Class} &
+ \textbf{Slots} &
+ \textbf{Methods} &
+ \textbf{Dynamic Dispatch}\\
+\cmidrule{1-4}
+Message & 2 & 20 & yes (field names)\\
+Descriptor & 2 & 16 & yes (field names, enum types, nested types)\\
+FieldDescriptor & 4 & 18 & no\\
+EnumDescriptor & 4 & 11 & yes (enum constant names)\\
+FileDescriptor & 3 & \phantom{1}6 & yes (message/field definitions)\\
+EnumValueDescriptor & 3 & \phantom{1}6 & no\\
+\bottomrule
+\end{tabular}
+\caption{\label{class-summary-table}Overview of Class, Slot, Method and
+ Dispatch Relationships}
+\end{table}
+
The \CRANpkg{Rcpp} package
\citep{eddelbuettel2011rcpp,eddelbuettel2013seamless} is used to
facilitate this integration of the R and C++ code for these objects.
@@ -744,33 +767,13 @@
\verb|object$method(arguments)|.
\end{itemize}
-Additionally, \texttt{RProtoBuf} implements the \texttt{.DollarNames} S3 generic function
-(defined in the \texttt{utils} package) for all classes to enable tab
-completion. Completion possibilities include pseudo-method names for all
-classes, plus dynamic dispatch on names or types specific to a given object.
+Additionally, \pkg{RProtoBuf} supports tab completion for all
+classes. Completion possibilities include pseudo-method names for all
+classes, plus dynamic dispatch on names or types specific to a given
+object. This functionality is implemented with the
+\texttt{.DollarNames} S3 generic function defined in the \pkg{utils}
+package.
-% TODO(ms): Add column check box for doing dynamic dispatch based on type.
-\begin{table}[h]
-\centering
-\begin{tabular}{lccl}
-\toprule
-\textbf{Class} &
- \textbf{Slots} &
- \textbf{Methods} &
- \textbf{Dynamic Dispatch}\\
-\cmidrule{1-4}
-Message & 2 & 20 & yes (field names)\\
-Descriptor & 2 & 16 & yes (field names, enum types, nested types)\\
-FieldDescriptor & 4 & 18 & no\\
-EnumDescriptor & 4 & 11 & yes (enum constant names)\\
-FileDescriptor & 3 & \phantom{1}6 & yes (message/field definitions)\\
-EnumValueDescriptor & 3 & \phantom{1}6 & no\\
-\bottomrule
-\end{tabular}
-\caption{\label{class-summary-table}Overview of Class, Slot, Method and
- Dispatch Relationships}
-\end{table}
-
\subsection{Messages}
The \texttt{Message} S4 class represents Protocol Buffer Messages and
@@ -840,14 +843,12 @@
then available on the search path.
<<>>=
-# field descriptor
-tutorial.Person$email
+tutorial.Person$email # field descriptor
-# enum descriptor
-tutorial.Person$PhoneType
+tutorial.Person$PhoneType # enum descriptor
-# nested type descriptor
-tutorial.Person$PhoneNumber
+
+tutorial.Person$PhoneNumber # nested type descriptor
# same as
tutorial.Person.PhoneNumber
@
@@ -855,7 +856,7 @@
Table~\ref{Descriptor-methods-table} provides a complete list of the
slots and available methods for Descriptors.
-\begin{table}[h]
+\begin{table}[tbp]
\centering
\begin{small}
\begin{tabular}{lp{10cm}}
@@ -901,12 +902,12 @@
\label{subsec-field-descriptor}
The class \emph{FieldDescriptor} represents field
-descriptor in R. This is a wrapper S4 class around the
+descriptors in R. This is a wrapper S4 class around the
\texttt{google::protobuf::FieldDescriptor} C++ class.
Table~\ref{fielddescriptor-methods-table} describes the methods
defined for the \texttt{FieldDescriptor} class.
-\begin{table}[h]
+\begin{table}[tbp]
\centering
\begin{small}
\begin{tabular}{lp{10cm}}
@@ -952,8 +953,9 @@
\subsection{Enum Descriptors}
\label{subsec-enum-descriptor}
-The class \emph{EnumDescriptor} is an R wrapper
-class around the C++ class \texttt{google::protobuf::EnumDescriptor}.
+The class \emph{EnumDescriptor} represents enum descriptors in R.
+This is a wrapper S4 class around the
+\texttt{google::protobuf::EnumDescriptor} C++ class.
Table~\ref{enumdescriptor-methods-table} describes the methods
defined for the \texttt{EnumDescriptor} class.
@@ -966,7 +968,7 @@
tutorial.Person$PhoneType$WORK
@
-\begin{table}[h]
+\begin{table}[tbp]
\centering
\begin{small}
\begin{tabular}{lp{10cm}}
@@ -1002,8 +1004,9 @@
\subsection{File Descriptors}
\label{subsec-file-descriptor}
-The class \emph{FileDescriptor} is an R wrapper
-class around the C++ class \texttt{google::protobuf::FileDescriptor}.
+The class \emph{FileDescriptor} represents file descriptors in R.
+This is a wrapper S4 class around the
+\texttt{google::protobuf::FileDescriptor} C++ class.
Table~\ref{filedescriptor-methods-table} describes the methods
defined for the \texttt{FileDescriptor} class.
@@ -1016,7 +1019,7 @@
f$Person
@
-\begin{table}[h]
+\begin{table}[tbp]
\centering
\begin{small}
\begin{tabular}{lp{10cm}}
@@ -1045,8 +1048,9 @@
\subsection{Enum Value Descriptors}
\label{subsec-enumvalue-descriptor}
-The class \emph{EnumValueDescriptor} is an R wrapper
-class around the C++ class \texttt{google::protobuf::EnumValueDescriptor}.
+The class \emph{EnumValueDescriptor} represents enumeration value
+descriptors in R. This is a wrapper S4 class around the
+\texttt{google::protobuf::EnumValueDescriptor} C++ class.
Table~\ref{EnumValueDescriptor-methods-table} describes the methods
defined for the \texttt{EnumValueDescriptor} class.
@@ -1058,7 +1062,7 @@
tutorial.Person$PhoneType$value(number=1)
@
-\begin{table}[h]
+\begin{table}[tbp]
\centering
\begin{small}
\begin{tabular}{lp{10cm}}
@@ -1468,7 +1472,7 @@
very large data sets on large compute clusters.
Many types of data analysis over large data sets may involve very rare
-phenomenon or be dealing with highly skewed data sets or inflexible
+phenomenon or deal with highly skewed data sets or inflexible
raw data storage systems from which unbiased sampling is not feasible.
In such situations, MapReduce and binning may be combined as a
pre-processing step for a wide range of statistical and scientific
@@ -1529,10 +1533,11 @@
\end{verbatim}
This generates a Python module called \texttt{histogram\_pb2.py}, containing both the
descriptor information as well as methods to read and manipulate the histogram
-message data.
+message data. The following simple Python script uses this generated
+module to create a histogram and write out the protocol buffer
+representation to a file:
\begin{Code}
-# Import modules
from histogram_pb2 import HistogramState;
# Create empty Histogram message
@@ -1549,9 +1554,10 @@
outfile.close()
\end{Code}
-We can then read in the histogram into R and plot it with :
+The protocol buffer can then be read into R and converted to a native
+R histogram object for plotting:
-\begin{verbatim}
+\begin{Code}
library(RProtoBuf)
library(HistogramTools)
@@ -1565,7 +1571,7 @@
# Convert to native R histogram object and plot
plot(as.histogram(hist))
-\end{verbatim}
+\end{Code}
<<echo=FALSE,fig=TRUE,width=8,height=4>>=
require(RProtoBuf)
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