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From: <wa...@us...> - 2008-02-29 15:40:13
|
Revision: 1245
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1245&view=rev
Author: warnes
Date: 2008-02-29 07:40:11 -0800 (Fri, 29 Feb 2008)
Log Message:
-----------
Update for release 1.2.3
Modified Paths:
--------------
trunk/SASxport/DESCRIPTION
trunk/SASxport/inst/ChangeLog
trunk/SASxport/inst/NEWS
Modified: trunk/SASxport/DESCRIPTION
===================================================================
--- trunk/SASxport/DESCRIPTION 2008-02-29 15:37:16 UTC (rev 1244)
+++ trunk/SASxport/DESCRIPTION 2008-02-29 15:40:11 UTC (rev 1245)
@@ -1,8 +1,8 @@
Package: SASxport
Type: Package
Title: Read and Write SAS XPORT Files
-Version: 1.2.2
-Date: 2007-11-07
+Version: 1.2.3
+Date: 2008-02-29
Description: This package provides functions for reading, listing
the contents of, and writing SAS xport format files.
The functions support reading and writing of either
Modified: trunk/SASxport/inst/ChangeLog
===================================================================
--- trunk/SASxport/inst/ChangeLog 2008-02-29 15:37:16 UTC (rev 1244)
+++ trunk/SASxport/inst/ChangeLog 2008-02-29 15:40:11 UTC (rev 1245)
@@ -1,3 +1,12 @@
+2008-02-29 15:37 warnes
+
+ * [r1244] man/write.xport.Rd: Correct typo in write.xport man page
+
+2007-11-09 22:45 warnes
+
+ * [r1227] inst/ChangeLog, inst/NEWS: Update NEWS and ChangeLog for
+ 1.2.2
+
2007-11-09 19:59 warnes
* [r1226] src/ibm2ieee.c, src/ieee2ibm.c: Apply patches to fix
Modified: trunk/SASxport/inst/NEWS
===================================================================
--- trunk/SASxport/inst/NEWS 2008-02-29 15:37:16 UTC (rev 1244)
+++ trunk/SASxport/inst/NEWS 2008-02-29 15:40:11 UTC (rev 1245)
@@ -1,3 +1,11 @@
+Version 1.2.3 2008-02-29
+------------------------
+
+Bug fixes:
+
+- Fix typo in manual page for write.xport() reported by Yinlai Meng.
+
+
Version 1.2.2 2007-11-09
------------------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2008-02-29 15:37:25
|
Revision: 1244
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1244&view=rev
Author: warnes
Date: 2008-02-29 07:37:16 -0800 (Fri, 29 Feb 2008)
Log Message:
-----------
Correct typo in write.xport man page
Modified Paths:
--------------
trunk/SASxport/man/write.xport.Rd
Modified: trunk/SASxport/man/write.xport.Rd
===================================================================
--- trunk/SASxport/man/write.xport.Rd 2008-02-07 17:10:27 UTC (rev 1243)
+++ trunk/SASxport/man/write.xport.Rd 2008-02-29 15:37:16 UTC (rev 1244)
@@ -39,8 +39,8 @@
converted to upper case. All characters outside of the set A-Z,
0-9, and '\_' are converted to '\_'.
\item Character variables are stored as characters.
- \item If \code{make.formats=TRUE} (the default), factor variables are stored as numeric with an appropriate SAS
- format specification. If \code{make.formats=FALSE}, factor
+ \item If \code{autogen.formats=TRUE} (the default), factor variables are stored as numeric with an appropriate SAS
+ format specification. If \code{autogen.formats=FALSE}, factor
variables are stored as characters.
\item All numeric variables are stored as double-precision floating
point values utilizing the IBM mainframe double precision floating
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2008-02-07 17:10:33
|
Revision: 1243
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1243&view=rev
Author: warnes
Date: 2008-02-07 09:10:27 -0800 (Thu, 07 Feb 2008)
Log Message:
-----------
Slides for Myriad visit
Modified Paths:
--------------
trunk/PathwayModeling/thesispaper/slides.tex
Added Paths:
-----------
trunk/PathwayModeling/thesispaper/figures/MSR16.pdf
Added: trunk/PathwayModeling/thesispaper/figures/MSR16.pdf
===================================================================
(Binary files differ)
Property changes on: trunk/PathwayModeling/thesispaper/figures/MSR16.pdf
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: trunk/PathwayModeling/thesispaper/slides.tex
===================================================================
--- trunk/PathwayModeling/thesispaper/slides.tex 2008-02-05 21:38:08 UTC (rev 1242)
+++ trunk/PathwayModeling/thesispaper/slides.tex 2008-02-07 17:10:27 UTC (rev 1243)
@@ -3,10 +3,7 @@
\mode<presentation>
{
\usetheme{Warsaw}
- % or ...
-
\setbeamercovered{transparent}
- % or whatever (possibly just delete it)
}
%\setbeameroption{show notes}
@@ -20,7 +17,6 @@
% \documentclass[doublespacing]{elsart}
\usepackage{graphicx}
\usepackage[nogin]{Sweave}
-\usepackage[numbers]{natbib} \bibliographystyle{plainnat}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{yfonts}
@@ -32,18 +28,20 @@
\usepackage{makeidx}
\usepackage{dchem}
\usepackage{color}
+\usepackage[numbers]{natbib}
+\bibliographystyle{plainnat}
\newcommand{\deriv}[2]{\ensuremath{\frac{\mathrm{d} #1}{\mathrm{d} #2}}}
\title{Statistical Modeling of Biochemical Pathways}
-\author{Robert B. Burrows\inst{1} \and Gregory R. Warnes\inst{2,3} }
+\author{Gregory R. Warnes\inst{1,2,3} }
\institute{
\inst{1}%
- New England Biometrics\\
- North Scituate, RI
+ Biostatistics and Computational Biology \\
+ University of Rochester
\and
\inst{2}%
- Biostatistics and Computational Biology \\
+ Center for Biodefense Immune Modeling \\
University of Rochester
\and
\inst{3}%
@@ -56,37 +54,56 @@
$ $Id$ $
}
-%\begin{abstract}
-%The usefulness of Markov chain Monte Carlo methods for the modeling
-%of biochemical reactions is examined. With simulated data, it is
-%shown that mechanistic models can be fit to sequences of enzymatic
-%reactions. These methods have the advantages of being relatively easy
-%to use and producing probability distributions for the model
-%parameters rather than point estimates.
-%Three Markov chain Monte Carlo algorithms are used to fit models to
-%data from a
-%sequence of 4 enzymatic reactions. The algorithms
-%are evaluated with respect to
-%the goodness-of-fit of the fitted models and the time to completion.
-%It is shown that the algorithms produce essentially the same
-%parameter distributions but the time to completion varies.
-%\end{abstract}
-
\frame{
\maketitle
}
+%%\section[Abstract]{}
+%%\begin{abstract}
+%\frame{
+% \frametitle{Abstract}
+% \small
+% We examine the usefulness of Bayesian statistical methods for
+% the modeling of biochemical reactions. With simulated data, it is
+% shown that these methods can effectively fit mechanistic models of
+% sequences of enzymatic reactions to experimental data. This
+% approach has the advantages of being flexible, relatively easy to use,
+% and producing full probability distributions for the model parameters
+% rather than point estimates, thus allowing more informative inferences
+% (including relationships between parameters) to be drawn. Further,
+% these methods perform well even when the mechanistic model leads
+% to multiple solution regions, high parameter correlations, and other
+% 'unfriendly' behavior.
+
+% The presentation will include a brief overview of Bayesian statistical
+% methods for those unfamiliar with these techniques, as well as a brief
+% discussion of the computational methods utilized.
+%}
+%%\end{abstract}
+
\section[Outline]{}
\frame{
\frametitle{Outline}
- \tableofcontents
+
+% \tableofcontents
+
+ \begin{columns}
+ \begin{column}{0.5\textwidth}
+ \tableofcontents[sections={1-4}]
+ \end{column}
+ \begin{column}{0.5\textwidth}
+ \tableofcontents[sections={5-8}]
+ \end{column}
+ \end{columns}
+
}
\section{Overview}
+\subsection{Goal}
\frame{
\frametitle{Overview}
- \begin{block}{Goal:}
+ \begin{block}{Goal: Model Biochemical Pathways}
Estimate key rate parameters of biological pathways, e.g
\includegraphics[width=0.75\textwidth]{figures/glycolysis}
@@ -95,16 +112,87 @@
changes, and understand the system.
\end{block}
}
+
+\subsection{Components}
\frame{
\frametitle{Overview}
- \begin{block}{Method:}
- ``Wrap'' standard deterministic mathematical model
- within a Bayesian statistical model
+ \begin{block}{Combine 3 components:}
+ \begin{tabular}{ll}
+ Biochemistry & Biochemical components \& relationships \\
+ Mathematical Model & Strucure of relationships between components \\
+ Bayesian Statistics & Relationship between previous information, \\
+ & model and measured data \\
+ \end{tabular}
+
+% \begin{block}{Method:}
+% \begin{center}
+% ``Wrap'' standard deterministic mathematical model describing a
+% biochemical pathway within a Bayesian statistical model
+% \end{center}
\end{block}
+
}
+\subsection{Intro to Bayesian Statistics}
+\frame{
+ \frametitle{Intro to Bayesian Statistics (1/2)}
+ \begin{enumerate}
+ \item Based on Decision Theory
+ \item Modeling Process:
+ \begin{enumerate}
+ \item Costruct a model for observed data: {\color{blue} ``Likelihood'':
+ $L(\mathit{Data}|\theta)$ }
+ \item Describe current information about model parameters:
+ { \color{green} ``Prior distribution'' $\pi(\theta)$ }
+ \item Run experiment \& collect data
+ \item Apply Bayes Rule $\to$ {\color{red}``Posterior distribution''}
+
+\begin{equation}\label{BayesRule}
+{\color{red}\pi(\theta|\mathit{Data})} = \frac{{\color{blue}L(\mathit{Data}|\theta)} {\color{green}\pi(\theta)}}{\int {L(\mathit{Data}|\theta) \pi(\theta)}d\theta}
+\end{equation}
+
+ \item Draw conclusions using Posterior
+ \end{enumerate}
+ \end{enumerate}
+}
+
+\frame{
+ \frametitle{Intro to Bayesian Statistics (2/2)}
+ \begin{itemize}
+ \item Strengths
+ \begin{itemize}
+ \item Very flexible
+ \item Consistent with human thinking
+ \item Allows inclusion of existing domain knowledge
+ \end{itemize}
+ \item Weaknesses
+ \begin{itemize}
+ \item Characterization of ``current information'' can be
+ controversial
+ \item Computationaly expensive
+ \item Less popular than Frequentist statistics
+ \end{itemize}
+ \end{itemize}
+}
+
+
+
\section{Evaluation Approach}
+
\frame{
+ \frametitle{Overview}
+ \begin{block}{Goal: Model Biochemical Pathways}
+ Estimate key rate parameters of biological pathways, e.g
+
+ \includegraphics[width=0.75\textwidth]{figures/glycolysis}
+
+ in order to estimate rate parameters, predict responses to
+ changes, and understand the system.
+ \end{block}
+}
+
+
+\frame{
\frametitle{Evaluation Approach}
\begin{enumerate}
\item{Create artificial model}
@@ -124,7 +212,7 @@
R3 \yields R4 \yields R5 \yields sink \end{reaction}
Chemical Equations:
- \begin{chemarray*} \small
+ \begin{chemarray*}
source &\yields^{k_1}& R1\\
R1 + E1 &\eqbm^{k_2}_{k_3}& R1E1 \yields^{k_4} R2 + E1\\
R2 + E2 &\eqbm^{k_5}_{k_6}& R2E2 \yields^{k_7} R3 + E2\\
@@ -324,7 +412,43 @@
}
\frame{
- \frametitle{Convergence Rates}
+\begin{block}{What is Markov Chain Monte Carlo?}
+
+\textcolor{blue}{Markov Chain Monte Carlo (MCMC)} is a technique for
+generating \textcolor{red}{dependent} samples (a Markov Chain) from a
+distribution without needing the \textcolor{blue}{normalizing constant}.
+
+\end{block}
+\begin{block}{When is MCMC useful?}
+
+\textcolor{blue}{MCMC} is useful when it is \textcolor{red}{difficult} to
+\textcolor{blue}{simulate} from the target distribution, such as when the
+\textcolor{blue}{normalizing constant} is difficult or impossible to
+compute and \textcolor{blue}{rejection sampling} is not possible.
+
+Examples:
+\begin{itemize}
+ \item Sampling from \textcolor{blue}{Bayesian Posterior Distributions}
+ \item Computing \textcolor{blue}{Maximum-Likelihood tests for intractable
+ likelihoods}
+\end{itemize}
+
+\end{block}
+
+}
+
+\frame{
+\frametitle{MCMC In pictures}
+\begin{center}
+\includegraphics[height=0.75\textheight]{MCMC-Picture}
+\hfill
+\includegraphics[height=0.75\textheight]{MCMC-Histogram}
+\end{center}
+}
+
+
+\frame{
+ \frametitle{Convergence Rates (1/2)}
\begin{center}
Mean Squared Residuals \\
~
@@ -343,6 +467,16 @@
\end{center}
}
+\frame{
+ \frametitle{Convergence Rates (2/2)}
+ \begin{center}
+ \includegraphics[scale=0.5]{figures/MSR16}
+ \end{center}
+
+
+}
+
+
\section{Results}
\frame{
\frametitle{Results}
@@ -377,22 +511,77 @@
\end{center}
}
-\section[]{References}
+\section{Acknowledgments}
\frame{
- \frametitle{For More Information}
- \begin{itemize}
- \item Greg Warnes \
+ \frametitle{Acknowledgments}
+
+ Robert "Bing" Burrows, Ph.D., who was primarily responsible for work
+ described here passed away unexpectedly on December 27, 2006.
+
+\begin{quote}
+\tiny
+ BURROWS, ROBERT BERNARD, II, 63, of North Scituate [Rhode Island],
+ died Wednesday, December 27, 2006. He was a long time resident of
+ Lexington, MA before moving to Rhode Island in 2001. After
+ graduating from Lexington High School, Dr. Burrows earned his
+ Bachelor of Arts from Northeastern University, a Ph.D. in
+ Biochemistry from the Massachusetts Institute of Technology, and a
+ Master of Science in Statistics from the University of Rhode Island.
+ He was a self-employed Research Biochemist and previously worked for
+ the Boston Biomedical Research Institute. He leaves his sister Ellen
+ Conner and her husband Donald of Coventry, his dearest friend Sally
+ Glanz of North Scituate and many cousins. (\emph{The Providence Journal/Evening
+ Bulletin} 2006 Dec. 31; Sec. B5)
+\end{quote}
+}
+
+\section[]{Reference \& Contact Information}
+\frame{
+ \frametitle{Reference \& Contact Information}
+ \begin{block}{Manuscript}
+ Burrows~RB, Warnes~GR, Hanumara~RC, ``Statistical Modeling of Biochemical Pathways'',
+ \emph{IET Systems Biology}, IET Syst. Biol. 1, 353 (2007)
+ \end{block}
+ \begin{block}{Contact Information}
\begin{itemize}
- \item Email: \texttt{wa...@bs...}
- \item Personal Web Page: \texttt{http://www.warnes.net}
- \item Research Web Page: \texttt{http://research.warnes.net}
+ \item Email: \texttt{gr...@wa...}
+ \item Personal Web Page: \texttt{http://www.warnes.net}
+ \item CBIM Web Page: \texttt{https://cbim.urmc.rochester.edu}
+ \item UR Biostat Web Page \texttt{http://www.urmc.rochester.edu/smd/biostat}
\end{itemize}
- \item Robert Burrows
- \begin{itemize}
- \item Email: \texttt{rb...@ne...}
- \item Web Page: \texttt{http://www.nebiometrics.com}
- \end{itemize}
- \end{itemize}
+ \end{block}
}
+%%\bibliography{./refs}
+%\begin{thebibliography}{99}
+% \bibitem{Oates02}%1
+% Oates,~P.J., 2002, Polyol pathway and diabetic peripheral
+% neuropathy, \emph{Int. Rev. Neurobiol.},
+% \textbf{50}, 325--392.
+% \bibitem{Gilks95} %5
+% Gilkes,~W.R., Richardson,~S., and Spiegelhalter,~D.J. (Ed.),
+% \emph{Markov Chain Monte Carlo in Practice} (Boca Raton, FL:
+% Chapman \& Hall/CRC)
+% \bibitem{R}%9
+% R Development Team, \emph{R: A Language and Environment for
+% Statistical Computing}, http://www.r-project.org (accessed 7 Nov 06)
+% \bibitem{Michaelis13} %10
+% Michaelis, L. and Menten, M.L., 1913, Die kinetic der
+% invertinwirkung, \emph{Biochem. Zeit.}, \textbf{49},
+% 333--369.
+% \bibitem{Hydra}%13
+% Warnes, G.R., Hydra {MCMC} {L}ibrary,
+% http://www.sourceforge.net/projects/hydra-mcmc
+% \bibitem{Warnes00} %14
+% Warnes, G.R., 2000, The {N}ormal {K}ernel {C}oupler: {A}n adaptive
+% {M}arkov chain {M}onte {C}arlo method for efficiently sampling
+% from multi-modal distributions, thesis, University of Washington.
+% \bibitem{projo}%16
+% OBITUARIES-SCITUATE-BURROWS. \emph{The Providence Journal/Evening
+% Bulletin} 2006 Dec. 31; Sec. B5
+%\end{thebibliography}
+
+
+
+
\end{document}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2008-02-05 21:38:12
|
Revision: 1242
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1242&view=rev
Author: warnes
Date: 2008-02-05 13:38:08 -0800 (Tue, 05 Feb 2008)
Log Message:
-----------
Update figure paths
Modified Paths:
--------------
trunk/PathwayModeling/thesispaper/figure2.Snw
trunk/PathwayModeling/thesispaper/paper.pdf
trunk/PathwayModeling/thesispaper/slides.tex
Modified: trunk/PathwayModeling/thesispaper/figure2.Snw
===================================================================
--- trunk/PathwayModeling/thesispaper/figure2.Snw 2008-01-30 19:55:08 UTC (rev 1241)
+++ trunk/PathwayModeling/thesispaper/figure2.Snw 2008-02-05 21:38:08 UTC (rev 1242)
@@ -1,14 +1,14 @@
<<fig2,echo=F,eval=F>>=2
-# source("R/pulse.R")
-# rawdata <- read.table("data/rawdata.dat",header=T)
-# attach(rawdata)
-# pdf(file="figures/tempDir/pulse.pdf",width=9,height=5)
-# pulse()
-# postscript(file="figures/tempDir/pulse.eps",width=9,height=5)
-# pulse()
-# N <- dev.off()
-# N <- dev.off()
-# detach(rawdata)
+#source("R/pulse.R")
+#rawdata <- read.table("data/rawdata.dat",header=T)
+#attach(rawdata)
+#pdf(file="figures/tempDir/pulse.pdf",width=9,height=5)
+#pulse()
+#postscript(file="figures/tempDir/pulse.eps",width=9,height=5)
+#pulse()
+#N <- dev.off()
+#N <- dev.off()
+#detach(rawdata)
source("R/pulse_nocolor.R")
rawdata.trimmed <- read.table("data/rawdata.trimmed.dat",header=T)
Modified: trunk/PathwayModeling/thesispaper/paper.pdf
===================================================================
(Binary files differ)
Modified: trunk/PathwayModeling/thesispaper/slides.tex
===================================================================
--- trunk/PathwayModeling/thesispaper/slides.tex 2008-01-30 19:55:08 UTC (rev 1241)
+++ trunk/PathwayModeling/thesispaper/slides.tex 2008-02-05 21:38:08 UTC (rev 1242)
@@ -43,12 +43,11 @@
North Scituate, RI
\and
\inst{2}%
- Statistical Applications \\
- Pfizer, Inc.
+ Biostatistics and Computational Biology \\
+ University of Rochester
\and
\inst{3}%
- Department of Computer Science \\
- Yale University
+ Random Technologies, LLC.
}
\begin{document}
@@ -166,7 +165,7 @@
\vspace{-0.125in}
\begin{center}
\label{pulse}
- \includegraphics[height=0.6\textheight]{figures/pulse}
+ \includegraphics[height=0.6\textheight]{figures/tempDir/pulse}
\end{center}
\vspace{-0.125in}
\item Triplicate estimates of reactant concentrations every minute
@@ -362,7 +361,7 @@
\column{2in}
- \includegraphics[width=2in]{figures/scatterPlot}
+ \includegraphics[width=2in]{figures/tempDir/scatterPlot}
\end{columns}
}
@@ -370,11 +369,11 @@
\frametitle{Actual vs Fitted}
\begin{center}
- \includegraphics[width=0.5\textwidth]{figures/V1fitted}
- \includegraphics[width=0.5\textwidth]{figures/V2fitted} \\
+ \includegraphics[width=0.5\textwidth]{figures/tempDir/V1fitted}
+ \includegraphics[width=0.5\textwidth]{figures/tempDir/V2fitted} \\
- \includegraphics[width=0.5\textwidth]{figures/V3fitted}
- \includegraphics[width=0.5\textwidth]{figures/V4fitted} \\
+ \includegraphics[width=0.5\textwidth]{figures/tempDir/V3fitted}
+ \includegraphics[width=0.5\textwidth]{figures/tempDir/V4fitted} \\
\end{center}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2008-01-30 19:55:13
|
Revision: 1241
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1241&view=rev
Author: warnes
Date: 2008-01-30 11:55:08 -0800 (Wed, 30 Jan 2008)
Log Message:
-----------
Update DESCRIPTION and NEWS for release 2.4.0
Modified Paths:
--------------
trunk/gdata/DESCRIPTION
trunk/gdata/inst/NEWS
Added Paths:
-----------
trunk/gdata/ChangeLog
Added: trunk/gdata/ChangeLog
===================================================================
--- trunk/gdata/ChangeLog (rev 0)
+++ trunk/gdata/ChangeLog 2008-01-30 19:55:08 UTC (rev 1241)
@@ -0,0 +1 @@
+link inst/ChangeLog
\ No newline at end of file
Property changes on: trunk/gdata/ChangeLog
___________________________________________________________________
Name: svn:special
+ *
Modified: trunk/gdata/DESCRIPTION
===================================================================
--- trunk/gdata/DESCRIPTION 2008-01-29 11:26:03 UTC (rev 1240)
+++ trunk/gdata/DESCRIPTION 2008-01-30 19:55:08 UTC (rev 1241)
@@ -3,8 +3,9 @@
Description: Various R programming tools for data manipulation
Depends: R (>= 2.4.0)
Imports: gtools
-Version: 2.3.1
-Author: Gregory R. Warnes. Includes R source code and/or documentation
- contributed by Ben Bolker, Gregor Gorjanc, and Thomas Lumley
+Version: 2.4.0
+Date: 2008-01-30
+Author: Gregory R. Warnes and Gregor Gorjanc. Includes R source code
+ and/or documentation contributed by Ben Bolker and Thomas Lumley.
Maintainer: Gregory Warnes <gre...@ur...>
License: GPL-2
Modified: trunk/gdata/inst/NEWS
===================================================================
--- trunk/gdata/inst/NEWS 2008-01-29 11:26:03 UTC (rev 1240)
+++ trunk/gdata/inst/NEWS 2008-01-30 19:55:08 UTC (rev 1241)
@@ -1,5 +1,40 @@
+CHANGES IN 2.4.0 (2008-01-30)
+-----------------------------
+
+- The keep() function now includes an 'all' argument to specify how
+ objects with names starting with '.' are handled.
+
+- keep() now shows an informative warning message when a requested
+ object does not exist
+
+- New vignette "Mapping Levels of a Factor" describing the use of
+ mapLevels().
+
+- New vignette "Working with Unknown Values" describing the use of
+ isUnknown() and unknownToNA().
+
+- Several enhancements to read.xls() (thanks to Gabor Grothendieck):
+
+ - New function xls2csv(), which handles converting an xls file
+ to a csv file and returns a connection to the
+ temporary csv file
+
+ - xls2csv() and read.xls() both allow a file or a url to be specified
+
+ - read.xls() has a new 'pattern' argument which, if supplied,
+ will ignore everything prior to the first line in th csv file
+ that matches the pattern. This is typically used if there
+ are a variable number of comment lines prior to the header
+ in which case one can specify one of the column
+ headings as the pattern. read.xls should
+ be compatible with the old read.xls.
+
+- Minor fixes to drop.levels(), is.what().
+
+- Implementation of unit tests for most functions.
+
CHANGES IN 2.3.1 (2006-10-29)
----------------------------------------
+-----------------------------
- Arguments as well as their position of reorder.factor have been changed
to conform with reorder.factor method in stats package, due to collision
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From: <ar...@us...> - 2008-01-29 11:26:16
|
Revision: 1240
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1240&view=rev
Author: arnima
Date: 2008-01-29 03:26:03 -0800 (Tue, 29 Jan 2008)
Log Message:
-----------
Added argument 'all'.
Modified Paths:
--------------
trunk/gdata/man/keep.Rd
Modified: trunk/gdata/man/keep.Rd
===================================================================
--- trunk/gdata/man/keep.Rd 2008-01-29 11:09:38 UTC (rev 1239)
+++ trunk/gdata/man/keep.Rd 2008-01-29 11:26:03 UTC (rev 1240)
@@ -7,12 +7,14 @@
Remove all objects from the default workspace, except those specified.
}
\usage{
-keep(..., list = character(0), sure = FALSE)
+keep(..., list = character(0), all = FALSE, sure = FALSE)
}
\arguments{
\item{...}{objects to be kept, specified one by one, quoted or
unquoted.}
\item{list}{character vector of object names to be kept.}
+ \item{all}{whether hidden objects (beginning with a \code{.}) should
+ be removed, unless explicitly kept.}
\item{sure}{whether to perform the removal, otherwise return names of
objects that would have been removed.}
}
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|
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From: <ar...@us...> - 2008-01-29 11:09:45
|
Revision: 1239
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1239&view=rev
Author: arnima
Date: 2008-01-29 03:09:38 -0800 (Tue, 29 Jan 2008)
Log Message:
-----------
Added argument 'all'.
Modified Paths:
--------------
trunk/gdata/R/keep.R
Modified: trunk/gdata/R/keep.R
===================================================================
--- trunk/gdata/R/keep.R 2008-01-04 18:59:56 UTC (rev 1238)
+++ trunk/gdata/R/keep.R 2008-01-29 11:09:38 UTC (rev 1239)
@@ -1,4 +1,4 @@
-keep <- function(..., list=character(0), sure=FALSE)
+keep <- function(..., list=character(0), all=FALSE, sure=FALSE)
{
if(missing(...) && missing(list))
{
@@ -8,7 +8,7 @@
}
names <- as.character(substitute(list(...)))[-1]
list <- c(list, names)
- keep.elements <- match(list, ls(1))
+ keep.elements <- match(list, ls(1,all.names=all))
if(any(is.na(keep.elements)))
{
warning("You tried to keep \"", list[which(is.na(keep.elements))[1]],
@@ -17,8 +17,8 @@
}
if(sure)
- rm(list=ls(1)[-keep.elements], pos=1)
+ rm(list=ls(1,all.names=all)[-keep.elements], pos=1)
else
- return(ls(1)[-keep.elements])
+ return(ls(1,all.names=all)[-keep.elements])
}
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From: <wa...@us...> - 2008-01-04 18:59:57
|
Revision: 1238
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1238&view=rev
Author: warnes
Date: 2008-01-04 10:59:56 -0800 (Fri, 04 Jan 2008)
Log Message:
-----------
Fix examples for overplot()
Modified Paths:
--------------
trunk/gplots/man/overplot.Rd
Modified: trunk/gplots/man/overplot.Rd
===================================================================
--- trunk/gplots/man/overplot.Rd 2008-01-02 16:58:01 UTC (rev 1237)
+++ trunk/gplots/man/overplot.Rd 2008-01-04 18:59:56 UTC (rev 1238)
@@ -67,11 +67,11 @@
# same scale
overplot( RQ ~ Conc..ug.ml. | Test.Substance,
data=rtPCR,
- subset=Detector=="ProbeType 7" & Conc..ug.ml. > 0,
+ subset=Detector=="ProbeType 1" & Conc..ug.ml. > 0,
same.scale=TRUE,
log="xy",
f=3/4,
- main="Detector=ProbeType 7",
+ main="Detector=ProbeType 1",
xlab="Concentration (ug/ml)",
ylab="Relative Gene Quantification"
)
@@ -79,10 +79,10 @@
# different scales, but force lower limit to 0.01
overplot( RQ ~ Conc..ug.ml. | Test.Substance,
data=rtPCR,
- subset=Detector=="ProbeType 7" & Conc..ug.ml. > 0,
+ subset=Detector=="ProbeType 8" & Conc..ug.ml. > 0,
log="xy",
f=3/4,
- main="Detector=ProbeType 7",
+ main="Detector=ProbeType 8",
xlab="Concentration (ug/ml)",
ylab="Relative Gene Quantification",
min.y=0.01
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From: <wa...@us...> - 2008-01-02 16:58:05
|
Revision: 1237
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1237&view=rev
Author: warnes
Date: 2008-01-02 08:58:01 -0800 (Wed, 02 Jan 2008)
Log Message:
-----------
Update Marc's email address
Modified Paths:
--------------
trunk/gplots/man/barplot2.Rd
Modified: trunk/gplots/man/barplot2.Rd
===================================================================
--- trunk/gplots/man/barplot2.Rd 2008-01-02 16:56:53 UTC (rev 1236)
+++ trunk/gplots/man/barplot2.Rd 2008-01-02 16:58:01 UTC (rev 1237)
@@ -213,7 +213,7 @@
midpoints of each \emph{group} of bars, see example.
}
\author{Original barplot() by R-Core. Enhancements by Marc
- Schwartz \email{msc...@mn...}
+ Schwartz \email{mar...@co...}
}
\note{
Prior to \R 1.6.0, \code{barplot} behaved as if \code{axis.lty = 1},
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From: <wa...@us...> - 2008-01-02 16:57:03
|
Revision: 1236
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1236&view=rev
Author: warnes
Date: 2008-01-02 08:56:53 -0800 (Wed, 02 Jan 2008)
Log Message:
-----------
Update Marc's email address
Modified Paths:
--------------
trunk/gmodels/man/CrossTable.Rd
Modified: trunk/gmodels/man/CrossTable.Rd
===================================================================
--- trunk/gmodels/man/CrossTable.Rd 2007-12-20 22:48:22 UTC (rev 1235)
+++ trunk/gmodels/man/CrossTable.Rd 2008-01-02 16:56:53 UTC (rev 1236)
@@ -116,11 +116,10 @@
resid/sresid/asresid: Pearson Residuals (from chi-square tests).
}
-\author{Marc Schwartz \email{msc...@mn...}. Original
+\author{Marc Schwartz \email{mar...@co...}. Original
version posted to r-devel on Jul 27, 2002. SPSS format
- modifications added by Nitin Jain \email{nit...@pf...}
- based upon code provided by Dirk Enzmann
- \email{dir...@ju...}}
+ modifications added by Nitin Jain based upon code provided
+ by Dirk Enzmann \email{dir...@ju...}}
\seealso{\code{\link{xtabs}},
\code{\link{table}},
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|
|
From: <wa...@us...> - 2007-12-20 22:48:31
|
Revision: 1235
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1235&view=rev
Author: warnes
Date: 2007-12-20 14:48:22 -0800 (Thu, 20 Dec 2007)
Log Message:
-----------
Two letter clarification of help text for heatmap.2()
Modified Paths:
--------------
trunk/gplots/man/heatmap.2.Rd
Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd 2007-12-20 22:24:40 UTC (rev 1234)
+++ trunk/gplots/man/heatmap.2.Rd 2007-12-20 22:48:22 UTC (rev 1235)
@@ -81,7 +81,7 @@
\item{Rowv}{determines if and how the \emph{row} dendrogram should be
reordered. By default, it is TRUE, which implies dendrogram is
computed and reordered based on row means. If NULL or FALSE, then no
- dendrogram is computed and reordering is done. If a
+ dendrogram is computed and no reordering is done. If a
\code{\link{dendrogram}}, then it is used "as-is", ie
without any reordering. If a vector of integers, then dendrogram is
computed and reordered based on the order of the vector.}
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From: <wa...@us...> - 2007-12-20 22:25:12
|
Revision: 1234
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1234&view=rev
Author: warnes
Date: 2007-12-20 14:24:40 -0800 (Thu, 20 Dec 2007)
Log Message:
-----------
Restore plot layout at end of ooplot() example
Modified Paths:
--------------
trunk/gplots/man/ooplot.Rd
Modified: trunk/gplots/man/ooplot.Rd
===================================================================
--- trunk/gplots/man/ooplot.Rd 2007-12-12 21:16:44 UTC (rev 1233)
+++ trunk/gplots/man/ooplot.Rd 2007-12-20 22:24:40 UTC (rev 1234)
@@ -229,6 +229,8 @@
ooplot(test3f,type="stackbar",col=c("red","blue","green"))
ooplot(test5r,type="stackbar",col=c("red","blue","green"))
+ # restore default layout (1 plot/page)
+ layout(1)
}
\keyword{hplot}
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From: <wa...@us...> - 2007-12-12 21:16:51
|
Revision: 1233
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1233&view=rev
Author: warnes
Date: 2007-12-12 13:16:44 -0800 (Wed, 12 Dec 2007)
Log Message:
-----------
Move copyright notice for Randall's contributions from License section to Author section of the DESCRIPTION file.
Modified Paths:
--------------
trunk/gmodels/DESCRIPTION
Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION 2007-12-07 22:21:41 UTC (rev 1232)
+++ trunk/gmodels/DESCRIPTION 2007-12-12 21:16:44 UTC (rev 1233)
@@ -3,16 +3,16 @@
Title: Various R programming tools for model fitting
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker, Thomas Lumley, and Randall C Johnson.
+ Contributions from Randall C. Johnson are Copyright (2005)
+ SAIC-Frederick, Inc. Funded by the Intramural Research Program,
+ of the NIH, National Cancer Institute, Center for Cancer Research
+ under NCI Contract NO1-CO-12400.
Maintainer: Gregory R. Warnes <wa...@bs...>
Description: Various R programming tools for model fitting
Depends: R (>= 1.9.0)
Suggests: gplots, Matrix, nlme, lme4, coda
Imports: MASS, gdata
-License: GPL-2. Contributions from Randall C. Johnson are
- Copyright (2005) SAIC-Frederick, Inc. Funded by
- the Intramural Research Program, of the NIH, National
- Cancer Institute, Center for Cancer Research under NCI
- Contract NO1-CO-12400.
+License: GPL-2.
URL: http://cran.r-project.org/src/contrib/PACKAGES.html
http://www.sf.net/projects/r-gregmisc
Date: 2007-07-24
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From: <wa...@us...> - 2007-12-07 22:21:45
|
Revision: 1232
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1232&view=rev
Author: warnes
Date: 2007-12-07 14:21:41 -0800 (Fri, 07 Dec 2007)
Log Message:
-----------
Update DESCRIPTION and NEWS for release 2.14.1
Modified Paths:
--------------
trunk/gmodels/DESCRIPTION
trunk/gmodels/NEWS
Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION 2007-12-07 22:10:30 UTC (rev 1231)
+++ trunk/gmodels/DESCRIPTION 2007-12-07 22:21:41 UTC (rev 1232)
@@ -1,5 +1,5 @@
Package: gmodels
-Version: 2.14.0
+Version: 2.14.1
Title: Various R programming tools for model fitting
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker, Thomas Lumley, and Randall C Johnson.
Modified: trunk/gmodels/NEWS
===================================================================
--- trunk/gmodels/NEWS 2007-12-07 22:10:30 UTC (rev 1231)
+++ trunk/gmodels/NEWS 2007-12-07 22:21:41 UTC (rev 1232)
@@ -1,6 +1,17 @@
-Version 2.13.2
+Version 2.14.1
--------------
+New features:
+
+- Add support for 'lme' objects to estimable().
+
+Other:
+
+- Fix minor typos in manual page for estimable().
+
+Version 2.14.0
+--------------
+
New Features:
- Add support for 'mlm' objects to estimable
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|
From: <wa...@us...> - 2007-12-07 22:10:32
|
Revision: 1231
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1231&view=rev
Author: warnes
Date: 2007-12-07 14:10:30 -0800 (Fri, 07 Dec 2007)
Log Message:
-----------
Correct minor typos in man page for estimable()
Modified Paths:
--------------
trunk/gmodels/man/estimable.Rd
Modified: trunk/gmodels/man/estimable.Rd
===================================================================
--- trunk/gmodels/man/estimable.Rd 2007-12-07 22:09:13 UTC (rev 1230)
+++ trunk/gmodels/man/estimable.Rd 2007-12-07 22:10:30 UTC (rev 1231)
@@ -23,7 +23,7 @@
%.to.est(obj, params)
}
\arguments{
- \item{obj}{Regression (lm,glm,lme,lmer,mlm) object. }
+ \item{obj}{Regression (lm, glm, lme, lmer, mlm) object. }
\item{cm}{Vector, List, or Matrix specifying estimable linear functions or
contrasts. See below for details.}
\item{beta0}{Vector of null hypothesis values}
@@ -80,7 +80,7 @@
%is not intended for direct use.
}
\note{
- The estimated fixed effect parameter of \code{lme} objects may have
+ The estimated fixed effect parameters of \code{lme} objects may have
different degrees of freedom. If a specified contrast includes
nonzero coefficients for parameters with differing degrees of freedom,
the smallest number of degrees of freedom is used and a warning
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From: <wa...@us...> - 2007-12-07 22:09:15
|
Revision: 1230
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1230&view=rev
Author: warnes
Date: 2007-12-07 14:09:13 -0800 (Fri, 07 Dec 2007)
Log Message:
-----------
Add support for lme models to estimable()
Modified Paths:
--------------
trunk/gmodels/R/estimable.R
Modified: trunk/gmodels/R/estimable.R
===================================================================
--- trunk/gmodels/R/estimable.R 2007-12-07 22:07:26 UTC (rev 1229)
+++ trunk/gmodels/R/estimable.R 2007-12-07 22:09:13 UTC (rev 1230)
@@ -184,14 +184,21 @@
else if ("lm" %in% class(obj))
{
cf <- summary.lm(obj)$coefficients[, 1]
- vcv <- summary.lm(obj)$cov.unscaled * summary.lm(obj)$sigma^2
if ("glm" %in% class(obj))
- {
- vcv <- summary(obj)$cov.scaled
- }
+ vcv <- summary(obj)$cov.scaled
+ else
+ vcv <- summary.lm(obj)$cov.unscaled * summary.lm(obj)$sigma^2
}
+ else if ("lme" %in% class(obj))
+ {
+ s.o <- summary(obj)
+ cf <- s.o$tTable[,1]
+ se <- s.o$tTable[, 2]
+ rho <- s.o$cor
+ vcv <- rho * outer(se, se)
+ }
else
- stop("obj must be of class 'lm', 'glm', 'aov', 'gee' or 'geese'")
+ stop("obj must be of class 'lm', 'glm', 'aov', 'gee', 'geese', or 'lme'.")
u <- (cm %*% cf)-beta0
vcv.u <- cm %*% vcv %*% t(cm)
W <- t(u) %*% solve(vcv.u) %*% u
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From: <wa...@us...> - 2007-12-07 22:07:29
|
Revision: 1229
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1229&view=rev
Author: warnes
Date: 2007-12-07 14:07:26 -0800 (Fri, 07 Dec 2007)
Log Message:
-----------
Replace non-ascii characters in Soren's name with (equivalent?) ascii character to avoid character encoding issues.
Modified Paths:
--------------
trunk/gmodels/man/estimable.Rd
Modified: trunk/gmodels/man/estimable.Rd
===================================================================
--- trunk/gmodels/man/estimable.Rd 2007-11-30 18:05:43 UTC (rev 1228)
+++ trunk/gmodels/man/estimable.Rd 2007-12-07 22:07:26 UTC (rev 1229)
@@ -96,7 +96,7 @@
\author{
BXC (Bendix Carstensen) \email{bxc\@novonordisk.com},
Gregory R. Warnes \email{wa...@bs...},
- S\xF8ren H\xF8jsgaard \email{so...@ag...}, and
+ Soren Hojsgaard \email{so...@ag...}, and
Randall C Johnson \email{rjo...@nc...}
}
\seealso{
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From: <wa...@us...> - 2007-11-30 18:05:45
|
Revision: 1228
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1228&view=rev
Author: warnes
Date: 2007-11-30 10:05:43 -0800 (Fri, 30 Nov 2007)
Log Message:
-----------
Update defnitions of odd() and even() to use modulus operator instead of division. Prettier, I think, :-D
Modified Paths:
--------------
trunk/gtools/R/oddeven.R
Modified: trunk/gtools/R/oddeven.R
===================================================================
--- trunk/gtools/R/oddeven.R 2007-11-09 22:45:58 UTC (rev 1227)
+++ trunk/gtools/R/oddeven.R 2007-11-30 18:05:43 UTC (rev 1228)
@@ -1,5 +1,5 @@
# $Id$
# detect odd/even integers
-odd <- function(x) x!=as.integer(x/2)*2
-even <- function(x) x==as.integer(x/2)*2
+odd <- function(x) x %% 2 == 1
+even <- function(x) x %% 2 == 0
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From: <wa...@us...> - 2007-11-09 22:46:04
|
Revision: 1227
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1227&view=rev
Author: warnes
Date: 2007-11-09 14:45:58 -0800 (Fri, 09 Nov 2007)
Log Message:
-----------
Update NEWS and ChangeLog for 1.2.2
Modified Paths:
--------------
trunk/SASxport/inst/ChangeLog
trunk/SASxport/inst/NEWS
Modified: trunk/SASxport/inst/ChangeLog
===================================================================
--- trunk/SASxport/inst/ChangeLog 2007-11-09 19:59:48 UTC (rev 1226)
+++ trunk/SASxport/inst/ChangeLog 2007-11-09 22:45:58 UTC (rev 1227)
@@ -1,16 +1,57 @@
+2007-11-09 19:59 warnes
+
+ * [r1226] src/ibm2ieee.c, src/ieee2ibm.c: Apply patches to fix
+ problems on 64 bit platforms, as sumitted by Brian Ripley.
+
+2007-11-07 19:01 warnes
+
+ * [r1225] tests/Alfalfa_Test.Rout.save,
+ tests/TestUnnamedComponents.Rout.save, tests/Theoph.Rout.save,
+ tests/cars.Rout.save, tests/testDates.Rout.save,
+ tests/testNegative.Rout.save, tests/testNumeric.Rout.save,
+ tests/test_fields.Rout.save, tests/xport.Rout.save,
+ tests/xxx.Rout.save: Update version number
+
+2007-11-07 18:59 warnes
+
+ * [r1224] DESCRIPTION: Bump version number
+
+2007-11-07 18:14 warnes
+
+ * [r1223] src/ibm2ieee.c, src/reverse.c, src/writeSAS.c,
+ src/writeSAS.h: Apply patches to fix problems on 64 bit
+ platforms, as sumitted by Brian Ripley, and to replace assert()
+ calls with calls a macro that maps to error() unless standalone
+ testing is being done, in which case assert() is used.
+
+2007-11-05 15:25 warnes
+
+ * [r1220] DESCRIPTION, inst/NEWS, src/writeSAS.c: Remove extraneous
+ ';' characters after function closing brace
+
+2007-11-01 16:42 warnes
+
+ * [r1211] DESCRIPTION: Remove dependency on foreign, since the
+ necessary functionality is now provided internally.
+
+2007-11-01 06:44 warnes
+
+ * [r1210] TODO, inst/ChangeLog: Update TODO file
+
2007-11-01 06:43 warnes
- * man/SASxport-package.Rd, man/label.Rd, man/read.xport.Rd,
+ * [r1209] man/SASxport-package.Rd, man/label.Rd, man/read.xport.Rd,
man/toSAS.Rd, man/write.xport.Rd: Update to match changes to
functions
2007-11-01 06:42 warnes
- * DESCRIPTION: Update to match package changes
+ * [r1208] DESCRIPTION: Update to match package changes
2007-11-01 06:42 warnes
- * tests/Alfalfa_Test.Rout.save, tests/TestUnnamedComponents.R,
+ * [r1207] tests/Alfalfa_Test.Rout.save,
+ tests/TestUnnamedComponents.R,
tests/TestUnnamedComponents.Rout.save, tests/Theoph.Rout.save,
tests/cars.Rout.save, tests/testDates.Rout.save,
tests/testNegative.Rout.save, tests/testNumeric.R,
@@ -20,21 +61,21 @@
2007-11-01 06:41 warnes
- * inst/NEWS: Update for new release
+ * [r1206] inst/NEWS: Update for new release
2007-11-01 06:16 warnes
- * NAMESPACE: Remove dependency on foreign
+ * [r1205] NAMESPACE: Remove dependency on foreign
2007-11-01 06:15 warnes
- * src/ieee2ibm.c, src/init.c, src/swap_bytes.h: Copy code from
- foreign for lookup.xport() and read.xport(), extend
+ * [r1204] src/ieee2ibm.c, src/init.c, src/swap_bytes.h: Copy code
+ from foreign for lookup.xport() and read.xport(), extend
lookup.xport() to show information about SAS format and iformat
2007-11-01 06:14 warnes
- * R/SASformat.R, R/SASiformat.R, R/formats.R, R/fstr.R,
+ * [r1203] R/SASformat.R, R/SASiformat.R, R/formats.R, R/fstr.R,
R/iformat.R, R/lookup.xport.R, R/make.formats.R, R/read.xport.R,
R/toSAS.R, R/write.xport.R: - Use of the attribute named 'format'
caused problems with chron
@@ -63,33 +104,33 @@
2007-11-01 06:01 warnes
- * R/xport.R, src/SASxport.c, src/SASxport.h: Copy code from foreign
- for lookup.xport() and read.xport(), extend lookup.xport() to
- show information about SAS format and iformat
+ * [r1202] R/xport.R, src/SASxport.c, src/SASxport.h: Copy code from
+ foreign for lookup.xport() and read.xport(), extend
+ lookup.xport() to show information about SAS format and iformat
2007-11-01 05:59 warnes
- * R/importConvertDateTime.R: Improve handling of SAS data and time
- formats, simplify code
+ * [r1201] R/importConvertDateTime.R: Improve handling of SAS data
+ and time formats, simplify code
2007-10-29 15:37 warnes
- * DESCRIPTION, R/xport.numeric.R, inst/ChangeLog, src/ibm2ieee.c,
- src/ieee2ibm.c, tests/testNegative.R: Fixes to correct handling
- storage of negative numbers
+ * [r1200] DESCRIPTION, R/xport.numeric.R, inst/ChangeLog,
+ src/ibm2ieee.c, src/ieee2ibm.c, tests/testNegative.R: Fixes to
+ correct handling storage of negative numbers
2007-10-29 15:35 warnes
- * R/zzz.R: Belatedly commit change to startup message to give path
- to SASxport product page rather than contact page
+ * [r1199] R/zzz.R: Belatedly commit change to startup message to
+ give path to SASxport product page rather than contact page
2007-10-29 15:34 warnes
- * src/reverse.c: Comment out debugging message in reverse()
+ * [r1198] src/reverse.c: Comment out debugging message in reverse()
2007-10-29 15:32 warnes
- * tests/Alfalfa_Test.Rout.save,
+ * [r1197] tests/Alfalfa_Test.Rout.save,
tests/TestUnnamedComponents.Rout.save, tests/Theoph.Rout.save,
tests/cars.Rout.save, tests/testDates.Rout.save,
tests/test_fields.Rout.save, tests/xport.Rout.save,
@@ -98,7 +139,8 @@
2007-10-22 02:24 warnes
- * branches/GenerateFORMATSfromFactorObjects/SASxport/DESCRIPTION,
+ * [r1196]
+ branches/GenerateFORMATSfromFactorObjects/SASxport/DESCRIPTION,
trunk/MSOfficeUtil/DESCRIPTION, trunk/RMCMC/DESCRIPTION,
trunk/Rlsf/DESCRIPTION, DESCRIPTION, trunk/bwRF/DESCRIPTION,
trunk/exp.ssize/DESCRIPTION, trunk/fork/DESCRIPTION,
@@ -108,7 +150,7 @@
2007-10-02 22:34 warnes
- * inst/ChangeLog, tests/Alfalfa_Test.Rout.save,
+ * [r1195] inst/ChangeLog, tests/Alfalfa_Test.Rout.save,
tests/TestUnnamedComponents.Rout.save, tests/Theoph.Rout.save,
tests/cars.Rout.save, tests/testDates.Rout.save,
tests/test_fields.Rout.save, tests/xport.Rout.save,
@@ -117,16 +159,16 @@
2007-10-02 22:30 warnes
- * R/zzz.R: Add information on how to get help to the startup
- message
+ * [r1194] R/zzz.R: Add information on how to get help to the
+ startup message
2007-10-02 21:21 warnes
- * NAMESPACE: Add dependenct on utils::packageDescription
+ * [r1193] NAMESPACE: Add dependenct on utils::packageDescription
2007-10-01 20:09 warnes
- * tests/Alfalfa_Test.Rout.save,
+ * [r1192] tests/Alfalfa_Test.Rout.save,
tests/TestUnnamedComponents.Rout.save, tests/Theoph.Rout.save,
tests/cars.Rout.save, tests/testDates.Rout.save,
tests/test_fields.Rout.save, tests/xport.Rout.save,
@@ -135,42 +177,45 @@
2007-09-25 19:58 warnes
- * DESCRIPTION, inst/ChangeLog: Update version number and date
+ * [r1191] DESCRIPTION, inst/ChangeLog: Update version number and
+ date
2007-09-25 19:54 warnes
- * man/SASxport-package.Rd, man/write.xport.Rd: Indicate that Metrum
- partially funded development
+ * [r1190] man/SASxport-package.Rd, man/write.xport.Rd: Indicate
+ that Metrum partially funded development
2007-09-25 19:53 warnes
- * R/zzz.R: Display version and support information on package load
+ * [r1189] R/zzz.R: Display version and support information on
+ package load
2007-09-18 17:42 warnes
- * DESCRIPTION: Spent more time than Metrum paid for
+ * [r1188] DESCRIPTION: Spent more time than Metrum paid for
2007-09-15 06:17 warnes
- * man/SASxport-package.Rd, man/lookup.xport.Rd, man/read.xport.Rd,
- man/toSAS.Rd, tests/TestUnnamedComponents.Rout.save: Improve
- formatting for pdf output
+ * [r1187] man/SASxport-package.Rd, man/lookup.xport.Rd,
+ man/read.xport.Rd, man/toSAS.Rd,
+ tests/TestUnnamedComponents.Rout.save: Improve formatting for pdf
+ output
2007-09-15 05:06 warnes
- * inst/ChangeLog: Update changelog
+ * [r1186] inst/ChangeLog: Update changelog
2007-09-15 04:55 warnes
- * tests/TestUnnamedComponents.R: Changes so test
+ * [r1185] tests/TestUnnamedComponents.R: Changes so test
TestUnnamedCompontents.R runs under R 2.4.1 on Win32
2007-09-15 04:01 warnes
- * DESCRIPTION, R/make.formats.R, R/toSAS.R, R/write.xport.R,
- R/xport.character.R, man/Alfalfa.Rd, man/lookup.xport.Rd,
- man/toSAS.Rd, man/write.xport.Rd, tests/Alfalfa_Test.R,
- tests/Alfalfa_Test.Rout.save,
+ * [r1184] DESCRIPTION, R/make.formats.R, R/toSAS.R,
+ R/write.xport.R, R/xport.character.R, man/Alfalfa.Rd,
+ man/lookup.xport.Rd, man/toSAS.Rd, man/write.xport.Rd,
+ tests/Alfalfa_Test.R, tests/Alfalfa_Test.Rout.save,
tests/TestUnnamedComponents.Rout.save, tests/Theoph.Rout.save,
tests/cars.R, tests/cars.Rout.save, tests/test.xpt,
tests/testDates.Rout.save, tests/test_fields.Rout.save,
@@ -180,8 +225,8 @@
2007-09-14 15:35 warnes
- * R/process.formats.R, R/read.xport.R, data, data/Alfalfa.R,
- data/Alfalfa.xpt, inst/ChangeLog, man/Alfalfa.Rd,
+ * [r1183] R/process.formats.R, R/read.xport.R, data,
+ data/Alfalfa.R, data/Alfalfa.xpt, inst/ChangeLog, man/Alfalfa.Rd,
man/lookup.xport.Rd, man/read.xport.Rd,
tests/TestUnnamedComponents.Rout.save: Add option to read.xport()
that permits inclusion of PROC CONTENTS format information in the
@@ -189,21 +234,23 @@
2007-09-13 17:36 warnes
- * R/read.xport.R: Ensure 'names.tolower' applies to dataset names
+ * [r1180] R/read.xport.R: Ensure 'names.tolower' applies to dataset
+ names
2007-09-13 01:55 warnes
- * tests/TestUnnamedComponents.Rout.save: Update test output to
- match recent changes.
+ * [r1179] tests/TestUnnamedComponents.Rout.save: Update test output
+ to match recent changes.
2007-09-13 01:19 warnes
- * R/write.xport.R: Add checking and handling for unnamed data
- frames or variables
+ * [r1178] R/write.xport.R: Add checking and handling for unnamed
+ data frames or variables
2007-09-13 01:14 warnes
- * tests/Alfalfa_Test.Rout.save, tests/TestUnnamedComponents.R,
+ * [r1177] tests/Alfalfa_Test.Rout.save,
+ tests/TestUnnamedComponents.R,
tests/TestUnnamedComponents.Rout.save, tests/Theoph.Rout.save,
tests/cars.Rout.save, tests/testDates.Rout.save,
tests/test_fields.Rout.save, tests/xport.Rout.save,
@@ -212,125 +259,125 @@
2007-09-12 22:27 warnes
- * NAMESPACE: Remove units() and units<-() functions since they
- arene't ever used.
+ * [r1176] NAMESPACE: Remove units() and units<-() functions since
+ they arene't ever used.
2007-09-12 22:25 warnes
- * R/units.R, man/label.Rd, man/units.Rd: Remove units() and
+ * [r1175] R/units.R, man/label.Rd, man/units.Rd: Remove units() and
units<-() functions since they arene't ever used.
2007-09-12 22:24 warnes
- * man/units.Rd: Remove units from manual page
+ * [r1174] man/units.Rd: Remove units from manual page
2007-09-11 23:08 warnes
- * man/read.xport.Rd: Add assertion to test that read.xport(..,
- as.list=TRUE) works properly
+ * [r1173] man/read.xport.Rd: Add assertion to test that
+ read.xport(.., as.list=TRUE) works properly
2007-09-11 23:05 warnes
- * R/write.xport.R: Forgot to save buffer before svn commit.
+ * [r1172] R/write.xport.R: Forgot to save buffer before svn commit.
2007-09-11 21:22 warnes
- * R/read.xport.R, man/read.xport.Rd: Correct error in handling
- 'verbose' argument, error when more than one dataset has the same
- name, and add 'as.list' argument to ensure return value is a
- list, even if there is only one dataset in the file
+ * [r1171] R/read.xport.R, man/read.xport.Rd: Correct error in
+ handling 'verbose' argument, error when more than one dataset has
+ the same name, and add 'as.list' argument to ensure return value
+ is a list, even if there is only one dataset in the file
2007-09-11 21:21 warnes
- * R/write.xport.R, man/write.xport.Rd: Improve handling of list
- argument. Also check that names are proper and unique.
+ * [r1170] R/write.xport.R, man/write.xport.Rd: Improve handling of
+ list argument. Also check that names are proper and unique.
2007-09-07 16:47 warnes
- * tests/Theoph.R, tests/Theoph.Rout.save: Add round-trip test for
- Theoph data set
+ * [r1167] tests/Theoph.R, tests/Theoph.Rout.save: Add round-trip
+ test for Theoph data set
2007-09-07 16:32 warnes
- * tests/Alfalfa_Test.Rout.save, tests/cars.Rout.save,
+ * [r1166] tests/Alfalfa_Test.Rout.save, tests/cars.Rout.save,
tests/testDates.Rout.save, tests/xxx.Rout.save: Change argument
name in write.xport from 'filename' to 'file' to match read.xport
2007-09-07 16:25 warnes
- * man/write.xport.Rd: Change argument name in write.xport from
- 'filename' to 'file' to match read.xport
+ * [r1165] man/write.xport.Rd: Change argument name in write.xport
+ from 'filename' to 'file' to match read.xport
2007-09-07 16:23 warnes
- * R/write.xport.R, man/read.xport.Rd, man/write.xport.Rd,
+ * [r1164] R/write.xport.R, man/read.xport.Rd, man/write.xport.Rd,
tests/Alfalfa_Test.R, tests/cars.R, tests/testDates.R,
tests/xxx.R: Change argument name in write.xport from 'filename'
to 'file' to match read.xport
2007-09-07 16:21 warnes
- * DESCRIPTION: Fix typo
+ * [r1163] DESCRIPTION: Fix typo
2007-08-29 02:24 warnes
- * DESCRIPTION: Update Version to 1.0, depend on current version of
- foreign
+ * [r1161] DESCRIPTION: Update Version to 1.0, depend on current
+ version of foreign
2007-08-22 19:21 warnes
- * ChangeLog, NEWS, inst/ChangeLog, inst/NEWS: Update ChangeLog and
- NEWS files
+ * [r1160] ChangeLog, NEWS, inst/ChangeLog, inst/NEWS: Update
+ ChangeLog and NEWS files
2007-08-22 18:11 warnes
- * R/read.xport.R, man/read.xport.Rd, tests/xport.Rout.save: Modify
- read.xport to preserve case of SAS names by default, as well as
- updating the example code.
+ * [r1159] R/read.xport.R, man/read.xport.Rd, tests/xport.Rout.save:
+ Modify read.xport to preserve case of SAS names by default, as
+ well as updating the example code.
2007-08-22 01:19 warnes
- * src/reverse.c: sprintf() was being used where printf() was
- intended.
+ * [r1158] src/reverse.c: sprintf() was being used where printf()
+ was intended.
2007-08-21 18:16 warnes
- * DESCRIPTION: Slight improvement to credits for BRL-CAD
+ * [r1157] DESCRIPTION: Slight improvement to credits for BRL-CAD
2007-08-21 18:13 warnes
- * TODO, man/lookup.xport.Rd, man/read.xport.Rd: Commit previous
- updates
+ * [r1156] TODO, man/lookup.xport.Rd, man/read.xport.Rd: Commit
+ previous updates
2007-08-21 18:12 warnes
- * src/htond.c, src/ibm2ieee.c, src/ieee2ibm.c, src/init.c,
+ * [r1155] src/htond.c, src/ibm2ieee.c, src/ieee2ibm.c, src/init.c,
src/reverse.c, src/test_fields.c: Commit previous updates
2007-08-15 07:02 warnes
- * DESCRIPTION, man/SASxport-package.Rd, src/cnxptiee.c,
+ * [r1146] DESCRIPTION, man/SASxport-package.Rd, src/cnxptiee.c,
src/cnxptiee.h, src/htond.c, src/init.c, src/reverse.c,
src/test_fields.c, src/writeSAS.c, src/writeSAS.h: Remove
dependency on SAS code
2007-08-15 06:06 warnes
- * src/reverse.c: Fix reverse.c because we need to swap everything
- to match Big-Endian, rather than Little-Endian. Also, dont' call
- the macro.
+ * [r1145] src/reverse.c: Fix reverse.c because we need to swap
+ everything to match Big-Endian, rather than Little-Endian. Also,
+ dont' call the macro.
2007-08-15 06:04 warnes
- * src/reverse.c: Restore reverse.c
+ * [r1144] src/reverse.c: Restore reverse.c
2007-08-15 03:17 warnes
- * DESCRIPTION: Minor reformatting
+ * [r1143] DESCRIPTION: Minor reformatting
2007-08-15 03:14 warnes
- * DESCRIPTION, inst/doc/SAS_TS140.txt, inst/doc/index.html,
+ * [r1142] DESCRIPTION, inst/doc/SAS_TS140.txt, inst/doc/index.html,
inst/doc/r2xpt.doc, man/SASxport-package.Rd, man/lookup.xport.Rd,
man/read.xport.Rd, man/toSAS.Rd, man/units.Rd,
man/write.xport.Rd: Make corrections for typos noted by Metrum
@@ -338,96 +385,98 @@
2007-08-12 03:22 warnes
- * DESCRIPTION, man/lookup.xport.Rd, src/cnxptiee.h,
+ * [r1138] DESCRIPTION, man/lookup.xport.Rd, src/cnxptiee.h,
src/test_fields.c, src/writeSAS.h: More updates
2007-08-12 03:13 warnes
- * src/B8.h, src/IEEEtoIBM.c, src/MASKS.h, src/main.c,
+ * [r1137] src/B8.h, src/IEEEtoIBM.c, src/MASKS.h, src/main.c,
src/reverse.c: Remove new stuff... use SAS's code instead
2007-08-12 03:12 warnes
- * src/B8.h, src/IEEEtoIBM.c, src/MASKS.h, src/cnxptiee.h,
+ * [r1136] src/B8.h, src/IEEEtoIBM.c, src/MASKS.h, src/cnxptiee.h,
src/main.c, src/reverse.c, src/test_fields.c, src/writeSAS.h: 1st
attempt at rewriting cnxptiee.[ch]
2007-08-11 23:48 warnes
- * R/read.xport.R: Explicitly check file header
+ * [r1135] R/read.xport.R: Explicitly check file header
2007-08-11 00:03 warnes
- * DESCRIPTION, man/SASxport-package.Rd: Improve package description
+ * [r1134] DESCRIPTION, man/SASxport-package.Rd: Improve package
+ description
2007-08-09 23:29 warnes
- * DESCRIPTION, NAMESPACE, TODO, man/lookup.xport.Rd,
+ * [r1133] DESCRIPTION, NAMESPACE, TODO, man/lookup.xport.Rd,
man/read.xport.Rd, man/units.Rd: More changes, esp to
lookup.xport() and friends
2007-08-09 23:28 warnes
- * tests/Alfalfa_Test.Rout.save, tests/cars.Rout.save,
+ * [r1132] tests/Alfalfa_Test.Rout.save, tests/cars.Rout.save,
tests/xport.Rout.save: More changes, esp to lookup.xport() and
friends
2007-08-09 23:28 warnes
- * R/AFirst.lib.s, R/all.is.numeric.R, R/in.opererator.R,
+ * [r1131] R/AFirst.lib.s, R/all.is.numeric.R, R/in.opererator.R,
R/lookup.xport.R, R/read.xport.R, R/write.xport.R: More changes,
esp to lookup.xport() and friends
2007-08-09 19:02 warnes
- * src/swap_bytes.h: Remove unused swap_bytes.h
+ * [r1130] src/swap_bytes.h: Remove unused swap_bytes.h
2007-08-09 19:02 warnes
- * man/SASxport-package.Rd: Add package description page
+ * [r1129] man/SASxport-package.Rd: Add package description page
2007-08-09 16:54 warnes
- * R/importConvertDateTime.R, R/makeNames.R, R/read.xport.R,
+ * [r1128] R/importConvertDateTime.R, R/makeNames.R, R/read.xport.R,
R/testDateTime.R: Add comment header indicating the source of
code from Hmisc
2007-08-09 16:53 warnes
- * tests/testDates.Rout.save, tests/test_fields.Rout.save,
+ * [r1127] tests/testDates.Rout.save, tests/test_fields.Rout.save,
tests/xport.Rout.save, tests/xxx.Rout.save: Update saved output
of test scripts
2007-08-08 18:54 warnes
- * DESCRIPTION, NAMESPACE: Updates
+ * [r1126] DESCRIPTION, NAMESPACE: Updates
2007-08-08 18:54 warnes
- * tests/Alfalfa_Test.R, tests/Alfalfa_Test.Rout.save, tests/cars.R,
- tests/cars.Rout.save, tests/datetime.xpt, tests/testDates.R,
- tests/test_fields.R, tests/test_fields.Rout.save, tests/xport.R,
- tests/xxx.R, tests/xxx.Rout.save: Updates
+ * [r1125] tests/Alfalfa_Test.R, tests/Alfalfa_Test.Rout.save,
+ tests/cars.R, tests/cars.Rout.save, tests/datetime.xpt,
+ tests/testDates.R, tests/test_fields.R,
+ tests/test_fields.Rout.save, tests/xport.R, tests/xxx.R,
+ tests/xxx.Rout.save: Updates
2007-08-08 18:54 warnes
- * src/SASxport.c, src/SASxport.h, src/foreign.h, src/init.c:
- Updates
+ * [r1124] src/SASxport.c, src/SASxport.h, src/foreign.h,
+ src/init.c: Updates
2007-08-08 18:53 warnes
- * R/AFirst.lib.s, R/formats.R, R/iformat.R,
+ * [r1123] R/AFirst.lib.s, R/formats.R, R/iformat.R,
R/importConvertDateTime.R, R/label.R, R/lookup.xport.R,
R/makeNames.R, R/read.xport.R, R/testDateTime.R, R/units.R,
R/xport.R: Updates
2007-08-08 18:53 warnes
- * man/assert.Rd, man/read.xport.Rd, man/units.Rd: Updates.
+ * [r1122] man/assert.Rd, man/read.xport.Rd, man/units.Rd: Updates.
2007-08-03 04:44 warnes
- * DESCRIPTION, NAMESPACE, R/scat.R, R/xport.R, R/zzz.R,
+ * [r1119] DESCRIPTION, NAMESPACE, R/scat.R, R/xport.R, R/zzz.R,
man/lookup.xport.Rd, man/read.xport.Rd, src/SASxport.c,
src/SASxport.h, src/cnxptiee.c, src/cnxptiee.h, src/foreign.h,
src/init.c, src/swap_bytes.h, src/test_fields.c, src/writeSAS.c,
@@ -439,41 +488,42 @@
2007-08-03 01:46 warnes
- * R/.Rhistory: Remove stray .Rhistory file
+ * [r1118] R/.Rhistory: Remove stray .Rhistory file
2007-08-03 01:45 warnes
- * DESCRIPTION: Acknowledge MetrumI support
+ * [r1117] DESCRIPTION: Acknowledge MetrumI support
2007-08-03 01:45 warnes
- * NAMESPACE: Add "assert" function
+ * [r1116] NAMESPACE: Add "assert" function
2007-08-03 01:44 warnes
- * R/assert.R, man/assert.Rd: Add "assert" function to avoid
+ * [r1115] R/assert.R, man/assert.Rd: Add "assert" function to avoid
dependenct on gtools.
2007-08-03 01:29 warnes
- * man/toSAS.Rd, src/cnxptiee.c, src/writeSAS.c: Correct some typos.
+ * [r1114] man/toSAS.Rd, src/cnxptiee.c, src/writeSAS.c: Correct
+ some typos.
2007-08-03 00:40 warnes
- * DESCRIPTION: Drop version number to 0.99 until testing
+ * [r1113] DESCRIPTION: Drop version number to 0.99 until testing
integration and is complete
2007-08-03 00:39 warnes
- * tests/test_fields.R: Add R test file to run c-level tests
+ * [r1112] tests/test_fields.R: Add R test file to run c-level tests
2007-08-03 00:36 warnes
- * src/SASxport.so: Remove .so from svn
+ * [r1111] src/SASxport.so: Remove .so from svn
2007-08-03 00:35 warnes
- * NAMESPACE, R/fromSASDate.R, R/parseFormat.R, R/toSAS.R,
+ * [r1110] NAMESPACE, R/fromSASDate.R, R/parseFormat.R, R/toSAS.R,
R/write.xport.R, R/xport.character.R, R/xport.file.header.R,
R/xport.member.header.R, R/xport.namestr.R, man/toSAS.Rd,
src/SASxport.so, src/writeSAS.c: More modifications. Should now
@@ -481,18 +531,18 @@
2007-08-03 00:35 warnes
- * tests/cars.R, tests/datetime.xpt, tests/testDates.R, tests/xxx.R:
- Add more tests
+ * [r1109] tests/cars.R, tests/datetime.xpt, tests/testDates.R,
+ tests/xxx.R: Add more tests
2007-07-29 01:15 warnes
- * tests/Alfalfa2.xpt, tests/cars.sas, tests/cars.xpt,
+ * [r1107] tests/Alfalfa2.xpt, tests/cars.sas, tests/cars.xpt,
tests/xxx.sas, tests/xxx.xpt: Add SAS code to create xport data
files for testing
2007-07-28 08:47 warnes
- * ., DESCRIPTION, NAMESPACE, R, R/.Rhistory, R/blanks.R,
+ * [r1106] ., DESCRIPTION, NAMESPACE, R, R/.Rhistory, R/blanks.R,
R/rawToDisplay.R, R/write.xport.R, R/xport.NA.R,
R/xport.character.R, R/xport.dateFMT.R, R/xport.file.header.R,
R/xport.fill.R, R/xport.member.header.R, R/xport.namestr.R,
Modified: trunk/SASxport/inst/NEWS
===================================================================
--- trunk/SASxport/inst/NEWS 2007-11-09 19:59:48 UTC (rev 1226)
+++ trunk/SASxport/inst/NEWS 2007-11-09 22:45:58 UTC (rev 1227)
@@ -1,3 +1,12 @@
+Version 1.2.2 2007-11-09
+------------------------
+
+Bug fixes:
+
+- Apply patches to fix problems on 64 bit platforms, as sumitted by
+ Brian Ripley.
+
+
Version 1.2.1 2007-11-05
-------------------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2007-11-09 19:59:51
|
Revision: 1226
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1226&view=rev
Author: warnes
Date: 2007-11-09 11:59:48 -0800 (Fri, 09 Nov 2007)
Log Message:
-----------
Apply patches to fix problems on 64 bit platforms, as sumitted by Brian Ripley.
Modified Paths:
--------------
trunk/SASxport/src/ibm2ieee.c
trunk/SASxport/src/ieee2ibm.c
Modified: trunk/SASxport/src/ibm2ieee.c
===================================================================
--- trunk/SASxport/src/ibm2ieee.c 2007-11-07 19:01:02 UTC (rev 1225)
+++ trunk/SASxport/src/ibm2ieee.c 2007-11-09 19:59:48 UTC (rev 1226)
@@ -73,7 +73,7 @@
*/
register int i;
for( i=count-1; i >= 0; i-- ) {
- register unsigned left, right, signbit;
+ register unsigned int left, right, signbit;
register int exp;
left = (in[0]<<24) | (in[1]<<16) | (in[2]<<8) | in[3];
Modified: trunk/SASxport/src/ieee2ibm.c
===================================================================
--- trunk/SASxport/src/ieee2ibm.c 2007-11-07 19:01:02 UTC (rev 1225)
+++ trunk/SASxport/src/ieee2ibm.c 2007-11-09 19:59:48 UTC (rev 1226)
@@ -53,7 +53,7 @@
*/
register int i;
for( i=count-1; i >= 0; i-- ) {
- register unsigned long left, right;
+ register unsigned int left, right;
register int fix, exp, signbit;
left = (in[0]<<24) | (in[1]<<16) | (in[2]<<8) | in[3];
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From: <wa...@us...> - 2007-11-07 19:01:05
|
Revision: 1225
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1225&view=rev
Author: warnes
Date: 2007-11-07 11:01:02 -0800 (Wed, 07 Nov 2007)
Log Message:
-----------
Update version number
Modified Paths:
--------------
trunk/SASxport/tests/Alfalfa_Test.Rout.save
trunk/SASxport/tests/TestUnnamedComponents.Rout.save
trunk/SASxport/tests/Theoph.Rout.save
trunk/SASxport/tests/cars.Rout.save
trunk/SASxport/tests/testDates.Rout.save
trunk/SASxport/tests/testNegative.Rout.save
trunk/SASxport/tests/testNumeric.Rout.save
trunk/SASxport/tests/test_fields.Rout.save
trunk/SASxport/tests/xport.Rout.save
trunk/SASxport/tests/xxx.Rout.save
Modified: trunk/SASxport/tests/Alfalfa_Test.Rout.save
===================================================================
--- trunk/SASxport/tests/Alfalfa_Test.Rout.save 2007-11-07 18:59:20 UTC (rev 1224)
+++ trunk/SASxport/tests/Alfalfa_Test.Rout.save 2007-11-07 19:01:02 UTC (rev 1225)
@@ -20,7 +20,7 @@
>
> library(SASxport)
-Loaded SASxport version 1.2.0 (2007-11-01).
+Loaded SASxport version 1.2.2 (2007-11-07).
Updates and technical support available from Random Technologies, LLC
<http://random-technologies-llc.com/products/SASxport>
Modified: trunk/SASxport/tests/TestUnnamedComponents.Rout.save
===================================================================
--- trunk/SASxport/tests/TestUnnamedComponents.Rout.save 2007-11-07 18:59:20 UTC (rev 1224)
+++ trunk/SASxport/tests/TestUnnamedComponents.Rout.save 2007-11-07 19:01:02 UTC (rev 1225)
@@ -17,7 +17,7 @@
> library(SASxport)
-Loaded SASxport version 1.2.0 (2007-11-01).
+Loaded SASxport version 1.2.2 (2007-11-07).
Updates and technical support available from Random Technologies, LLC
<http://random-technologies-llc.com/products/SASxport>
Modified: trunk/SASxport/tests/Theoph.Rout.save
===================================================================
--- trunk/SASxport/tests/Theoph.Rout.save 2007-11-07 18:59:20 UTC (rev 1224)
+++ trunk/SASxport/tests/Theoph.Rout.save 2007-11-07 19:01:02 UTC (rev 1225)
@@ -22,7 +22,7 @@
>
> library(SASxport)
-Loaded SASxport version 1.2.0 (2007-11-01).
+Loaded SASxport version 1.2.2 (2007-11-07).
Updates and technical support available from Random Technologies, LLC
<http://random-technologies-llc.com/products/SASxport>
Modified: trunk/SASxport/tests/cars.Rout.save
===================================================================
--- trunk/SASxport/tests/cars.Rout.save 2007-11-07 18:59:20 UTC (rev 1224)
+++ trunk/SASxport/tests/cars.Rout.save 2007-11-07 19:01:02 UTC (rev 1225)
@@ -17,7 +17,7 @@
> library(SASxport)
-Loaded SASxport version 1.2.0 (2007-11-01).
+Loaded SASxport version 1.2.2 (2007-11-07).
Updates and technical support available from Random Technologies, LLC
<http://random-technologies-llc.com/products/SASxport>
Modified: trunk/SASxport/tests/testDates.Rout.save
===================================================================
--- trunk/SASxport/tests/testDates.Rout.save 2007-11-07 18:59:20 UTC (rev 1224)
+++ trunk/SASxport/tests/testDates.Rout.save 2007-11-07 19:01:02 UTC (rev 1225)
@@ -17,7 +17,7 @@
> library(SASxport)
-Loaded SASxport version 1.2.0 (2007-11-01).
+Loaded SASxport version 1.2.2 (2007-11-07).
Updates and technical support available from Random Technologies, LLC
<http://random-technologies-llc.com/products/SASxport>
Modified: trunk/SASxport/tests/testNegative.Rout.save
===================================================================
--- trunk/SASxport/tests/testNegative.Rout.save 2007-11-07 18:59:20 UTC (rev 1224)
+++ trunk/SASxport/tests/testNegative.Rout.save 2007-11-07 19:01:02 UTC (rev 1225)
@@ -17,7 +17,7 @@
> library(SASxport)
-Loaded SASxport version 1.2.0 (2007-11-01).
+Loaded SASxport version 1.2.2 (2007-11-07).
Updates and technical support available from Random Technologies, LLC
<http://random-technologies-llc.com/products/SASxport>
Modified: trunk/SASxport/tests/testNumeric.Rout.save
===================================================================
--- trunk/SASxport/tests/testNumeric.Rout.save 2007-11-07 18:59:20 UTC (rev 1224)
+++ trunk/SASxport/tests/testNumeric.Rout.save 2007-11-07 19:01:02 UTC (rev 1225)
@@ -89,4 +89,4 @@
>
> proc.time()
user system elapsed
- 0.994 0.071 1.106
+ 1.123 0.119 2.017
Modified: trunk/SASxport/tests/test_fields.Rout.save
===================================================================
--- trunk/SASxport/tests/test_fields.Rout.save 2007-11-07 18:59:20 UTC (rev 1224)
+++ trunk/SASxport/tests/test_fields.Rout.save 2007-11-07 19:01:02 UTC (rev 1225)
@@ -17,7 +17,7 @@
> library(SASxport)
-Loaded SASxport version 1.2.0 (2007-11-01).
+Loaded SASxport version 1.2.2 (2007-11-07).
Updates and technical support available from Random Technologies, LLC
<http://random-technologies-llc.com/products/SASxport>
Modified: trunk/SASxport/tests/xport.Rout.save
===================================================================
--- trunk/SASxport/tests/xport.Rout.save 2007-11-07 18:59:20 UTC (rev 1224)
+++ trunk/SASxport/tests/xport.Rout.save 2007-11-07 19:01:02 UTC (rev 1225)
@@ -17,7 +17,7 @@
> library(SASxport)
-Loaded SASxport version 1.2.0 (2007-11-01).
+Loaded SASxport version 1.2.2 (2007-11-07).
Updates and technical support available from Random Technologies, LLC
<http://random-technologies-llc.com/products/SASxport>
Modified: trunk/SASxport/tests/xxx.Rout.save
===================================================================
--- trunk/SASxport/tests/xxx.Rout.save 2007-11-07 18:59:20 UTC (rev 1224)
+++ trunk/SASxport/tests/xxx.Rout.save 2007-11-07 19:01:02 UTC (rev 1225)
@@ -17,7 +17,7 @@
> library(SASxport)
-Loaded SASxport version 1.2.0 (2007-11-01).
+Loaded SASxport version 1.2.2 (2007-11-07).
Updates and technical support available from Random Technologies, LLC
<http://random-technologies-llc.com/products/SASxport>
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From: <wa...@us...> - 2007-11-07 18:59:23
|
Revision: 1224
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1224&view=rev
Author: warnes
Date: 2007-11-07 10:59:20 -0800 (Wed, 07 Nov 2007)
Log Message:
-----------
Bump version number
Modified Paths:
--------------
trunk/SASxport/DESCRIPTION
Modified: trunk/SASxport/DESCRIPTION
===================================================================
--- trunk/SASxport/DESCRIPTION 2007-11-07 18:14:58 UTC (rev 1223)
+++ trunk/SASxport/DESCRIPTION 2007-11-07 18:59:20 UTC (rev 1224)
@@ -1,8 +1,8 @@
Package: SASxport
Type: Package
Title: Read and Write SAS XPORT Files
-Version: 1.2.1
-Date: 2007-11-01
+Version: 1.2.2
+Date: 2007-11-07
Description: This package provides functions for reading, listing
the contents of, and writing SAS xport format files.
The functions support reading and writing of either
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From: <wa...@us...> - 2007-11-07 18:14:59
|
Revision: 1223
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1223&view=rev
Author: warnes
Date: 2007-11-07 10:14:58 -0800 (Wed, 07 Nov 2007)
Log Message:
-----------
Apply patches to fix problems on 64 bit platforms, as sumitted by Brian Ripley, and to replace assert() calls with calls a macro that maps to error() unless standalone testing is being done, in which case assert() is used.
Modified Paths:
--------------
trunk/SASxport/src/ibm2ieee.c
trunk/SASxport/src/reverse.c
trunk/SASxport/src/writeSAS.c
trunk/SASxport/src/writeSAS.h
Modified: trunk/SASxport/src/ibm2ieee.c
===================================================================
--- trunk/SASxport/src/ibm2ieee.c 2007-11-06 16:24:50 UTC (rev 1222)
+++ trunk/SASxport/src/ibm2ieee.c 2007-11-07 18:14:58 UTC (rev 1223)
@@ -73,7 +73,7 @@
*/
register int i;
for( i=count-1; i >= 0; i-- ) {
- register unsigned long left, right, signbit;
+ register unsigned left, right, signbit;
register int exp;
left = (in[0]<<24) | (in[1]<<16) | (in[2]<<8) | in[3];
Modified: trunk/SASxport/src/reverse.c
===================================================================
--- trunk/SASxport/src/reverse.c 2007-11-06 16:24:50 UTC (rev 1222)
+++ trunk/SASxport/src/reverse.c 2007-11-07 18:14:58 UTC (rev 1223)
@@ -1,4 +1,4 @@
-//#include "writeSAS.h"
+#include "writeSAS.h"
#include <stdio.h>
#include <string.h>
@@ -34,7 +34,6 @@
return;
}
-
/* test code */
void test_reverse()
{
@@ -54,28 +53,25 @@
/* byte */
reverse( &byte_value, sizeof(unsigned char) );
- assert( (unsigned char) *byte_pattern == byte_value );
+ ASSERT( (unsigned char) *byte_pattern == byte_value );
/* short */
reverse( (unsigned char*) &short_value, sizeof(short) );
- assert( *((short *) short_pattern) == short_value );
+ ASSERT( *((short *) short_pattern) == short_value );
/* int */
reverse( (unsigned char*) &int_value, sizeof(int) );
- assert( *((int *) int_pattern) == int_value );
+ ASSERT( *((int *) int_pattern) == int_value );
/* long */
reverse( (unsigned char*) &long_value, sizeof(long) );
- assert( *((long*) long_pattern) == long_value );
+ ASSERT( *((long*) long_pattern) == long_value );
}
-
#ifdef DO_TEST
int main(int argc, char *argv)
{
test_reverse();
}
-
-
#endif
Modified: trunk/SASxport/src/writeSAS.c
===================================================================
--- trunk/SASxport/src/writeSAS.c 2007-11-06 16:24:50 UTC (rev 1222)
+++ trunk/SASxport/src/writeSAS.c 2007-11-07 18:14:58 UTC (rev 1223)
@@ -250,14 +250,14 @@
blankCopy(namestr_record.niform, 8, niform[0]); /* NAME OF INPUT FORMAT */
namestr_record.nifl = (short) *nifl; /* INFORMAT LENGTH ATTRIBUTE */
namestr_record.nifd = (short) *nifd; /* INFORMAT NUMBER OF DECIMALS */
- namestr_record.npos = (long) *npos; /* POSITION OF VALUE IN OBSERVATION */
+ namestr_record.npos = (int) *npos; /* POSITION OF VALUE IN OBSERVATION */
zeroFill(namestr_record.rest, 52); /* remaining fields are irrelevant */
/* Flip byte order if necessary */
#define SHORTREV(a) REVERSE( &a, sizeof(short) )
-#define LONGREV(a) REVERSE( &a, sizeof(long) )
+#define INTREV(a) REVERSE( &a, sizeof(int) )
SHORTREV( namestr_record.ntype );
SHORTREV( namestr_record.nhfun );
@@ -269,7 +269,7 @@
SHORTREV( namestr_record.nifl );
SHORTREV( namestr_record.nifd );
- LONGREV ( namestr_record.npos );
+ INTREV ( namestr_record.npos );
/* copy filled struct to return area */
memcpy( raw_buffer, &namestr_record, sizeof(namestr_record) );
Modified: trunk/SASxport/src/writeSAS.h
===================================================================
--- trunk/SASxport/src/writeSAS.h 2007-11-06 16:24:50 UTC (rev 1222)
+++ trunk/SASxport/src/writeSAS.h 2007-11-07 18:14:58 UTC (rev 1223)
@@ -56,6 +56,11 @@
*****/
#define MIN(x,y) (x>y?y:x)
+#ifdef DO_TEST
+#define ASSERT(x) assert(x)
+#else
+#define ASSERT(x) if(!(x)) error("Assertion failed: x")
+#endif
/*****
@@ -128,7 +133,7 @@
short nifl; /* INFORMAT LENGTH ATTRIBUTE */
short nifd; /* INFORMAT NUMBER OF DECIMALS */
- long npos; /* POSITION OF VALUE IN OBSERVATION */
+ int npos; /* POSITION OF VALUE IN OBSERVATION */
char rest[52]; /* remaining fields are irrelevant */
};
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From: <wa...@us...> - 2007-11-06 16:25:00
|
Revision: 1222
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1222&view=rev
Author: warnes
Date: 2007-11-06 08:24:50 -0800 (Tue, 06 Nov 2007)
Log Message:
-----------
Remove extraneous closing brace in the hist2d documentation file
Modified Paths:
--------------
trunk/gplots/man/hist2d.Rd
Modified: trunk/gplots/man/hist2d.Rd
===================================================================
--- trunk/gplots/man/hist2d.Rd 2007-11-05 15:32:36 UTC (rev 1221)
+++ trunk/gplots/man/hist2d.Rd 2007-11-06 16:24:50 UTC (rev 1222)
@@ -23,7 +23,7 @@
\alias{hist2d}
\title{ Compute and Plot a 2-Dimensional Histogram }
\description{
- Compute and plot a 2-dimensional histogram. }
+ Compute and plot a 2-dimensional histogram.
}
\usage{
hist2d(x,y=NULL, nbins=200, same.scale=FALSE, na.rm=TRUE, show=TRUE,
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From: <wa...@us...> - 2007-11-05 15:32:37
|
Revision: 1221
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1221&view=rev
Author: warnes
Date: 2007-11-05 07:32:36 -0800 (Mon, 05 Nov 2007)
Log Message:
-----------
Fix typo in NEWS: col2hex() is the new function, not col2rgb() which is part of grDevices
Modified Paths:
--------------
trunk/gplots/inst/NEWS
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2007-11-05 15:25:38 UTC (rev 1220)
+++ trunk/gplots/inst/NEWS 2007-11-05 15:32:36 UTC (rev 1221)
@@ -7,7 +7,7 @@
avoid problems with computing height and width of text that includes
tabs.
-- Add col2rgb() function to convert color names to rgb hex codes
+- Add col2hex() function to convert color names to rgb hex codes
Bug Fixes:
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