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[R-gregmisc-users] SF.net SVN: r-gregmisc: [971] trunk/OpenSourceInPharma/talk.tex
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From: <wa...@us...> - 2006-07-28 23:21:13
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Revision: 971 Author: warnes Date: 2006-07-28 16:20:45 -0700 (Fri, 28 Jul 2006) ViewCVS: http://svn.sourceforge.net/r-gregmisc/?rev=971&view=rev Log Message: ----------- Updates to get ready for JSM Modified Paths: -------------- trunk/OpenSourceInPharma/talk.tex Modified: trunk/OpenSourceInPharma/talk.tex =================================================================== --- trunk/OpenSourceInPharma/talk.tex 2006-07-24 21:23:26 UTC (rev 970) +++ trunk/OpenSourceInPharma/talk.tex 2006-07-28 23:20:45 UTC (rev 971) @@ -28,28 +28,35 @@ \title{Open Source Software in Pharmaceutical Research} \author{ - Gregory R. Warnes\inst{1} \and + Gregory R. Warnes\inst{1}\inst{2}\inst{3} \and James A. Rogers\inst{2} \and - A. Max Kuhn\inst{2} + Max Kuhn\inst{2} } -\institute[U. Rochester, Pfizer]{ - \inst{1}% +\institute{ + \inst{1}% + Center for Biodefense Immune Modeling, University of Rochester \vspace{-5pt} + \and + \inst{2}% Department of Biostatistics and Computational Biology, University of Rochester \vspace{-5pt} \and - \inst{2}% - Statistical Applications, Pfizer, Inc. \vspace{-5pt} + \inst{3}% + REvolution Computing, Inc.\vspace{-5pt} + \and + \inst{4}% + Research Statistics, Pfizer, Inc. \vspace{-5pt} } \date[2006 JSM]{Joint Statistical Meetings, Seattle, WA, Aug 6-9, 2006} +%\date[UseR! 2006]{UseR! 2006, Vienna, Austria, June 15-19, 2006} \begin{document} \frame{\titlepage} \frame{ \begin{abstract} -\setbeamerfont{small}{size=\tiny} +\setbeamerfont{small}{size=\small} \usebeamerfont{small} Open-Source statistical software is being used with increasing @@ -62,7 +69,7 @@ \vspace{1em} -We will focus on R, a full-featured open-source statistical +We will focus on \textsc{R}, a full-featured open-source statistical software package. We'll briefly outline the benefits it provides, as seen from the perspective of a discovery statistician, show some example areas in which it may be used, and then discuss the @@ -73,10 +80,10 @@ Next we will discuss what is needed for organizations to be comfortable with employing open-source statistical software for regulatory use within clinical, safety, or manufacturing. We will -then talk about how well or poorly R meets these requirements, +then talk about how well or poorly \textsc{R} meets these requirements, highlighting current issues. Finally, we will discuss options for -third-party commercial support for R, and evaluate how well they -meet the requirements for use of R within both regulated and +third-party commercial support for \textsc{R}, and evaluate how well they +meet the requirements for use of \textsc{R} within both regulated and non-regulated contexts. \end{abstract} @@ -84,7 +91,7 @@ \frame{ \frametitle{Outline} - \tableofcontents[pausesections] + \tableofcontents%[pausesections] } @@ -117,149 +124,324 @@ \item Documentable \item Auditable \item Stable + \item Supported \end{enumerate} } \frame{ -\frametitle{Requirements (detail)} +\frametitle{Requirements: Details (I)} \begin{description}[<+->] -\item[Functional] Performs the reqiured tasks +\item[Functional] Performs the required tasks -\item[Verifiable] Demonstrate that computer output is correct, or at least consustent.. +\item[Verifiable] Demonstrate that computer output is correct, or at least consistent.. \item[Repeatable] Given the same data, the same results can be obtained, potentially much later in time. -\item[Documentable] Documentation is avaiable or can easily be - generated for the entire software lifecycle: Specification, Design, +\item[Documentable] Documentation is available or can easily be + generated for the entire software life-cycle: Specification, Design, Development. Testing, Deployment, Change Management + \end{description} - } \frame{ - \frametitle{Requirements (detail, cont)} +\frametitle{Requirements: Details (II)} -\begin{description} +\begin{description}[<+->] \item[Auditable] Track everything done to data and the system \item[Stable] Doesn't change too fast, so that there is enough time to develop required documentation + +\item[Supported] Guaranteed (by \$\$) availability of external expense + for installation, problem resolution, bug fixes, feature + development, training, application development, consulting -\item[Supported] Guaranteed (by \$\$) availability of external expense for - \begin{itemize} - \item installation - \item problem resolution - \item bug fixes - \item feature development - \item training - \item application development - \item consulting - \end{itemize} - \end{description} } -\section{What is R?} +\section{What is \textsc{R}?} \frame{ - \frametitle{What is R?} + \frametitle{What is \textsc{R}?} + + \begin{itemize}[<+->] - \begin{itemize} - \item{foo} - \end{itemize} + \item System for statistical computing and graphics + + \item Language is very similar to the S-Plus + + \item Full featured support for statistical and graphical techniques: + + \begin{itemize}[<1->] + \item linear and nonlinear modeling, + \item classical statistical tests, + \item time-series analysis, + \item classification, + \item clustering + \item ... + \end{itemize} + + \item Highly extensible with good development tools + + \item \emph{Huge} library of user-contributed add-on packages: $>850$ ! + + \item Source code is freely available + +\end{itemize} } +\section{Status of \textsc{R}} -\section{ Status of R} - \frame{ - \frametitle{Status of R} + \frametitle{Status of \textsc{R} (I)} -\begin{description} +\begin{description}[<+->] -\item[Functional] +++ This is R's strength, and is largely provided by - user-supplied add on packages. R currently provides more +\item[Functional] +++ This is \textsc{R}'s strength. Largely provided by + the $>850$ user-supplied add-on packages. \textsc{R} currently provides more functionality than any other statistical software system and is growing rapidly. -\item[Verifiable] --- Most of the functionality of R comes from - user-developed add-on packages, but there is currently no formal - mechanism for evaluating the level of quality of these packages (eg: +\item[Verifiable] --- Most of the functionality of \textsc{R} comes from + user-developed add-on packages ($>850$!), but there is currently no formal + mechanism for evaluating the level of quality of these packages (e.g.: development, test, production, peer reviewed, validated) or documentation that they accomplish the required tasks. + +\item[Repeatable] --- Currently, add on packages do not display + version information when loaded, making it difficult to know what + versions were utilized for a given analysis, and thus impossible to + reliably replicated. -\item[Repeatable] --- +\end{description} +} +\frame{ +\frametitle{Status of \textsc{R} (II)} -\item[Documentable] --- While the R core team has a well defined and +\begin{description}[<+->] + +\item[Documentable] --- While the \textsc{R} core team has a well defined and managed process for design, development, testing, release, and change management, no formal documentation of this process appears to exists (aside from the specifications of the language itself). No centrally defined or managed process appears to exist for add-on packages. + +\item[Auditable] --- \textsc{R} has no built-in no audit log, either for data + analysis steps or for changes to the system (e.g.: package updates, + patches) + \end{description} } - \frame{ +\frametitle{Status of \textsc{R} (III)} - \frametitle{Status of R (cont)} +\begin{description}[<+->] -\begin{description} - -\item[Auditable] --- R has no built-in no audit log, either for data - analysis steps or for changes to the system (e.g.: package updates, - patches) - -\item[Stable] --- The R core team releases minor (major.minor.patch) +\item[Stable] --- The \textsc{R} core team releases minor (major.minor.patch) versions twice a year. Since bug fixes are currently applied only to the latest released version of the system, it is difficult to properly support embedded and validated systems where one may need - to resolve bugs in R, but must constrain the R version to remain + to resolve bugs in \textsc{R}, but must constrain the \textsc{R} version to remain constant for long periods due to the burden of documentation and testing that must be performed. -\item[Supported] While there is an increasingly large pool of - statisticians and statistical consulting groups that have R - expertise, no organization formally supports R at this time. +\item[Supported] --- While there is an increasingly large pool of + statisticians and statistical consulting groups that have \textsc{R} + expertise, no organization formally supports \textsc{R} at this time. \end{description} } -\section{ What needs to be done?} +\section{Moving Forward} \frame{ - \frametitle{Status of R (cont)} + \frametitle{Moving Forward (I)} +\begin{description}[<+->] + \item[Functional] Already a strength. Continue! + \item[Verifiable] \textsc{RForge} proposal + \begin{enumerate} + \item Develop a SourceForge-like system for contributed packages: +% \begin{itemize} +% \item version control system (subversion) +% \item issue tracking system +% \item file release area +% \item web page +% \item news lists +% \end{itemize} for each individual package. + \item Support package status categories, including clear standards + \begin{itemize}[<1->] + \item development, + \item testing, + \item production, or + \item peer-reviewed/validated. + \end{itemize} + \end{enumerate} + \item[Repeatable] Display versions of packages on load + +\end{description} } -\begin{frame}[allowframebreaks] - \frametitle<presentation>{For Further Reading} +\frame{ + \frametitle{Moving Forward (II)} + +\begin{description}[<+->] + + \item[Documentable] ~ + \begin{enumerate} + \item Formally document the development process used for \textsc{R} + \item Provide tools to perform and document this process for + add-on packages + \item Develop validation templates for use by organizations + \item Encourage commercial vendors to support \textsc{R} and to provide + additional validation effort and associated documentation. + \end{enumerate} + \item[Auditable] Add an audit-log facility + \item[Stable] Establish a system for back-porting bug fixes to + previous versions. + \item[Supported] Encourage commercial vendors to formally support \textsc{R}. +\end{description} +} + +\section{News Flash!} + +\frame{ + \frametitle{News Flash!: \textsc{RPro} from \emph{REvolution Computing} } + + \setbeamerfont{small}{size=\small} + \usebeamerfont{small} + + + 2006-08-01 {\bf New Haven, CT}: \emph{REvolution Computing} + announces the immediate availability of \textsc{RPro}, an enterprise-strength + statistical computing environment providing the strengths of the + open source \textsc{R} statistical software system from the R-Project coupled + with the enterprise-level support and high-performance computing + expertise of \emph{REvolution Computing}. + + \vspace{1em} + + \begin{columns}[c] + \begin{column}{0.5\textwidth} + Additions to \textsc{R}: + + \begin{itemize} + + \item Technical Support + + \item Simple Installation and Maintenance + + \item Performance Tuning + + \item Documentation and Training + + \item Validation Materials + + \item Consulting and Services + + \end{itemize} + + \end{column} + \begin{column}{0.5\textwidth} + \includegraphics*[width=\textwidth]{RevolutionComputingInfo.pdf} + \end{column} + \end{columns} + +} + +\frame{ + +\frametitle{News Flash!: \textsc{NetWorkSpaces} from + \emph{REvolution Computing} + } + + \setbeamerfont{small}{size=\small} + \usebeamerfont{small} + + 2006-08-01 {\bf New Haven, CT}: \emph{REvolution Computing} + announces the immediate availability of \textsc{NetWorkSpaces} for + \textsc{RPro} (\textsc{NWS}). \textsc{NWS} enables calculations to + be automatically distributed across multiple processors in clusters. + Distributing the data and/or work across multiple processors permits + a dramatic decrease in time to completion of large computational + tasks or permits a dramatic increase in those calculations size, + length or complexity. \textsc{NWS} fully supports Microsoft Windows + Compute Cluster Server 2003 (\textsc{CCS}), which provides a + security enhanced and affordable high performance computing + solution. + +\begin{columns}[c] +\begin{column}{0.5\textwidth} + \includegraphics*[width=\textwidth]{MicrosoftWindowsClusterComputeServer2003.pdf} +\end{column} +\begin{column}{0.5\textwidth} + \includegraphics*[width=\textwidth]{RevolutionComputingInfo.pdf} +\end{column} +\end{columns} + +} + + +\section{More Information} + +\frame{ + \frametitle<presentation>{Contact Information} + +\begin{itemize} + \item Personal: + \begin{description} + \item[Email] gr...@wa... + \item[Web] http://www.warnes.net/Research + \end{description} + \vspace{1em} + + \item University of Rochester: + \begin{description} + \item[Email] wa...@bs... + \item[Web] http://www.urmc.rochester.edu/smd/biostat + \end{description} + \vspace{1em} - \begin{thebibliography}{10} + \item REvolution Computing: + \begin{description} + \item[Email] gr...@re... + \item[Web] http://www.revolution-computing.com + \end{description} + \vspace{1em} + + \end{itemize} + +} + +% \frame{ +% \begin{thebibliography}{10} - \beamertemplatebookbibitems - % Start with overview books. +% \beamertemplatebookbibitems +% % Start with overview books. - \bibitem{Author1990} - A.~Author. - \newblock {\em Handbook of Everything}. - \newblock Some Press, 1990. +% \bibitem{Warnes2006} +% G.~Warnes. +% \newblock {\em Handbook of Everything}. +% \newblock Some Press, 1990. - \beamertemplatearticlebibitems - % Followed by interesting articles. Keep the list short. +% \beamertemplatearticlebibitems +% % Followed by interesting articles. Keep the list short. - \bibitem{Someone2000} - S.~Someone. - \newblock On this and that. - \newblock {\em Journal of This and That}, 2(1):50--100, - 2000. - \end{thebibliography} -\end{frame} +% \bibitem{Someone2000} +% S.~Someone. +% \newblock On this and that. +% \newblock {\em Journal of This and That}, 2(1):50--100, +% 2000. +% \end{thebibliography} +% +% } - \end{document} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
