Decimaker: A statistical software using R, Microsoft.NET, R (D)COM Server and graphical libraries

Transcription

1 Decimaker: A statistical software using R, Microsoft.NET, R (D)COM Server and graphical libraries Julien Vanwinsberghe, ClinBAY, France Francois Vandenhende, ClinBAY, Belgium

2 Plan Decimaker software highlight Build a software using R: Why & How? Open Source components that can be useful Decimaker demonstration Installation & required components Some tools used during development Conclusion

3 Decimaker software highlight Decimaker: software for Adaptive Dose-Response Trials and Bayesian Decision Analysis Designed to assist clinical development teams protocol design, trial simulations and analysis User-friendly graphical interface Components Statistics: R and Open Bugs GUI: C# and.net Framework 2.0 Connection to R: R(D)COM Server

4 Build a software using R: Why & How?

5 Build a software using R: Part 1 - Why? R is command- line statistical software widely used by researchers A lot of statistical methods have been developed in R R is open- source Number of packages steadily increasing Fast and robust lack of an intuitive graphical interface for novices - >develop an interface easily understandable around the R programs Decimaker: kernel is a set of R programs, enhanced by a graphical interface

6 Build a software using R: Part 2 - How? R (D)COM Server: COM server used to connect a client application (e.g. Microsoft Excel) with R Environment: MS Windows Methods to transfer data to/from R Add the COM references to the C#.NET project Use the methods of the StatConnector object to evaluate R commands STATCONNECTORSRVLib.StatConnector R = new STATCONNECTORSRVLib.StatConnector(); R.Init("R"); R.EvaluateNoReturn("a<-12"); object ret = R.Evaluate("a");

7 Graphical open source components that can be useful Because adding a professional and pleasant interface to an application can be the most time-consuming part of the development

8 Open Source components that can be useful: Part 1 R Server ActiveX components R (D)COM Server includes two ActiveX controls Easy to implement To show R graphical output To Show R text output Display plots Transmit text outputs

9 Open Source components that can be useful: Part 1 R Server ActiveX components R (D)COM Server includes two ActiveX controls public void TestAxStatConnectors() { // Create an instance of the StatConnector STATCONNECTORSRVLib.StatConnector R = new STATCONNECTORSRVLib.StatConnector(); // Initialize R R.Init("R"); // Connect graphical and text devices R.AddGraphicsDevice("gfx", axstatconnectorgraphicsdevice.getgfx()); R.SetCharacterOutputDevice((StatConnectorCommonLib.IStatConnectorCharacterDevice)ax StatConnectorCharacterDevice.GetOcx()); // Test with R commands R.EvaluateNoReturn("print(\"plot(sin(1:100))\")"); R.EvaluateNoReturn("plot(sin(1:100))"); R.EvaluateNoReturn("print(\"Done.\")"); }

10 Open Source components that can be useful: Part 2 Charting and Gauge controls ZedGraph and A.J. Bauer Gauge are open-source charting and gauge libraries ZedGraph 2D line and bar charts of arbitrary datasets High degree of flexibility A.J. Bauer gauge Fast and performing Several themes Fully customizable Necessitates more code, but as a result, the quality of the graphical outputs is significantly improved

11 Open Source components that can be useful: Part 3 Icons FAMFAMFAM Silk icon library To add a final polish Smooth, colourful icons for any purpose > x16 px icons

12 Decimaker Demonstration Website :

13 Decimaker installation & required components

14 Decimaker required components Platform: Microsoft Windows Required components: R and required packages R (D)COM Server.NET Framework 2.0 Very complicated Errors in the first attempt to execute the application

15 Decimaker required components Test the proper installation of required external components string Rpath; // Variable that will contain R install path Microsoft.Win32.RegistryKey key = Microsoft.Win32.Registry.LocalMachine.OpenSubKey(@"SOFTWARE\R-core\R"); if (key!= null) { Rpath = key.getvalue("installpath", "").ToString(); // Can be in DOS format if (System.IO.Directory.Exists(Rpath)) // Transform to complete path Rpath = (new System.IO.DirectoryInfo(installedPath)).FullName; }

16 Some tools used during software development

17 Some tools used during development Subversion: version control system used on many open source projects (Apache, KDE, Pyton, ) manages current and historical versions of files BugTracker.NET: open-source, web-based bug tracker particularly easy to handle permits to keep track of reported software bugs supports integration with Subversion FxCop: Microsoft application that analyzes managed code to find possible improvements that can be made Testlink: test tool web based interface create, manage and plan tests

18 Conclusion Significant time was spent on searching, assessing and in integrating existing components Accurate results, fast computations and very nice and usable graphical outputs. The open source community provides key products The power of R Quality of results, speed up development Decimaker is not a black-box: import statistical models, define R formulas and queries, export results as R objects A downside: users are bound to install all required R components

19 Thank you! Julien Vanwinsberghe

20 To do list Complete validation report Wizards to assist users and make the use of the software easier Automatized reports

21 Licenses R (D)COM Server R ZedGraph FamFamFam Silk Icons A.J. Bauer Gauge Krypton Toolkit Not included in Decimaker Lesser General Public License (LGPL) Creative Commons Attribution 2.5 License No license (just keep included code header) Free to use runtime

22 Another tool to access R from and application: R Serve Rserve is a TCP/IP server supports remote connection, authentication and file transfer Easy integration: Rconnection c = new Rconnection(); double d[]=c.eval("rnorm(10)").asdoublearray(); Not advised for windows servers

23 Open Source components that can be useful: Part 3 Windows Form Controls Component Factory Toolkit library Improved versions of common used form controls Pretty design More functionalities Often updated