Executable papers for the R community: The R2 platform for reproducible research

Procedia Computer Science

Volumn 4, Issue , 2011, Pages 618-626

  Leisch, Friedrich ^a   Eugster, Manuel ^b   Hothorn, Torsten ^b  

^a UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

R; Reproducible research; Statistical computing; Sweave

Indexed keywords

COMPUTATIONAL RESULTS; R; REPRODUCIBLE RESEARCH; SCIENTIFIC PAPERS; SOFTWARE REPOSITORIES; STATISTICAL COMPUTING; SWEAVE; THIRD PARTIES;

SOFTWARE TESTING; USER INTERFACES; WEB SERVICES;

PAPER;

EID: 79958264004     PISSN: None     EISSN: 18770509     Source Type: Conference Proceeding    
DOI: 10.1016/j.procs.2011.04.065     Document Type: Conference Paper

References (20)

1. J. Buckheit, D. Donoho, WaveLab and reproducible research, statistics Department, Stanford University, CA, USA (1995). URL http://www-stat.stanford. edu/donoho/.
2. J. de Leeuw, Reproducible research: the bottom line, statistics Program, Unniversity of California, Los Angeles, CA, USA (2001). URL http://preprints. stat.ucla.edu/.
3. T. Hothorn, F. Leisch, Case studies in reproducibility, Briefings in BioinformaticsAccepted for publication on 2010-12-01. doi:10.1093/bib/bbq084.
4. R Development Core Team, R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, ISBN 3-900051-07-0 (2010). URL http://www.R-project.org.
5. K. Hornik, F. Leisch, Vienna and R: Love, marriage and the future, in: R. Dutter (Ed.), Festschrift 50 Jahre Österreichische Statistische Gesellschaft, Österreichische Statistische Gesellschaft, 2002, pp. 61-70, iSSN 1026-597X.
6. S. Theüsl, U. Ligges, K. Hornik, Prospects and challenges in R package development, Computational Statistics Accepted for publication. doi:10.1007/s00180-010-0205-5. URL http://dx.doi.org/10.1007/s00180-010-0205-5.
7. F. Leisch, Sweave: Dynamic generation of statistical reports using literate data analysis, in: W. Härdle, B. R̈onz (Eds.), Compstat 2002 - Proceedings in Computational Statistics, Physica Verlag, Heidelberg, 2002, pp. 575-580, iSBN 3-7908-1517-9. URL http://www.stat.uni-muenchen.de/leisch/Sweave.
8. D. E. Knuth, Literate programming, The Computer Journal 27 (2) (1984) 97111.
9. F. Leisch, A. J. Rossini, Reproducible statistical research, Chance 16 (2) (2003) 46-50.
10. R. C. Gentleman, V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J. Y. Yang, J. Zhang, Bioconductor: Open software development for computational biology and bioinformatics, Genome Biology 5 (10) (2004) R80.1-16. URL http://genomebiology.com/2004/5/10/R80.
11. G. J. Williams, Rattle: A Data Mining GUI for R, The R Journal 1 (2) (2009) 45-55.
12. R. Koenker, A. Zeileis, On reproducible econometric research, Journal of Applied Econometrics 24 (5) (2009) 833-847. doi:10.1002/jae.1083.
13. P. Vandewalle, J. Kovacevic, M. Vetterli, Reproducible research in signal processing [what, why, and how], IEEE Signal Processing Magazine (2009) 37-47.
14. K. A. Baggerly, K. R. Coombes, Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in highthroughput biology, The Annals of Applied Statistics 3 (4) (2009) 1309-1334. doi:10.1214/09-AOAS291.
15. K. A. Baggerly, K. R. Coombes, E. S. Neeley, Run Batch Effects Potentially Compromise the Usefulness of Genomic Signatures for Ovarian Cancer, Journal of Clinical Oncology 26 (7) (2008) 1186-1187. doi:10.1200/JCO.2007.15. 1951.
16. H. K. Dressman, A. Berchuck, G. Chan, J. Zhai, A. Bild, R. Sayer, J. Cragun, J. Clarke, R. S. Whitaker, L. Li, J. Gray, J. Marks, G. S. Ginsburg, A. Potti, M. West, J. R. Nevins, J. M. Lancaster, An Integrated Genomic-Based Approach to Individualized Treatment of Patients With Advanced-Stage Ovarian Cancer, Journal of Clinical Oncology 25 (5) (2007) 517-525. doi:10.1200/JCO. 2006.06.3743. (Pubitemid 350002958)
17. V. J. Carey, V. Stodden, Reproducible research concepts and tools for cancer bioinformatics, in: M. F. Ochs, J. T. Casagrande, R. V. Davuluri (Eds.), Biomedical Informatics for Cancer Research, Springer, 2010, pp. 149-175.
18. A. J. Rossini, R. M. Heiberger, R. Sparapani, M. Mächler, K. Hornik, Emacs speaks statistics: A multiplatform, multipackage development environment for statistical analysis, Journal of Computational and Graphical Statistics 13 (1) (2004) 247-261. (Pubitemid 38422443)
19. Object Management Group, Inc., Business Process Modeling Notation, v2.0 (January 2011). URL http://www.bpmn.org.
20. R Development Core Team, Writing R Extensions, R Foundation for Statistical Computing, Vienna, Austria, ISBN 3-900051-11-9 (2011). URL http://www.R-project.org.