Knitr: A comprehensive tool for reproducible research in R

Implementing Reproducible Research

Volumn , Issue , 2014, Pages 3-32

  Xie, Yihui ^a  

^a Department of Statistics Center for Statistics and Applications in Forensic Evidence Iowa State University 2438 Osborn Dr Ames   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85055520225     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/b16868     Document Type: Chapter

References (29)

1. D. Adler and D. Murdoch. rgl: 3D visualization device system (OpenGL), 2013. R package version 0.93.929/r929.
2. K.A. Baggerly, J.S. Morris, and K.R. Coombes. Reproducibility of SELDI-TOF protein patterns in serum: Comparing datasets from different experiments. Bioinformatics, 20(5):777–785, 2004.
3. C. Bracken and C. Sharpsteen. pgfSweave: Quality speedy graphics compilation and caching with Sweave, 2012. R package version 1.3.0.
4. D.B. Dahl. xtable: Export tables to LaTeX or HTML, 2013. R package version 1.7-1.
5. D. Eddelbuettel. digest: Create cryptographic hash digests of R objects, 2013. R package version 0.6.3.
6. S. Falcon. weaver: Tools and extensions for processing Sweave documents, 2013. R package version 1.24.0.
7. R. Gentleman. Reproducible research: A bioinformatics case study. Statistical Applications in Genetics and Molecular Biology, 4(1):1034, 2005.
8. R. Gentleman and D. Temple Lang. Statistical analyses and reproducible research. Bioconductor Project Working Papers, 2004.
9. M. Gesmann and D. de Castillo. googleVis: Interface between R and the Google chart tools, 2013. R package version 0.4.2.
10. J. Gruber. The Markdown project, 2004. http://daringfireball.net/projects/markdown/
11. R. Ihaka and R. Gentleman. R: A language for data analysis and graphics. Journal of Computational and Graphical Statistics, 5(3):299–314, 1996.
12. D.E. Knuth. The WEB system of structured documentation. Technical report, Department of Computer Science, Stanford University, Stanford, CA, 1983.
13. D.E. Knuth. Literate programming. The Computer Journal, 27(2):97–111, 1984.
14. F. Leisch. Sweave: Dynamic generation of statistical reports using literate data analysis. In COMPSTAT 2002 Proceedings in Computational Statistics, Vol. 69, pp. 575–580. Physica Verlag, Heidelberg, Germany, 2002.
15. P. Murrell. R Graphics, 2nd ed. Chapman & Hall/CRC, Boca Raton, FL, 2011.
16. R.D. Peng. cacheSweave: Tools for caching Sweave computations, 2012. R package version 0.6-1.
17. R.D. Peng. filehash: Simple key-value database, 2012. R package version 2.2-1.
18. R Core Team. R Language Definition. R Foundation for Statistical Computing. Vienna, Austria, 2012.
19. R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2013. ISBN 3-900051-07-0.
20. N. Ramsey. Literate programming simplified. IEEE Software, 11(5): 97–105, 1994.
21. A.J. Rossini, R.M. Heiberger, R.A. Sparapani, M. Maechler, and K. Hornik. Emacs speaks statistics: A multiplatform, multipackage development environment for statistical analysis. Journal of Computational and Graphical Statistics, 13(1):247–261, 2004.
22. A. Rossini. Literate statistical analysis. In Proceedings of the 2nd International Workshop on Distributed Statistical Computing, Hornik, K. and Leisch, F. (Eds.), Technische Universität Wien, Vienna, Austria, 2001. http://www.ci.tuwien.ac.at/Conferences/DSC-2001/Proceedings/
23. RStudio, Inc. shiny: Web Application Framework for R, 2013. R package version 0.4.0.99.
24. C. Sharpsteen and C. Bracken. tikzDevice: R graphics output in LaTeX format, 2012. R package version 0.6.3/r49.
25. T. Tantau. The TikZ and PGF packages, 2008. http://sourceforge.net/projects/pgf/
26. H. Wickham. evaluate: Parsing and evaluation tools that provide more details than the default, 2013. R package version 0.4.3.
27. Y. Xie. formatR: Format R code automatically, 2012. R package version 0.7.2.
28. Y. Xie. Dynamic Documents with R and knitr. Chapman & Hall/CRC, Boca Raton, FL, 2013. ISBN 978-1482203530.
29. Y. Xie. knitr: A general-purpose package for dynamic report generation in R, 2013. R package version 1.1.8.