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The Nuts and Bolts of Sweave/Knitr for Reproducible Research

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The Nuts and Bolts of Sweave/Knitr for Reproducible Research The nuts and bolts of Sweave/Knitr for reproducible research Marcus W. Beck ORISE Post-doc Fellow USEPA NHEERL Gulf Ecology Division, Gulf Breeze, FL Email: [email protected], Phone: 850 934 2480 January 15, 2014 M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 1 / 25 From Wikipedia... `The ultimate product is the paper along with the full computational environment used to produce the results in the paper such as the code, data, etc. that can be used to reproduce the results and create new work based on the research.' Concept is strongly based on the idea of literate programming such that the logic of the analysis is clearly represented in the final product by combining computer code/programs with ordinary human language [Knuth, 1992]. Reproducible research In it's most general sense... the ability to reproduce results from an experiment or analysis conducted by another. M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 2 / 25 Concept is strongly based on the idea of literate programming such that the logic of the analysis is clearly represented in the final product by combining computer code/programs with ordinary human language [Knuth, 1992]. Reproducible research In it's most general sense... the ability to reproduce results from an experiment or analysis conducted by another. From Wikipedia... `The ultimate product is the paper along with the full computational environment used to produce the results in the paper such as the code, data, etc. that can be used to reproduce the results and create new work based on the research.' M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 2 / 25 Reproducible research In it's most general sense... the ability to reproduce results from an experiment or analysis conducted by another. From Wikipedia... `The ultimate product is the paper along with the full computational environment used to produce the results in the paper such as the code, data, etc. that can be used to reproduce the results and create new work based on the research.' Concept is strongly based on the idea of literate programming such that the logic of the analysis is clearly represented in the final product by combining computer code/programs with ordinary human language [Knuth, 1992]. M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 2 / 25 3. Report 1. Gather data 2. Analyze data results Begins with general Import data into Create research question or research stats program or report using Word objectives analyze directly in or other software Data collected in Excel Manually insert raw format (hard Create results into report copy) converted to figures/tables Change final report digital (Excel directly in stats by hand if spreadsheet) program methods/analysis Save relevant altered output Non-reproducible research M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 3 / 25 3. Report 2. Analyze data results Import data into Create research stats program or report using Word analyze directly in or other software Excel Manually insert Create results into report figures/tables Change final report directly in stats by hand if program methods/analysis Save relevant altered output Non-reproducible research 1. Gather data Begins with general question or research objectives Data collected in raw format (hard copy) converted to digital (Excel spreadsheet) M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 3 / 25 3. Report results Create research report using Word or other software Manually insert results into report Change final report by hand if methods/analysis altered Non-reproducible research 1. Gather data 2. Analyze data Begins with general Import data into question or research stats program or objectives analyze directly in Data collected in Excel raw format (hard Create copy) converted to figures/tables digital (Excel directly in stats spreadsheet) program Save relevant output M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 3 / 25 Non-reproducible research 3. Report 1. Gather data 2. Analyze data results Begins with general Import data into Create research question or research stats program or report using Word objectives analyze directly in or other software Data collected in Excel Manually insert raw format (hard Create results into report copy) converted to figures/tables Change final report digital (Excel directly in stats by hand if spreadsheet) program methods/analysis Save relevant altered output M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 3 / 25 Reproducible research 3. Report 1. Gather data 2. Analyze data results Begins with general Create integrated Create research question or research script for importing report using RR objectives data (data path is software Data collected in known) Automatically raw format (hard Create include results into copy) converted to figures/tables report digital (text file) directly in stats Change final report program automatically if No need to export methods/analysis (reproduced on the altered fly) M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 4 / 25 Essentially a LATEX document that incorporates R code... Uses Sweave (or Knitr) to convert .Rnw file to .tex file, then LATEX to create pdf Sweave comes with utils package, may have to tell R where it is Reproducible research in R Easily adopted using RStudio [http://www.rstudio.com/] Also possible w/ Tinn-R or via command prompt but not as intuitive Requires a LATEX distribution system - use MikTex for Windows [http://miktex.org/] M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 5 / 25 Reproducible research in R Easily adopted using RStudio [http://www.rstudio.com/] Also possible w/ Tinn-R or via command prompt but not as intuitive Requires a LATEX distribution system - use MikTex for Windows [http://miktex.org/] Essentially a LATEX document that incorporates R code... Uses Sweave (or Knitr) to convert .Rnw file to .tex file, then LATEX to create pdf Sweave comes with utils package, may have to tell R where it is M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 5 / 25 Sweave pdfLatex 1. myfile.Rnw 2. myfile.tex 3. myfile.pdf A .tex file but with .Rnw file is .tex file converted .Rnw extension converted to a .tex to pdf (or other Includes R code as file using Sweave output) for final `chunks' or inline .tex file contains format expressions output from R, no Include biblio with raw R code bibtex Reproducible research in R Use same procedure for compiling a LATEX document with one additional step M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 6 / 25 Sweave pdfLatex 2. myfile.tex 3. myfile.pdf .Rnw file is .tex file converted converted to a .tex to pdf (or other file using Sweave output) for final .tex file contains format output from R, no Include biblio with raw R code bibtex Reproducible research in R Use same procedure for compiling a LATEX document with one additional step 1. myfile.Rnw A .tex file but with .Rnw extension Includes R code as `chunks' or inline expressions M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 6 / 25 pdfLatex 3. myfile.pdf .tex file converted to pdf (or other output) for final format Include biblio with bibtex Reproducible research in R Use same procedure for compiling a LATEX document with one additional step Sweave 1. myfile.Rnw 2. myfile.tex A .tex file but with .Rnw file is .Rnw extension converted to a .tex Includes R code as file using Sweave `chunks' or inline .tex file contains expressions output from R, no raw R code M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 6 / 25 Reproducible research in R Use same procedure for compiling a LATEX document with one additional step Sweave pdfLatex 1. myfile.Rnw 2. myfile.tex 3. myfile.pdf A .tex file but with .Rnw file is .tex file converted .Rnw extension converted to a .tex to pdf (or other Includes R code as file using Sweave output) for final `chunks' or inline .tex file contains format expressions output from R, no Include biblio with raw R code bibtex M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 6 / 25 Reproducible research in R .Rnw file \documentclass{article} \usepackage{Sweave} \begin{document} Here's some R code: <<eval=true,echo=true>>= options(width=60) set.seed(2) rnorm(10) @ \end{document} M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 7 / 25 Reproducible research in R .tex file \documentclass{article} \usepackage{Sweave} \begin{document} Here's some R code: \begin{Schunk} \begin{Sinput} > options(width=60) > set.seed(2) > rnorm(10) \end{Sinput} \begin{Soutput} [1] -0.89691455 0.18484918 1.58784533 -1.13037567 [5] -0.08025176 0.13242028 0.70795473 -0.23969802 [9] 1.98447394 -0.13878701 \end{Soutput} \end{Schunk} \end{document} M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 8 / 25 Reproducible research in R The final product: Here’s some R code: > options(width=60) > set.seed(2) > rnorm(10) [1] -0.89691455 0.18484918 1.58784533 -1.13037567 [5] -0.08025176 0.13242028 0.70795473 -0.23969802 [9] 1.98447394 -0.13878701 M. Beck (USEPA NHEERL) Nuts and bolts of Sweave/Knitr January 15, 2014 9 / 25 1 eval: evaluate code, default T echo: return source code, default T results: format of output (chr string), default is `include' (also `tex' for tables or `hide' to suppress) fig: for creating figures, default F Sweave - code chunks R code is entered in the LATEX document using `code chunks' <<>>= @ Any text within the code chunk is interpreted as R code Arguments for the code chunk are entered within <<here>> M.
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