Reproducible Research

1
Reproducible Research

• Lisa Pappas
• 10/21/10
• SDBC meeting

2
Goals

• Be able to reproduce your own results
• Allow others to reproduce your results
• Time turns each one of us into another person,
• and by making eort to communicate with
• strangers, we help ourselves to communicate
• with our future selves. (Schwab and Claerbout)
• Reproduce an entire report, manuscript,
  dissertation, book
• with a single system command when changes occur
  in
• operating system, stat software, graphics
  engines, source
• data, derived variables, analysis, interpretation
• Save time
• Provide the ultimate documentation of work done
  for a
• paper

Frank E Harrell Jr
3
Prior to running Sweave

• Install MiKTeX it is free and is necessary for
  creating PDF files from the TeX files that
  Sweave generates.
• http//miktex.org/
• Consider using the trial version or purchasing
  WinEdt 6.0. There are built in functions for
  generating PDF files . http//www.winedt.com/
•  
• If you are using Windows, have R installed in a
  path with no spaces (C\R vs. the default
  C\Program files\R) OR- make sure you include
  \usepackageSweave in your program and have the
  file Sweave.sty in your working directory.
  Sweave.sty can be found R_HOME\share\texmf\tex\
  latex
• Have packages tools and Hmisc installed in R.

4
Diagram of process
http//biostat.mc.vanderbilt.edu/wiki/pub/Main/The
resaScott/ReproducibleResearch.TAScott.handout.pdf
5
Running the example Sweave file in R

• gtSweave(example.Rnw)
• gttexi2dvi(example.tex, pdfTRUE)

6
Good Sweave references

• Sweave homepage http//www.statistik.lmu.de/leis
  ch/Sweave/
• Reproducible Research with R, LaTeX Sweave
  http//biostat.mc.vanderbilt.edu/wiki/pub/Main/The
  resaScott/ReproducibleResearch.TAScott.handout.pdf
  
• Additional links http//gettinggeneticsdone.blogs
  pot.com/2010/05/using-r-latex-and-sweave-for.html