Difference: StatReport (24 vs. 25)

Revision 25
30 Jul 2011 - Main.FrankHarrell
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META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data | Reproducible Research | RR Planet | Department Reproducible Reporting Activities

  • Statistical Tables and Plots using S and LaTeX; FE Harrell (PDF with hyperlinks and bookmarks). This document shows all of the LaTeX and S code needed to produce the entire document. Heavy use is made of the Hmisc library's summary.formula function for semi-advanced table making and conversion of selected tables to graphics. The document shows how to automatically get hyperlinks in the final .pdf file using the LaTeX hyperref style. It also shows how easy it is to use the LaTeX \input command to include tables and computed values created by S, which allows a report to easily be updated, reassembled, re-cross-referenced, etc., if any component tables or plots change. The Heiberger-Harrell latex function in Hmisc is used to interface S with LaTeX.
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  • Converting Sweave LaTeX documents for use in word and posting on web pages, and using the R odfWeave package to create OpenOffice documents
  • The Statdocs project at UC Berkeley, based on integrating XMLS, HTML, JavaScript, and R
  • Managing analysis projects using conditional processing of sections of S code: see Chapter 13 of Alzola & Harrell for information about the S do function and using Makefiles on Windows. (This text also contains an example of using another, more flexible, tool for managing program execution: Perl). do makes it easy to run only the sections of the analysis that you want to re-do. Each section can automatically generate its own listing output file which is not overwritten by output files from other sections. The graphics files generated by each code section can automatically be given a section-specific file name prefix. do works especially well with batch job processing.
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  • Reproducible electronic documents from Matt Schwab and Jon Claerbout of Stanford University. This approach is based on the make utility readily available for Unix, Linux, and Win95/98/NT. Final figures and calculations are easily regenerated by running make, which senses file dependencies and creation/modification dates to re-run whatever needs to be re-run to build the final product. Quoting Schwab and Claerbout, "It takes some effort to organize your research to be reproducible. We found that although the effort seems to be directed to helping other people stand up on your shoulders, the principal beneficiary is generally the author herself. This is because time turns each one of us into another person, and by making effort to communicate with strangers, we help ourselves to communicate with our future selves."
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  • Reproducible electronic documents from Matt Schwab and Jon Claerbout of Stanford University. This approach is based on the make utility readily available for Unix, Linux, and Win95/98/NT. Final figures and calculations are easily regenerated by running make, which senses file dependencies and creation/modification dates to re-run whatever needs to be re-run to build the final product. Quoting Schwab and Claerbout, "It takes some effort to organize your research to be reproducible. We found that although the effort seems to be directed to helping other people stand up on your shoulders, the principal beneficiary is generally the author herself. This is because time turns each one of us into another person, and by making effort to communicate with strangers, we help ourselves to communicate with our future selves."
 
 
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