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---+ Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data  | [[http://www.reproducibleresearch.org Reproducible Research]] | [[http://rrplanet.com RR Planet]] | Department [[ReReport][Reproducible Reporting]] Activities

*Note*: This page is out of date.  Go to https://hbiostat.org/rr 

   * [[%ATTACHURL%/summary.pdf][Statistical Tables and Plots using S and LaTeX]]; FE Harrell (PDF with hyperlinks and bookmarks). This document shows all of the <nop>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 <nop>LaTeX =hyperref= style. It also shows how easy it is to use the <nop>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 <nop>LaTeX. 
      * [[%ATTACHURL%/summary.zip Zipped Word version]] of =summary.pdf= created by http://www.pdftoword.com | [[%ATTACHURL%/summary.doc.pdf PDF version created by Word]]
      * [[%ATTACHURL%/s6a.odt OpenOffice Example]] of Table 12 of the above document, created by opening the html document created by the =htlatex= command of the =TeX4ht= package (see SweaveConvert) and removing links to images so they are saved in-line.  !LaTeX code for that table was first saved into a file and a prologue containing =\usepackage{color,calc,epic}= was inserted (for tables using the =ctable= style, =ctable= would have to be included in this prologue).
      * [[%ATTACHURL%/latexFineControl.pdf Examples]] of [[mailto:david.whiting@ncl.ac.uk][David Whiting]]'s additions to the =latex= function to allow more fine control of typesetting
   * The [[Rreport][rreport]] package for reporting clinical trials analyses

Features of <nop>LaTeX that make it excellent for report composition include:
   * the =\input{filename}= command for assembling <nop>LaTeX-coded tables created by S or SAS, or for including definitions of variable values to be included in the report (e.g., a P-value to insert in the text) 
   * the =\verbatimtabinput{filename}= command (part of the <nop>LaTeX =moreverb= package) for including verbatim tabular listings that are not to be reformatted by <nop>LaTeX 
   * the =\includegraphics{filename}= command for including graphics files (usually postscript for <nop>LaTeX and pdf for =pdflatex)= 
   * automatic recompilation of the entire report by re-running the =latex= or =pdflatex= command whenever any of the component figures, variable values, or tables change, with automatic regeneration of cross-references, page numbers, etc. 
   * excellent facilities for cross-referencing, table of contents, table of tables, table of figures, indexes, and bibliographic citations 
   * the =hyperref= style in <nop>LaTeX makes all bibliographic citations, references, sections, subsections, tables of contents, indexes, etc., automatically hyperlinked in the final pdf document, with no work by the user; the table of contents is bookmarked 
   * you can have "if-then" constructs in <nop>LaTeX for conditional output generation 
   * by adding the =pdfscreen= style to the <nop>LaTeX master file you can produce a hyperlinked pdf document specially formatted for on-screen viewing 
   * you can produce somewhat complex tables, e.g., tables showing small numerators and denominators next to percents, that are very readable

One of many features of S that makes it an excellent tool for producing statistical reports is its object orientation. By writing both a table-producing method and a plot method for each type of analysis you can convert tables to plots. See the =[[Hmisc]]= library's =[[http://biostat.mc.vanderbilt.edu/s/Hmisc/html/summary.formula.html][summary.formula]]= function for many examples of this.

Click [[http://www.biostat.wisc.edu/Clinical_Trials/sdacindex.htm][here]] for information about how the University of Wisconsin Statistical Data Analysis Center uses S and <nop>LaTeX for producing primarily graphical reports for Safety and Data Monitoring Committees.  
   * [[http://www.literateprogramming.com][Literate programming]]: Writing documentation containing computer code. Documentation (and perhaps a statistical report) and code are maintained in one file. An extractor program such as [[http://www.ross.net/funnelweb/][FunnelWeb]] splits out the code to compile. [[mailto:pwolf@wiwi.uni-bielefeld.de <nop>H.P. <nop>Wolf]] and P. Naeve have done a lot of work in this area. In Peter Wolf's words
      * Some years ago we have developed a system for reporting the steps of a data analysis.  The system is based on the ideas of literate programming. =Noweb= and <nop>LaTeX are used to  generate nice output. The result of the tangle path can be reloaded by our function  =revive()= into the S-Plus interpreter. Then you can select and extract the elements of the  old analysis, you can modify them and you can activate the statements again. Therefore, our  tool can be used for teaching, demonstrations, case studies, ... We have constructed a lot of  papers for our statistics courses in this way.
Click [[http://www.wiwi.uni-bielefeld.de/StatCompSci/software/e-papers/e-papers.html][here]] for their papers that are written in English. These include a nice "live" statistics text (_A Revivable Book of Statistics_) in which their =revive()= function is used to extract S-Plus code from the book for interactive replay by the user who is connected to an S-Plus session. 
   * The [[http://www.ci.tuwien.ac.at/~leisch/Sweave][Sweave]] approach to literate programming using R | SweaveLatex
   * [[SweaveConvert][Converting Sweave LaTeX documents]] for use in word and posting on web pages, and using the R =odfWeave= package to create <noc>OpenOffice documents
   * The [[http://www.statdocs.org][Statdocs]] project at UC Berkeley, based on integrating XMLS, HTML, <nop>JavaScript, and R 
   * Managing analysis projects using *conditional processing of sections of S code*: see Chapter 13 of [[%ATTACHURL%/sintro#chapter.13][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: [[http://www.perl.org][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. 
   * [[http://sepwww.stanford.edu/lib/exe/fetch.php?media=sep:research:reproducible:cip.pdf][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." 
   * [[http://biomserv.univ-lyon1.fr/~necsulea/repro Example]] of a reproducible publication and [[http://pbil.univ-lyon1.fr/members/lobry/repro here]]
   * [[http://www.bepress.com/uwbiostat/paper194][Literate statistical practice]] by Anthony Rossini and Friedrich Leisch
   * Papers on reproducible research from the [[http://www.bepress.com/bioconductor][Bioconductor]] project
   * [[http://preprints.stat.ucla.edu/301/301.pdf][ Reproducible research: The Bottom Line]] by Jan de Leeuw 
   * Charles Geyer's excellent page on [[http://www.stat.umn.edu/~charlie/Sweave literate programming]] and related areas
   * Roger Peng's examples of [[http://www.biostat.jhsph.edu/~rpeng/reproducible reproducible research]]
   * [[http://fmwww.bc.edu/GStat/docs/pointclick.html][Why should you avoid using point-and-click methods in statistical software packages]] by C Baum and S Sirin, Boston College 
   * [[http://www.phor.com/perspective.html][PERSPECTIVE]], Hypertext Data Analysis Mapping software from Pharmaceutical Outcomes Research, Inc. This software allows analysts to track, review, communicate, and document analysis results using HTML. 
   * [[http://www.econ.uiuc.edu/~roger/repro.html][Reproducibility in Econometrics Research]] by Roger Koenker. A document on that page describes many useful approaches, including an S-Plus function =how.created= that makes it easy to attach to an object the following information: comments, user name, date, and the environment in effect (e.g., the search list) when the object was created. 
   * [[http://www.biostat.washington.edu/~rossini/][Tony Rossini]], a developer of [[http://ess.stat.wisc.edu/][ESS]] ("Emacs Speaks Statistics") is working on using =Noweb= with Emacs bookmarking facilities for tying S output chunks and figures to reports. 
   * [[http://www.icpsr.umich.edu/files/ICPSR/access/dataprep.pdf][University of Michigan ICPSR Guide to Social Sciences Data Preparation and Archiving]] - includes information on data entry, quality control, data management, codebooks and other documentation, and archiving 
   * [[EmacsTeX/index.html][Emacs/LaTeX/UNIX tools Information]] 
   * [[http://www.stat.sc.edu/rsrch/gasp/][Globally Accessible Statistical Procedures]] (web-based statistical programs)  
   * [[http://ged.msu.edu/papers/2012-diginorm/]["A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data"]] by Titus Brown, a benchmark example of reproducible research in genomics
   * Excellent =knitr= examples from [[http://www.math.smith.edu/~nhorton/sleuth The Statistical Sleuth]]

Topic attachments
I	Attachment	Action	Size	Date	Who	Comment
pdf	latexFineControl.pdf	manage	187.3 K	19 Dec 2005 - 08:01	FrankHarrell	Fine Control of LaTeX Typesetting with latex()
odt	s6a.odt	manage	16.6 K	20 Jul 2007 - 16:17	FrankHarrell	OpenOffice version of advanced table translated from LaTeX
pdf	summary.doc.pdf	manage	561.0 K	24 Nov 2009 - 13:35	FrankHarrell	summary.pdf -> summary.doc -> pdf created with Word
pdf	summary.pdf	manage	567.0 K	20 Jul 2007 - 16:46	FrankHarrell	Statistical Tables and Reports using S and LaTeX
zip	summary.zip	manage	357.9 K	28 Oct 2009 - 18:01	FrankHarrell	summary.pdf from pdflatex converted to Word using PDFtoWord - zipped .doc file
pdf	summaryPDF2doc2PDF.pdf	manage	770.8 K	21 Dec 2011 - 13:21	FrankHarrell	summary.doc converted to pdf using wordtopdf.com

Topic revision: r29 - 23 Jun 2020, FrankHarrell

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