Difference: StatReport (1 vs. 28)

Revision 28
14 Aug 2012 - Main.FrankHarrell
Line: 1 to 1
 
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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-- FrankHarrell
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META FILEATTACHMENT attr="" comment="Statistical Tables and Reports using S and LaTeX" date="1184967978" name="summary.pdf" path="summary.pdf" size="580656" user="FrankHarrell" version="1.3"
META FILEATTACHMENT attr="" comment="Fine Control of LaTeX Typesetting with latex()" date="1135000892" name="latexFineControl.pdf" path="latexFineControl.pdf" size="191762" user="FrankHarrell" version="1.3"
Revision 27
20 Jul 2012 - Main.ChrisFonnesbeck
Line: 1 to 1
 
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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-- FrankHarrell
Revision 26
21 Dec 2011 - Main.FrankHarrell
Line: 1 to 1
 
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.
Line: 50 to 50
 
META FILEATTACHMENT attr="" comment="OpenOffice version of advanced table translated from LaTeX" date="1184966227" name="s6a.odt" path="s6a.odt" size="17039" user="FrankHarrell" version="1.1"
META FILEATTACHMENT attachment="summary.zip" attr="" comment="summary.pdf from pdflatex converted to Word using PDFtoWord - zipped .doc file" date="1256770870" name="summary.zip" path="summary.zip" size="366505" stream="IO::File=GLOB(0x94b8dcc)" tmpFilename="/tmp/apreqGiM3XD" user="FrankHarrell" version="1"
META FILEATTACHMENT attachment="summary.doc.pdf" attr="" comment="summary.pdf -> summary.doc -> pdf created with Word" date="1259091347" name="summary.doc.pdf" path="summary.doc.pdf" size="574461" stream="IO::File=GLOB(0x8c501f0)" tmpFilename="/tmp/apreqCWmiTr" user="FrankHarrell" version="1"
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META FILEATTACHMENT attachment="summaryPDF2doc2PDF.pdf" attr="" comment="summary.doc converted to pdf using wordtopdf.com" date="1324495315" name="summaryPDF2doc2PDF.pdf" path="summaryPDF2doc2PDF.pdf" size="789281" stream="IO::File=GLOB(0x95a2e24)" tmpFilename="/tmp/9H4kgb3AMe" user="FrankHarrell" version="1"
Revision 25
30 Jul 2011 - Main.FrankHarrell
Line: 1 to 1
 
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.
Line: 28 to 28
 
  • 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."
 
Revision 24
22 Jul 2011 - Main.FrankHarrell
Line: 1 to 1
 
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.
Line: 20 to 20
 

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 summary.formula function for many examples of this.
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Click here for a short article about how the University of Wisconsin Statistical Data Analysis Center uses S-Plus and LaTeX for producing primarily graphical reports for Safety and Data Monitoring Committees.
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Click here for information about how the University of Wisconsin Statistical Data Analysis Center uses S and LaTeX for producing primarily graphical reports for Safety and Data Monitoring Committees.
 
  • 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 FunnelWeb splits out the code to compile. H.P. 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 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 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.
Line: 39 to 39
 
  • 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.
  • 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.
  • Tony Rossini, a developer of ESS ("Emacs Speaks Statistics") is working on using Noweb with Emacs bookmarking facilities for tying S output chunks and figures to reports.
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Revision 23
24 Nov 2009 - Main.FrankHarrell
Line: 1 to 1
 
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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    • 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).
    • Examples of David Whiting's additions to the latex function to allow more fine control of typesetting
  • The rreport package for reporting clinical trials analyses
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META FILEATTACHMENT attr="" comment="Fine Control of LaTeX Typesetting with latex()" date="1135000892" name="latexFineControl.pdf" path="latexFineControl.pdf" size="191762" user="FrankHarrell" version="1.3"
META FILEATTACHMENT attr="" comment="OpenOffice version of advanced table translated from LaTeX" date="1184966227" name="s6a.odt" path="s6a.odt" size="17039" user="FrankHarrell" version="1.1"
META FILEATTACHMENT attachment="summary.zip" attr="" comment="summary.pdf from pdflatex converted to Word using PDFtoWord - zipped .doc file" date="1256770870" name="summary.zip" path="summary.zip" size="366505" stream="IO::File=GLOB(0x94b8dcc)" tmpFilename="/tmp/apreqGiM3XD" user="FrankHarrell" version="1"
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META FILEATTACHMENT attachment="summary.doc.pdf" attr="" comment="summary.pdf -> summary.doc -> pdf created with Word" date="1259091347" name="summary.doc.pdf" path="summary.doc.pdf" size="574461" stream="IO::File=GLOB(0x8c501f0)" tmpFilename="/tmp/apreqCWmiTr" user="FrankHarrell" version="1"
Revision 22
28 Oct 2009 - Main.FrankHarrell
Line: 1 to 1
 
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.
Added:
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    • 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).
    • Examples of David Whiting's additions to the latex function to allow more fine control of typesetting
  • The rreport package for reporting clinical trials analyses
Line: 47 to 48
 
META FILEATTACHMENT attr="" comment="Statistical Tables and Reports using S and LaTeX" date="1184967978" name="summary.pdf" path="summary.pdf" size="580656" user="FrankHarrell" version="1.3"
META FILEATTACHMENT attr="" comment="Fine Control of LaTeX Typesetting with latex()" date="1135000892" name="latexFineControl.pdf" path="latexFineControl.pdf" size="191762" user="FrankHarrell" version="1.3"
META FILEATTACHMENT attr="" comment="OpenOffice version of advanced table translated from LaTeX" date="1184966227" name="s6a.odt" path="s6a.odt" size="17039" user="FrankHarrell" version="1.1"
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META FILEATTACHMENT attachment="summary.zip" attr="" comment="summary.pdf from pdflatex converted to Word using PDFtoWord - zipped .doc file" date="1256770870" name="summary.zip" path="summary.zip" size="366505" stream="IO::File=GLOB(0x94b8dcc)" tmpFilename="/tmp/apreqGiM3XD" user="FrankHarrell" version="1"
Revision 21
10 Aug 2009 - Main.FrankHarrell
Line: 1 to 1
 
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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Revision 20
03 Mar 2009 - Main.FrankHarrell
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META TOPICPARENT name="RS"
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Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data | Reproducible Research | Department Reproducible Reporting Activities

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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.
    • 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).
    • Examples of David Whiting's additions to the latex function to allow more fine control of typesetting
Revision 19
24 Jun 2008 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"
Changed:
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Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data | Reproducible Research

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Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data | Reproducible Research | 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.
    • 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).
    • Examples of David Whiting's additions to the latex function to allow more fine control of typesetting
Revision 18
30 May 2008 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"
Changed:
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Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

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

 
  • 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.
    • 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).
    • Examples of David Whiting's additions to the latex function to allow more fine control of typesetting
Revision 17
20 Jul 2007 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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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    • 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).
 
  • Examples of David Whiting's additions to the latex function to allow more fine control of typesetting
  • The rreport package for reporting clinical trials analyses
Line: 42 to 43
 

-- FrankHarrell
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META FILEATTACHMENT attr="" comment="Statistical Tables and Reports using S and LaTeX" date="1184882331" name="summary.pdf" path="summary.pdf" size="577909" user="FrankHarrell" version="1.2"
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META FILEATTACHMENT attr="" comment="Statistical Tables and Reports using S and LaTeX" date="1184967978" name="summary.pdf" path="summary.pdf" size="580656" user="FrankHarrell" version="1.3"
 
META FILEATTACHMENT attr="" comment="Fine Control of LaTeX Typesetting with latex()" date="1135000892" name="latexFineControl.pdf" path="latexFineControl.pdf" size="191762" user="FrankHarrell" version="1.3"
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META FILEATTACHMENT attr="" comment="OpenOffice version of advanced table translated from LaTeX" date="1184966227" name="s6a.odt" path="s6a.odt" size="17039" user="FrankHarrell" version="1.1"
Revision 16
19 Jul 2007 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 42 to 42
 

-- FrankHarrell
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META FILEATTACHMENT attr="" comment="Statistical Tables and Reports using S and LaTeX" date="1076854417" name="summary.pdf" path="summary.pdf" size="530624" user="FrankHarrell" version="1.1"
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META FILEATTACHMENT attr="" comment="Statistical Tables and Reports using S and LaTeX" date="1184882331" name="summary.pdf" path="summary.pdf" size="577909" user="FrankHarrell" version="1.2"
 
META FILEATTACHMENT attr="" comment="Fine Control of LaTeX Typesetting with latex()" date="1135000892" name="latexFineControl.pdf" path="latexFineControl.pdf" size="191762" user="FrankHarrell" version="1.3"
Revision 15
02 Mar 2007 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 31 to 31
 
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Revision 14
20 Nov 2006 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 22 to 22
 
  • 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 FunnelWeb splits out the code to compile. H.P. 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 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 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.
Changed:
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  • The Sweave approach to literate programming using R
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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.
Revision 13
13 Sep 2006 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
  • Examples of David Whiting's additions to the latex function to allow more fine control of typesetting
Added:
>
>
  • The rreport package for reporting clinical trials analyses
 

Features of LaTeX that make it excellent for report composition include:
  • the \input{filename} command for assembling 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)
Revision 12
26 Jul 2006 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 22 to 22
 
    • 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 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 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 Sweave approach to literate programming using R
Changed:
<
<
>
>
 
  • 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.
  • 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."
Revision 11
25 Jul 2006 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 22 to 22
 
    • 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 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 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 Sweave approach to literate programming using R
Added:
>
>
 
  • 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.
  • 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."
Revision 10
19 Jul 2006 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 25 to 25
 
  • 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.
  • 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."
Added:
>
>
 
Revision 9
27 Feb 2006 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 18 to 18
  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 summary.formula function for many examples of this.

Click here for a short article about how the University of Wisconsin Statistical Data Analysis Center uses S-Plus and LaTeX for producing primarily graphical reports for Safety and Data Monitoring Committees.
Changed:
<
<
  • Literate programming (or here).: Writing documentation containing computer code. Documentation (and perhaps a statistical report) and code are maintained in one file. An extractor program such as FunnelWeb splits out the code to compile. H.P. Wolf and P. Naeve have done a lot of work in this area. In Peter Wolf's words
>
>
  • 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 FunnelWeb splits out the code to compile. H.P. 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 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 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 Sweave approach to literate programming using R
Revision 8
19 Dec 2005 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 39 to 39
  -- FrankHarrell

META FILEATTACHMENT attr="" comment="Statistical Tables and Reports using S and LaTeX" date="1076854417" name="summary.pdf" path="summary.pdf" size="530624" user="FrankHarrell" version="1.1"
Changed:
<
<
META FILEATTACHMENT attr="" comment="Fine Control of LaTeX Typesetting with latex()" date="1114478881" name="latexFineControl.pdf" path="latexFineControl.pdf" size="187117" user="FrankHarrell" version="1.2"
>
>
META FILEATTACHMENT attr="" comment="Fine Control of LaTeX Typesetting with latex()" date="1135000892" name="latexFineControl.pdf" path="latexFineControl.pdf" size="191762" user="FrankHarrell" version="1.3"
Revision 7
25 Apr 2005 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 39 to 39
  -- FrankHarrell

META FILEATTACHMENT attr="" comment="Statistical Tables and Reports using S and LaTeX" date="1076854417" name="summary.pdf" path="summary.pdf" size="530624" user="FrankHarrell" version="1.1"
Changed:
<
<
META FILEATTACHMENT attr="" comment="Fine Control of LaTeX Typesetting with latex()" date="1114191098" name="latexFineControl.pdf" path="latexFineControl.pdf" size="168229" user="FrankHarrell" version="1.1"
>
>
META FILEATTACHMENT attr="" comment="Fine Control of LaTeX Typesetting with latex()" date="1114478881" name="latexFineControl.pdf" path="latexFineControl.pdf" size="187117" user="FrankHarrell" version="1.2"
Revision 6
22 Apr 2005 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Added:
>
>
 

Features of LaTeX that make it excellent for report composition include:
  • the \input{filename} command for assembling 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)
Line: 14 to 15
 
  • by adding the pdfscreen style to the 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
Changed:
<
<
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 summary.formula function for many examples of this.
>
>
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 summary.formula function for many examples of this.
 

Click here for a short article about how the University of Wisconsin Statistical Data Analysis Center uses S-Plus and LaTeX for producing primarily graphical reports for Safety and Data Monitoring Committees.
Deleted:
<
<
  • Utilities for maintaining S code and narrative text in one file, and automatically creating a LaTeX document from this code and converting it to a pdf report, making it easy to include postscript graphics in the report
 
  • Literate programming (or here).: Writing documentation containing computer code. Documentation (and perhaps a statistical report) and code are maintained in one file. An extractor program such as FunnelWeb splits out the code to compile. H.P. 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 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 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 Sweave approach to literate programming using R
  • The Statdocs project at UC Berkeley, based on integrating XMLS, HTML, JavaScript, and R
Changed:
<
<
  • 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
    Makefile=s
    on Windows/NT. (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.
>
>
  • 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.
 
  • 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."
  • Literate statistical practice by Anthony Rossini and Friedrich Leisch
  • Papers on reproducible research from the Bioconductor project
Line: 36 to 36
 
Changed:
<
<
-- FrankHarrell - 15 Feb 2004
>
>
-- FrankHarrell
 

META FILEATTACHMENT attr="" comment="Statistical Tables and Reports using S and LaTeX" date="1076854417" name="summary.pdf" path="summary.pdf" size="530624" user="FrankHarrell" version="1.1"
Added:
>
>
META FILEATTACHMENT attr="" comment="Fine Control of LaTeX Typesetting with latex()" date="1114191098" name="latexFineControl.pdf" path="latexFineControl.pdf" size="168229" user="FrankHarrell" version="1.1"
Revision 5
07 Apr 2005 - Main.StephenWeigand
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 23 to 23
  Click 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 Sweave approach to literate programming using R
  • The Statdocs project at UC Berkeley, based on integrating XMLS, HTML, JavaScript, and R
Changed:
<
<
  • 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
    Makefile=s
    on Windows/NT. (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.
>
>
  • 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
    Makefile=s
    on Windows/NT. (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.
 
  • 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."
  • Literate statistical practice by Anthony Rossini and Friedrich Leisch
  • Papers on reproducible research from the Bioconductor project
Revision 4
01 Apr 2005 - Main.StephenWeigand
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 23 to 23
  Click 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 Sweave approach to literate programming using R
  • The Statdocs project at UC Berkeley, based on integrating XMLS, HTML, JavaScript, and R
Changed:
<
<
  • 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 Makefile=s on Windows/NT. (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.
>
>
  • 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
    Makefile=s
    on Windows/NT. (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.
 
  • 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."
  • Literate statistical practice by Anthony Rossini and Friedrich Leisch
  • Papers on reproducible research from the Bioconductor project
Line: 32 to 32
 
  • 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.
  • 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.
  • Tony Rossini, a developer of ESS ("Emacs Speaks Statistics") is working on using Noweb with Emacs bookmarking facilities for tying S output chunks and figures to reports.
Changed:
<
<
>
>
 
Revision 3
09 Nov 2004 - Main.FrankHarrell
Line: 1 to 1
 
META TOPICPARENT name="RS"

Statistical Reporting, Linking S Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data

  • 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.
Line: 26 to 26
 
  • 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 Makefile=s on Windows/NT. (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.
  • 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."
  • Literate statistical practice by Anthony Rossini and Friedrich Leisch
Added:
>
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  • Papers on reproducible research from the Bioconductor project
 
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05 Aug 2004 - 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

  • 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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  • 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."
  • Literate statistical practice by Anthony Rossini and Friedrich Leisch
  • Reproducible research: The Bottom Line by Jan de Leeuw
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  • 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.
  • 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.
  • Tony Rossini, a developer of ESS ("Emacs Speaks Statistics") is working on using Noweb with Emacs bookmarking facilities for tying S output chunks and figures to reports.
 
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