DocProcess < Main < Vanderbilt Biostatistics Wiki

---+ General Information about <nop>LaTeX and other Document Processing Tools
   * [[http://www.ctan.org Comprehensive TeX Archive Network]]
   * [[http://www.latex-project.org/guides Online LaTeX Documentation]] | [[http://www.tex.ac.uk/cgi-bin/texfaq2html?introduction=yes FAQ]] | [[http://www.lecb.ncifcrf.gov/~toms/latex.html Schneider's Resources]]
   * [[LaTeXCollab][Notes]] on editing !LaTeX knitr documents by collaborators
   * [[http://www.ctan.org/tex-archive/info/epslatex.pdf Using Imported Graphics in LaTeX and pdfLaTeX]]
   * [[http://www-h.eng.cam.ac.uk/help/tpl/textprocessing/LaTeX_intro.html Text Processing using LaTeX]] from University of Cambridge
   * [[http://www.tug.org TeX Users Group]]
   * [[ftp://ctan.unsw.edu.au/tex-archive/info/lshort/english/lshort.pdf Not So Short Introduction to LaTeX]]
   * The [[http://en.wikibooks.org/wiki/LaTeX LaTeX Wikibook]]
   * [[http://www.latex-community.org LaTeX Community]]
   * [[http://www.stdout.org/~winston/latex/latexsheet.pdf LaTeX reference card]]
   *  [[http://webdemo.visionobjects.com/equation.html?locale=default Online converter]] from hand-drawn math to !LaTeX markup
   * How to produce [[LatexGraphLayout][posters and other layouts]]
   * A good handout about [[http://www.tug.org/tutorials/tugindia/chap09-prn.pdf floating figure placement]]
   * [[http://yihui.name/knitr knitr]]
   * [[SweaveLatex][Sweave]]
   * [[SweaveConvert][Methods for converting from !LaTeX to other formats]]
   * %N% [[http://gforge.se/2014/01/fast-track-publishing-using-knitr-part-v Max Gordon's blog]] on the use of =knitr=, nice html tables with footnotes, and markdown for manuscripts
   * JabRef - a comprehensive !BibTeX database manager and reference import/export facility
   * [[http://jo.irisson.free.fr/bstdatabase !BibTeX style database]]
   * [[http://www.sbg.bio.ic.ac.uk/~mueller/TeXMed <nop>PubMed bibliographic search engine with <nop>BibTeX output]]
   * =[[http://pybliographer.org pybliographer]]= : =apt-get -t testing install pybliographer= then type =pybliographic= at the command line.  Select =File -> Medline Query= then =File -> Save= and save the result as a <noc>BibTeX file with a suffix of =.bib=.  To view all the articles found, pull down on the bar separating the upper and lower panels.
   * Adding a non-included style macro such as =ctable= or =multibib= to a Linux <nop>LaTeX installation:
      * Put =[[%ATTACHURL%/getlatex][getlatex]]= in =/usr/local/bin= and set it to be executable
      * Run it, as root, using e.g. =su -c "getlatex ctable"=
      * This creates a new directory in the proper place in the =tex= installation, downloads all needed files from http://www.tug.org into this new directory, runs =latex= on the =.ins= file to create the =.sty= file, and runs =mktexlsr= to update =tex= indexes.
      * A [[GetLatex][simpler solution]] that may be more reliable 
   * [[http://www.research.att.com/sw/tools/graphviz graphviz]] for drawing diagrams and an [[http://www.linuxjournal.com/article.php?sid=7275 article]] about it in [[http://www.linuxjournal.com Linux Journal]]<br>To install under Debian Linux get the package from http://packages.debian.org/unstable/graphics/graphviz.html and install it using =KPackage= or save to disk then as root run =dpkg -i graphviz*.deb= where * is the version.  Documentation may then be found in =/usr/share/doc/graphviz=.  Under KDE you can do Alt-F2 =#dot= to launch the browser with the man page for =dot=.  Click [[http://biostat.mc.vanderbilt.edu/twiki/pub/Main/StatCompCourse/sCompGraph.pdf here]] for an example of the use of =dot= and for possible <nop>LaTeX alternatives.
   * *Best* approach to convert !LaTeX documents to =html= then to !OpenOffice or Word: [[SweaveConvert][TeX4ht]]
   * <noc>[[http://pauillac.inria.fr/~maranget/hevea HeVeA]]: an excellent program for converting <noc>LaTeX code to HTML without using graphics.  This may be installed with a standard Debian =apt-get= and is preinstalled on our Linux computers.
   * [[http://latex2rtf.sourceforge.net latex2rtf]]: a <noc>LaTeX to =RTF= convertor
   * <noc>[[http://hutchinson.belmont.ma.us/tth/mml TtM]]: a <noc>LaTeX to =html,xml,mathml= convertor with elegant rendering of complex equations.  You can save output in =html= and import in Word.
   * html to latex converter: =apt-get install gnuhtml2latex=
   * [[http://www.google.com/search?hl=en&ie=UTF-8&oe=UTF-8&q=writer2latex&spell=1 OpenOffice to LaTeX convertor]]
   * A Perl script [[%ATTACHURL%/../EmacsLaTeXTools/s2latx.pl.txt][s2latx.pl]] when used with <noc>LaTeX can process S source code to automatically convert to a form ready to =\input{}= into <noc>LaTeX for pretty printing if your system allows (through the =latex --shell-escape= system command) external program to be invoked by <noc>LaTeX. Store the <noc>LaTeX style macro [[%ATTACHURL%/../EmacsLaTeXTools/sinput.sty][sinput.sty]] where <noc>LaTeX can find it (this version of =sinput.sty= is for Linux/Unix). Here is an example <noc>LaTeX file to include and pretty-print S code. It assumes that =s2latx.pl= is in your system path. Invoke <noc>LaTeX using =latex --shell-escape myfilename=. 
<verbatim> 
\usepackage{sinput} % User must define \scom to specify how S comments are typeset 
\newcommand{\scom}[1]{{\rm\scriptsize \# #1}} 
\begin{document} 
\sinput{mysprog.s} % myprog.s is an ordinary S script
\end{document} 
</verbatim>
Thanks to [[mailto:TAC@nei.nih.gov][Terry Cox]] for showing me how to do this.  
   * [[http://www.andre-simon.de Highlight]], converts source code to formatted text with syntax highlighting
   * <noc>AucTeX: This Emacs/Xemacs mode makes it easy to run programs associated with <noc>LaTeX from within Emacs. You can also run =latex= on a highlighted region of your document if you only want to compile part of the text.
   * Using <noc>LaTeX for making presentations
      * Tutorial on the <noc>LaTeX [[http://astronomy.sussex.ac.uk/~eddie/soft/tutorial.html seminar style]] (link broken)
      * FrankHarrell's <noc>LaTeX setup for [[FHLaTeXSetup][slides and handouts]] (using seminar style) and handouts (using report style)
      * Sample slides using the Seminar class: [[%ATTACHURL%/Measures.tex][The tex file]], [[%ATTACHURL%/Measures.ps][the postscript file]], and the [[%ATTACHURL%/plots.q][R file (to generate figures).]] 
      * [[http://prosper.sourceforge.net][Prosper]], a <noc>LaTeX-based tool for making Powerpoint-type presentations
      * [[http://latex-beamer.sourceforge.net Beamer]] - a competitor of Prosper | [[http://www.math.temple.edu/tex/latex/beamer/examples/beamerexample5.pdf Example]] | [[http://www.math.temple.edu/tex/latex/beamer/examples/beamerexample5.tex Source Code]] | [[BeamerTemplate][Template]] | [[BeamerTips][Tips]]
      * [[http://www.paulhurley.co.uk/index.php/categories/computing-geek/27-r-stats/72-creating-science-posters-using-r-latex-beamer-and-beamerposter-2][Creating Scientific Posters using R, Latex, Beamer and Beamerposter]]
   * [[LaTeXExamples][LaTeX examples and templates]], including <noc>LaTeX macros for insertion of postscript graphics (the Hmisc =setps= and =ps.slide= functions work especially well for this), templates for <noc>NIH grant proposals, and a template making slides for talks. Don't forget to look at our report [[%ATTACHURL%/../StatReport/summary.pdf][ Statistical Tables and Plots using S-Plus and <noc>LaTeX]]. Note that the section on converting to HTML in this report has not been updated to describe Hevea. It does contain a lot of <noc>LaTeX code for your viewing pleasure.
   * More useful table tricks: http://www.tug.org/pracjourn/2007-1/mori/mori.pdf | http://tug.ctan.org/cgi-bin/ctanPackageInformation.py?id=siunitx  |  http://nepsweb.co.uk/docs/tableTricks.pdf
   * [[http://www.mackichan.com/index.html?techtalk/414.htm Wrapping text around a floating object]]
   * [[PsFrag][Inserting general !LaTeX code inside graphics]] 
-----
   * Go to the [[http://www.emacs.org/][GNU Emacs]] home page or to the [[http://www.delorie.com/gnu/docs/emacs/emacs_toc.html][GNU Emacs Manual]] or to the [[http://www.emacs.org/tutorial.html][GNU Emacs Tutorial]] 
   * Go to the [[http://sunsite.auc.dk/auctex/][AUCTeX]] home page 
   * Go to the [[http://www.strw.LeidenUniv.nl/~dominik/Tools/reftex/index.html][ RefTeX]] home page or directly to [[http://www.strw.LeidenUniv.nl/~dominik/Tools/reftex/reftex.html][RefTeX documentation.]] 
   * Dalhousie University's [[http://www.mscs.dal.ca/tutorials.html][Software Tutorials]], including <noc>LaTeX, UNIX, and S-Plus 
   * Go to the [[StatReport][Statistical Reporting, Linking S-Plus Output with Report Documents, Literate Programming, Managing Analyses, and Documenting Programs and Data]] home page 


-- Main.FrankHarrell - 08 Apr 2004, modified 13 May 2004, 20 Jun, 5 Sep, 12 Sep, 3 Oct, 11 Oct 2004, 1 Jan, 23 Feb, 11 May 2005, 6 Apr, 21 Oct 2006, 15 Mar, 19 Jul, 5 Aug, 21 Aug, 17 Sep 2007, 17 Jan, 28 May 2009, 1 Mar, 16 Mar, 27, 31 May 2010, 16 Feb, 2 Oct 2012, 2014-07-19
Topic attachments
I	Attachment	Action	Size	Date	Who	Comment
ps	Measures.ps	manage	320.4 K	06 Dec 2004 - 13:37	JonathanSchildcrout
tex	Measures.tex	manage	37.1 K	06 Dec 2004 - 13:46	JonathanSchildcrout
EXT	getlatex	manage	0.5 K	01 Mar 2014 - 08:36	FrankHarrell	Authors: Hans Ekbrand & Frank Harrell
EXT	getlatexfrom	manage	0.2 K	01 Mar 2014 - 08:38	FrankHarrell	Get LaTeX package from a specific locatiion
q	plots.q	manage	2.6 K	06 Dec 2004 - 13:46	JonathanSchildcrout
This topic: Main > WebHome > StatComp > DocProcess
Topic revision: 06 Jun 2015, FrankHarrell (raw view)
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