The document outlines a course on reproducible research using LaTeX and R. The course will cover installing LaTeX software, writing collaborative documents, writing a PhD thesis in LaTeX, combining R and LaTeX code, and converting LaTeX documents to other formats like Word and HTML. The goal is to teach researchers how to produce work that allows others to reproduce and validate their results.

1. Reproducible research with LATEX + R
(for PhD students)
Tomislav Hengl
ISRIC — World Soil Information, Wageningen University
In Wageningen, 26 September 2013

2. Outline I
Important points
Disclaimer
The programme
Reproducible research is beautiful!
Software in use
Web-services of interest
What is TEX?
TEX philosophy
What is LATEX?
LATEX versus MS Word
Comparison
Literature
In Wageningen, 26 September 2013

3. What you need to know about me
I am not really familiar with TEX programming (I never
developed any LATEX package).
LATEX has a steep learning curve.
I also still use Google docs and MS Word (e.g.to write short
documents).
LATEX comes (as any GNU) without any warranty.
In Wageningen, 26 September 2013

4. The course programme (1)
Block 1 (2 hours)
Introduction to TEX (philosophy, history).
Installation of software and first steps.
Common LATEX commands (graphics, tables, BibTEX, math).
Generate your first document with LATEX.
In Wageningen, 26 September 2013

5. The course programme (2)
Block 2 (2 hours)
Collaborative writing using LATEX— the DropBox approach.
Collaborative writing using LATEXon-line LATEXeditors
(ShareLaTeX, LaTeXLab)
Finding the right template for a PhD thesis
Writing a PhD thesis with LATEX(tips and tricks).
In Wageningen, 26 September 2013

6. The course programme (3)
Block 3 (2 hours)
Reproducible research — why? how? where?
Combining R and LATEXcode -> Sweave.
Preparing presentations using the Beamer package.
Converting LATEXdocs to MS Word and HTML.
In Wageningen, 26 September 2013

7. What is reproducible research?1
Ideally, each paper submitted for publication that contains some
type of statistical analysis or summaries of results should allow for
checking / validation.
Anybody should be able to reproduce your results. . . of course —
this is one of the main principles of science! But most of the
articles you find (>95%) do not satisfy the reproducibility principle!
Science is still largely based on trust and authorities.
1
https://en.wikipedia.org/wiki/Reproducibility
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8. Kligl & Bates (2011)
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9. Reproducible research is beautiful!
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10. Another example: JSS
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11. See also: UG4A
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12. Another leitmotif of this course: collaboration
The best papers are the ones written through creative team
work — creative brainstorming and discussion!
But how to collaborate on LATEXdocuments?
And how to monitor progress? (or“who do I turn on
track-changes in LATEX?!”)
In Wageningen, 26 September 2013

13. Software
You should have installed these already!
MikTEX (LATEX engine);
WinEdt (TEX editor);
(recommended) a number of WinEdt plugins:
JabRef — references editor;
BibTEX menu — WinEdt menu for references;
MathType — Equation editor;
R-Sweave — full WinEdt–R integration;
optional: Scientific Word — the commercial programme for
producing LATEX documents under Windows; word2tex — a
shareware programme that converts MS WORD documents to
LATEX.
In Wageningen, 26 September 2013

14. Websites (on-line services)
You can make an account and test things out
On-line TEXeditor: https://www.sharelatex.com;
Shared documents: http://DropBox.com;
Annotation of PDF docs: http://a.nnotate.com;
On-line equation editors;
In Wageningen, 26 September 2013

15. TEX history I
In 1978, Donald Knuth (one of the most famous and well
respected computer scientists) embarked on a project to
create a typesetting system, called TEX (pronounced ‘tech’),
after being disappointed with the quality of his acclaimed The
Art of Programming series.
TEXis an abbreviation of τ χνη (TEXNH — techn¯e), Greek
for both“art”and“craft”, which is also the root word of
‘technical’2.
Around 10 years later, he froze the language after originally
anticipating spending a single year!
In Wageningen, 26 September 2013

16. TEX history II
In the mid-80s Leslie Lamport created a set of macros that
abstracted away many of the complexities (this allowed for a
simpler approach for creating documents, where content and
style were separate). This extension became LATEX
(pronounced ‘lay-tech’);
MiKTEX (pronounced ‘mick-tech’) is an up-to-date
implementation of TEX and related programs for Windows.
2
https://en.wikipedia.org/wiki/TeX
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17. LATEXis not latex!
=
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18. TEX philosophy
Donald Knuth designed TEXwith two main goals in mind:
1. (perfectionism) to allow anybody to produce high-quality
books using a reasonably minimal amount of effort, and
2. (continuity) to provide a system that would give exactly the
same results on all computers, now and in the future.
The creator“offers monetary awards to people who find and report
a bug in TEX. The award per bug started at $2.56 (one
‘hexadecimal dollar’) and doubled every year until it was frozen at
its current value of $327.68. . . recipients have been known to
frame their check as proof that they found a bug in TEXrather than
cashing it.”
In Wageningen, 26 September 2013

19. What is LATEX?
essentially a markup language;
analogous to HTML with CSS;
programming environment with many contributed packages
and styles;
renders the content into a document (PDF);
the code must be error-free from the beginning till the end!
otherwise you do not see any PDF.
In Wageningen, 26 September 2013

20. Who is it for?
Anybody writing anything maths related will not find a richer
and better quality system.
Anybody planning to write research articles, PhD or MSc
thesis and make professional and stable overheads;
If you are in academia, you really ought to be using it!
Even WikiPedia uses LATEX for rendering any formulas that
appear on their site.
See also: “LATEX isn’t for everyone but it could be for you”by
Andy Roberts.
In Wageningen, 26 September 2013

21. Why TEX?
. . . portability, lightness, security;
it is easier than XML (and has less bugs);
it is for free
it is one of the most sophisticated digital typographical
systems in the world (MS Word is not a press software!);
You can get LATEX to do just about anything you can think of!
(it’s just a question of time / effort)
In Wageningen, 26 September 2013

22. TEX saves time
focus on content, let LATEX bother about the layout;
the software takes care of the actual typesetting, structuring,
numbering, referencing and cross-referencing, indexing and
page formatting;
compile documents in PDF (export to HTML, RTF);
hyphenation, typesetting, fine-tuned control;
In Wageningen, 26 September 2013

23. LATEX versus MS Word
MS Word
WYSIWYG world;
XML;
nonstandard styles;
not-suited for large
(collaborative)
documents;
compatibility problems
(MS Word 97, 2000, XP,
2003, 2007);
LATEX
code world;
TEX language;
standard styles;
suited for large
collaborative documents;
the syntax staid the same
ever since the beginning!
. . .and the winner is. . .
In Wageningen, 26 September 2013

24. MS Word
MS Word does in fact have a similar Styles feature (but people
don’t often know it exists).
Microsoft has a software to prepare documents for press —
Microsoft Office Publisher, but even this can not be compared with
e.g.Adobe InDesign (do you have money to use this software?)
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25. TEX versus MS Word3
3
http://www.pinteric.com/miktex.html
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26. TEX versus MS Word
Andy Roberts’ Laws on Word:
1. Likelihood of a crash is directly proportional to the importance
of a document.
2. Likelihood of a crash is inversely proportional to the time left
before its deadline.
3. Likelihood of a crash is directly proportional to the duration
since you last saved.
4. Likelihood of you throwing your computer out of the window
is directly proportional to the number of times Clippy pops up.
5. That’s enough laws for now. . .
See also: “LATEX vs.MS Word”
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27. Literature
Lamport, L., 1994. LATEX: A Document Preparation System.
Addison-Wesley, 291 p.
Oetiker, T. 2008. The (Not So) Short Introduction to LATEX2e.
self-published, 155 p.
Talbot, N.L.C. 2013. Using LaTeX to Write a PhD Thesis,
Dickimaw LATEXSeries
LATEX on wikibooks.
http://en.wikibooks.org/wiki/LaTeX
In Wageningen, 26 September 2013

28. Layout galleries
The TEX showcase;
Page and chapter headings by Vincent Zoonekynd;
LATEX font catalogue;
Text Processing using LATEX by University of Cambridge
Copernicus publications (HESS);
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29. LATEX to HTML/KML
convert your LATEX document to HTML (install TtH);
install some KML editor (or use WinEdt);
Put the slides as HTML in the description field;
to get some idea what you can do with KML, look at the
KML interactive sampler and/or Google Earth Outreach;
You can also convert from LATEX document to Wiki (e.g.using
this Python script);
In Wageningen, 26 September 2013