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  • 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 ( 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 rst steps. Common LATEX commands (graphics, tables, BibTEX, math). Generate your rst 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 nd (>95%) do not satisfy the reproducibility principle! Science is still largely based on trust and authorities. 1 In Wageningen, 26 September 2013 8. Kligl & Bates (2011) In Wageningen, 26 September 2013 9. Reproducible research is beautiful! In Wageningen, 26 September 2013 10. Another example: JSS In Wageningen, 26 September 2013 11. See also: UG4A In Wageningen, 26 September 2013 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? (orwho 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 WinEdtR integration; optional: Scientic 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:; Shared documents:; Annotation of PDF docs:; 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 (TEXNH techne), Greek for bothartandcraft, which is also the root word of technical2. 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 In Wageningen, 26 September 2013 17. LATEXis not latex! = In Wageningen, 26 September 2013 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 eort, and 2. (continuity) to provide a system that would give exactly the same results on all computers, now and in the future. The creatoroers monetary awards to people who nd 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 nd 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 isnt for everyone but it could be for youby 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! (its just a question of time / eort) 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, ne-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 dont often know it exists). Microsoft has a software to prepare documents for press Microsoft Oce Publisher, but even this can not be compared with e.g.Adobe InDesign (do you have money to use this software?) In Wageningen, 26 September 2013 25. TEX versus MS Word3 3 In Wageningen, 26 September 2013 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. Thats enough laws for now. . . See also: LATEX vs.MS Word In Wageningen, 26 September 2013 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. 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); In Wageningen, 26 September 2013 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 eld; 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