Markdown

I'm a sucker for simplicity. I found Word too multifunctional, I found LaTeX too hard. Then Markdown appeared, the language used on Wikipedia, on my Trello app, and - commonly - in emails.

Markdown syntax

There are some complication, like hyperlinks that I don't want to mention here, in order not to obscure the absolute simplicity of Markdown. This is what you'll use:

# Heading 1
## Heading 2
### Heading 3 (you get the point)
*bold*
**italic**
 

Nothing more.

Markdown on OS X

One address: MacDown. It is a beautiful program that has a split screen set-up: left you have a WYSIWYM interface, right there is a live preview. Did I say it is beautiful? It's free.

Markdown on Windows

I have tried a few, but on Windows with no luck. There is always some premium function for sale and I don't like that. WriteMonkey is a good idea, but the pdf support is ... not included. There are also a bunch of web apps, most notably Dillinger and StackEdit. They look good, but I like to open a file from windows explorer and then that's just a pain.

In fact, gVim will do all you want, but there's a learning curve as it doesn't behave like normal textpads (I like notepad++ for instance as an in-between solution).

Two programs however will do the job, and they are software packages! Obviously, R is free, and Stata is not. You will know that I love Stata - I think it's the best, albeit expensive, textbook in statistics and it also has free software with it.

Markdown in R and Rstudio

Rstudio is brilliant software. Use the -knitr- package to enjoy writing markdown files and exporting to pdf. It's made for that and it's used by millions.

• About: http://yihui.name/knitr/
• How to install -knitr-: https://github.com/yihui/knitr#readme3
• Options: http://rmarkdown.rstudio.com/pdf_document_format.html

Markdown in Stata

Stata is a different beast. In a way it is less flexible and the markdown integration doesn't feel as native as in R. However, it is also easier.

You output an smlc log file, then you parse the file with the user command -markdoc- (Converting SMCL to Markdown and other formats using Pandoc). That's all there is to it. Remember to put your markdown code between command /* beginnings and endings */ which you put on separate lines. Also use - quietly - to reduce output.

There are a couple of other Stata programs doing a similar job:

• Weaver: HTML and PDF dynamic report producer
• Ketchup: HTML and PDF dynamic report producer
• Synlight: SMCL to HTML convertor and syntax highlighter

Just -ssc install- those and discover their help files.

For the Markdoc command, see:

• Markdoc author: http://haghish.com/statistics/stata-blog/reproducible-research/dynamic_documents/markdown.php
• IDEAS: https://ideas.repec.org/c/boc/bocode/s457868.html
• Alternatives: https://hopstat.wordpress.com/2014/01/11/stata-markdown-2/

LaTeX: personal walk through the preamble

Introduction

LaTeX is much like the R statistical package: it forces you to load the parts of the program you will need. In contrast, most word processors load these options straight away in a standard installation - yet you may have noticed that you need to install language packs separately, for example. In LaTeX, you need to load all of it. Brilliant.

There is a good reason for this bad behaviour. It's not necessarily speed, because that doesn't seem to be a restricting factor anymore. It's rather the extensibility of the program, as well as the problems that go with it: sometimes one package conflicts with another, so we can't have both. I still think it's a serious design flaw, but it's not going to change anytime soon, I guess. So here's how to (learn to) live with it.

Packages

This is the list of packages I use in my most complex document. 

Lay-out

• Framed: provides the commans -shaded-, -snugshade- and -leftbar-. I use snugshade for background-filled boxes. You need to define the 'shadecolor' with the color-package.
• Color: define the colours you will use when loading this package

http://www.slideshare.net/linjaaho/how-to-make-boxed-text-with-latex

http://en.wikibooks.org/wiki/LaTeX/Colors

Fonts

• Inputenc: allows French characters with option utf8
• Fontenc: I don't know what it does but I set the option to T1. I believe it matters for BibLaTeX
• Csquotes: use option autostyle=try. This interpretes quotes, so you don't need LaTeX code to use them.

% styles: http://www.emerson.emory.edu/services/latex/latex_168.html#SEC168D

% Option clash

Tables and figures

• Graphicx
• Caption
• Tabularx
• Booktabs
• Array - permits justification options and fixed column width
• Pgfplots: this load the TikZ language

In the preamble, specify \graphicspath{{/Users/macuser/folder/}} or anything similar on Windows so LaTeX knows where you put your graphics. I honestly love this orderly behaviour.

Bibliography

I have written a separate post on BibLaTeX. It's a pain in the X$$.

%http://texblog.org/2007/11/14/hyper-links-to-the-pdfs/

% ISSUE !!! Several capital letters in a row.

% http://forums.zotero.org/discussion/19721/bibtex-export-for-corporate-authors-single-name-only/

% http://tex.stackexchange.com/questions/69594/biber-fails-at-supporting-in-author-names

% Info BibLaTeX http://tex.stackexchange.com/questions/5091/what-to-do-to-switch-to-biblatex

%\usepackage[dutch]{babel}

\usepackage[american]{babel}

%\selectlanguage{dutch} 

\selectlanguage{american} 

\usepackage[style=apa, backend=biber, url=false, doi=false]{biblatex} 

% , natbib=true

% , style=apa/authoryear/verbose/numeric(default)/alphabetic/authortitle

% \usepackage[safeinputenc]{biblatex}

\DeclareLanguageMapping{american}{american-apa}  % for apa

% \DeclareLanguageMapping{dutch}{dutch-apa}   % for apa

%\addbibresource{/Users/name/Dropbox/KeepCloud/zoterobibtex.bib} % MAC

\addbibresource{C:/Users/name/Dropbox/KeepCloud/zoterobibtex.bib} % PC

% zotero biblatex exporter misses out on dates

% problem with zotero bib files: too many brackets 

% solution: biber.conf in working folder or anjo biblatex translator / robintan bibtex translator

%\usepackage[backend=biber, style=authoryear-icomp, sortlocale=nl_NL, natbib=true, url=false, 

%    doi=true, eprint=false]{biblatex}

% http://tex.stackexchange.com/questions/54833/biblatex-apa-biber

%%% Language %%%

% http://www.kronto.org/thesis/tips/multiple-languages.html

Math

• Amsmath: it's more or less mandatory
• Amsfonts
• Amssymb
• Xfrac: provides slant frac / through \sfrac{}

User modifcations

There are a lot of tweaks you may way to do to make your work look good. In doing so, you change the LaTeX wonderful defaults, so you may have used Word after all. But once you got that far, you're probably to tired to start over and you'll fuck up LaTeX till you get results without visible collateral damage.

%\usepackage[all]{nowidow}

%\clubpenalty=9996

%\widowpenalty=9999

%\usepackage[hmargin=3cm,vmargin=3.5cm]{geometry}

%\newcommand{\myparagraph}[1]{\paragraph{#1}\mbox{}\\}

%http://hapticity.net/2007/03/23/latex-itemize-bullet-characters/

\def\labelitemi{--}

%\usepackage{needspace}

%\needspace{8\baselineskip}

%$\newcommand{\E}{\mathrm{E}}$

\newcommand{\E}{\mathbb E}

\newcommand{\Var}{\mathrm{Var}}

\newcommand{\Cov}{\mathrm{Cov}}

\synctex=1

Meta-info

\author{name}

\title{title}

\date{date}

PGF/TikZ

For a while now I was wondering how on earth those neat vector graphics in textbooks are made. I remember my professor of international economics producing graphs in CorelDraw, which is not the state of the art software I had expected.

Because I'm studying distributions at the moment, I was looking for a LaTeX bell shaped curve. I found the GPF/TikZ package and boy, this is what I needed for so long! Within TeX/LaTeX, it's a fairly recent addition. Its predecessor is PStricks, a postscript based graphical language that can't live in a PDF world.

Unlike much of the LaTeX manuals, the TikZ documentation is very instructive and even starts with 80 pages of tutorials. By the way, up to date manuals can always be found at:

http://texdoc.net/pkg/<packagename>

Another tongue for BibLaTeX

This is a post in English, about getting LaTeX to speak Dutch. As such, it may be interesting for other rare languages.

In my last post I discussed the awkward natbib package. That was pretty bad. Now natbib is actually the old fashioned way of referencing. The advantage: it does the job for simple tasks. The disadvantage: everything else. So here's the hip new way of referencing: biblatex.

Yes, I'm being a cynic here. It's a big mess again. But for all of you who like a decent walkthrough, here you are.

Compiling BibTex

First of all, biblatex relies on the biber code, not bibtex. This means that you have to reset your editor to instruct biber where it asks for the bibtex path. Obvious? Not at all. I use TexMaker.

• On a Windows machine: options > configure TM > commands > bibtex %
• On the Mac: same, ending in > usr/texbin/bibtex % (or something like that. No .aux!)

Next, you'll need a sequens of parsing. I do this, repeating step 2 and 3 twice if it doesn't work the way I expected.

1. pdflatex
2. bibtex
3. pdflatex
4. view pdf

Note that you can define the parsing sequens as a user command in TexMaker/TexStudio.

Citing in line and bibliography

Ok, so let's turn back to your .tex file. You'll basically need this syntax in the preamble (before \begin{document}:

\usepackage[american]{babel}
\usepackage{csquotes}
\usepackage[style=apa, natbib=true]{biblatex}
\DeclareLanguageMapping{american}{american-apa}
%\addbibresource{/Users/username/folder/database.bib} %MAC
\addbibresource{D:/folder/database.bib} %PC

There's no need to specify backend=biber in the biblatex options, yet it does no harm. The standard style is numeric, an alternative is authoryear-comp, or you can follow some journal style, like the APA in this case. Because of the biblatex-apa call here, we need babel, csquotes and \DeclareLanguageMapping. You can change american for a language of your choice, such as dutch, german or french. Do this everywhere it appears in this block of syntax. Do not use multiple languages. This is a shame, as many non-English authors may want to quote in English. Well, you can't.

In the body of your text, after \begin{document} you use the biblatex commands \cite, \textcite and \parencite, or the old natbib commands \cite, \citet and \citep for reasons of compatibility or demands from the publisher. To make the latter work, I specified the option natbib=true. there are a number of other options, such as the suppression of urls and ISBN or DOI numbers, you may want to add.

Before \end{document}, you put \printbibliography. This generates a bibliography, with appropriate translation: 'october' (EN) becomes 'oktober' (NL) in datas, 'references' becomes 'referenties' as heading, etc.

It took me a full day to find this out. I hope you found this post quick enough to keep some time for the real work.

End note

If along the way you get stuck, three things you may want to do:

• Update your editor and your packages. Use TexLive. It's a fat ugly program, but it's made to be updated (the program you need is texutility on OS X and tl-tray-menu on windows)
• Restart your editor. Sometimes it remembers old lines for no reason.
• Erase all latex files except the database (.bib), the text (.tex) and maybe the pdf to save your ass if you miss out on the first two.

BibTeX (natbib)

The much praised reference program BibTeX is an essential part of all academic LaTeX work. It took me some time to understand what it does. You should keep the following sequens in mind:

• First you process an .aux file from you .tex text using LaTeX (i.e. compile > LaTeX)
• That thing is full of code you need to parse through BibTeX to turn the reference fields into references (i.e. compile > BibTeX)
• Doing each step twice may be a good idea to get cross references right
• Next, you parse again using LaTeX
• Finally, you parse the whole thing using pdfLaTeX, to get a pdf (it's a miracle...)

You will agree with me that this is a very cumbersome operation. It is one of the reasons I would recommend using Zotero with a word processor plugin, if you don't really need LaTeX.

But it gets worse. This is how you set up your .tex file.

• In the preamble, so before \begin{document}, you need to load the BibTeX package. The old and safe way is \usepackage{natbib}. It seems there is a new and more flexible BibTeX connection called biblatex. So you heard it right: natbib won't let you make bibliographies for chapter, for example. Whence the praise, I wouldn't know.
• Also in the preamble, although some write it elsewhere, you need to mention the bibliography style. It is \bibliographystyle{plainnat}. In some sciences, this is just plain, and for some journals this will be a specific style. You can't modify this, as the .sty files with the definition are very hard to decypher. LaTeX guys would say: 'Why would you?' Honestly, because I like simple languages. I use Stata instead of SAS, and that's why.
• Obviously, in the standard format, you'll want your bibliography at the end. That's where you'll have it, just type \bibliography{library path}. Library path may be just the name of the library if it's in the same folder, but if you have a copy of your Zotero or Mendeley library at a fixed place, you should give the full path, and beware not to have spaces in it. Also, change backslash for slashes. Usability, you know?

Having gone through all that, you may want to start quoting. Luckily, that's the good part. You need not click any buttons, just type \cite{ and you have a list of labels to choose from. The handy thing is the AutoZotBib plugin for Zotero simply labels entries with the name of the first author, the first word of the title and the year. So it's pretty easy to call in your references. There's a few elegant options to quote:

• \citep{ : this numbers references, if you like that. If you care less about names, do it wiki-style.
• \citeauthor{ : obviously, you'll just get the author
• \citeyear{ : well... you get it

So in sum, it's a pain in the ass, but it works.

One note: you may have weird characters in your references, like Swedish names. You know that LaTeX is English based so you may go down because of your Swedish friends. I haven't really figured out yet, I will in time, but maybe some fontpackage, such as \usepackage[T1]{fontenc}, may help you out. Good Lord, this ain't how it was meant to be.

Good luck referencing!

LaTeX Tables

updated September 2013

I am not a big believer of LaTeX, but I do use it. One reason to dislike LaTeX is the way you need to make tables. It is very easy to mess up and very hard to debug.

From your stats package to LaTeX

My workflow is the following: make every table with just data in Excel, then convert using excel2latex and paste it in your .tex file. If you happen to have crazy formulas in your table, do the same but use codes in your excel table which you then replace by the formulas in LaTeX.

Do not, as a rule, use tabout-like output that Stata delivers. I prefer a little adjustment of Excel matrix output, which is good nowadays, over the burden to look into the LaTeX puzzle. Face it: when we use tables, it's generally for several models or with a combination of different analyses. So for me -tabout- is worthless.

Adjustments to LaTeX tables

The standard LaTeX-layout, which is good enough, has very large margins. That's nice, but it limits your tables. To cope with that, I've read about two solutions:

• The tabularx package
• Put the table inside a minipage and scale it to fit

We're left with just a few more issues: 

• Landscape pages (fear, anger, hate!)
• Wrapping lines
• Wide tables (through -tabularx-)

As for landscapes, I have no clue for the moment. You may want to check here. And pdflscape may be it.

Wrapping lines I've done. It's cumbersome. Basically, you will want to limit the size of a column. You do that through specifying p{3 cm} in your {l l l c r r r c} series of column specifications, where each of l, r, c refers to a column that is left aligned, right aligned or centered. p{} replaces such a specification, so you lose your control over alignment! To solve this issue, you need yet another package: arrays. Then, and I'm not joking, your wrapped left aligned column should be specified as:

>{\raggedright\arraybackslash}p{width}

It is really that stupid. Never saw a > in LaTeX syntax before? Neither did I. As always, there will be some logic behind it, for which a Ph.D. level IQ will suffice, but even if it is understandable, we don't want to waste our time figuring out. 

Links

If you don't want to google, hit some old bookmarks (2010):

• http://programming.itags.org/tex/126082/
• http://www.latex-community.org/forum/viewtopic.php?f=45&t=5089
• http://radio.wihome.net/wiki/?article=LaTeX:tablefootnotes
• http://www.vision.ime.usp.br/~jmena/misc/latex/tables_with_latex.pdf
• http://www.latex-community.org/forum/viewtopic.php?f=45&t=6322&p=24742
• http://www.math.uiuc.edu/~hildebr/tex/packages.html
• http://people.csail.mit.edu/jrennie/latex/

Word of LaTeX?

Dingen die goed werken, interesseren mij, en men zegt dat LaTeX goed werkt. Effectief, de output ziet er behoorlijk uit. Saai, maar consistent. Die twee dingen gaan samen en zijn voor bepaalde opdrachten gewenst.

Maar wat er bij mij niet ingaat is hoe je een tekst kunt schrijven in LaTeX. De markup code stuurt je in de war en tijdens het typen is de bladspiegel niet om aan te zien. Hou er rekening mee dat veel, zo niet de meeste, teksten vooral gelezen worden vóór ze afgedrukt of gefinaliseerd worden. Dat heet dan een werkdocument.

Eén optie is te starten in Word, en de finale versie in LaTeX te maken indien nodig. In veel gevallen zal dat niet kunnen, omdat er bijvoorbeeld een template opgelegd wordt door een consortium of een opdrachtgever.

• Type de tekst in Word, tenzij er wiskundige afleidingen in voorkomen, dan ga je meteen aan de slag in LaTeX.
• Exporteer het bestand (.doc) naar LaTeX (.tex) met Word-to-LaTeX
• Maak de tabellen altijd in Excel
• Converteer de tabel naar LaTeX met Excel2latex
• Voeg de tabellen in en check de cross-references
• Kuis de opmaak
• \title{titel hier} in de heading
• \data{datum hier} in de heading
• \maketitle als titel
• \section{} en \subsection{} als titels van de paragrafen
• \usepackage{verbatim} in de heading en \begin{comment} \end{comment} om tijdelijk syntax weg te laten (vb. uit Word overgenomen marges)

Voordeel: je ziet meteen een behoorlijke tekst en moet alleen kleine wijzigingen doorvoeren in de .tex-file.

Nadeel: met het gratis programma worden formules overgenomen als afbeeldingen. Je kan ze dus niet bewerken. Er zijn enkele betalende alternatieven, zoals GrindEQ, die dit wel kunnen. Ze doen het echter niet noodzakelijk beter voor andere omzettingen.

De tweede optie is meteen een LaTeX document maken.

• Werken met twee schermen is een must.
• Voor documenten met veel verwijzingen, grafieken en formules is dit een must.
• Grafieken kan je in één map plaatsen als pdf's, aangeduid via graphicspath. De kwaliteit van vectorafbeeldingen is niet te evenaren met .jpg/.bmp/.png of zelfs .tiff. Word kan overweg met .emf en .wmf, maar microsoft ontmoedigt deze formaten zelf in de recentere windows versies. Bovendien blijft consistent schalen een probleem in MS Office en is de controle over de bladspiegel onmogelijk. LaTeX daarentegen heeft eigen algoritmes om figuren een plaats te geven, die je desnoods kan overrulen.
• Je kan de tex-file altijd downgraden naar een ander soort tekstbestand. Er is een optie om te exporten naar html en naar rdf, maar ik heb die nog niet aan de praat gekregen.
• Het grootste probleem zijn de vreemde tekens, waar LaTeX niet mee overweg kan: een ö wordt in LaTeX \"{o}. Voor ç, û, etc. gelden gelijkaardige problemen. LaTeX verstaat deze karakters echt wél mits het oproepen van inputenc: \usepackage[utf8]{inputenc}. Dat kon gebruiksvriendelijker, natuurlijk.
• Ik heb geen idee of de bibliografie dan ineens mee geëxporteerd wordt. Laten we het hopen.

Links

• Een overzicht van de packages van LaTeX: http://philippleser.de/physics/latex

Reference managers

This post has been updated 9 November 2013: added JabRef

Routine work should be automatized. I remember writing my master thesis using a not so legal copy of Endnot X, which had a terrible memory leak. As a result, I had to restart my computer every hour - which took about 10 minutes! I didn't smoke cigarettes, so what a waste of time... However, the best part of my thesis was probably the bibliography.

Today we get all the fun for free. You may get rid of your boxes of EndNote and Reference Manager. They're too expensive and little innovative. There are two fresh, hip reference managers that rule the scientific world nowadays: Zotero and Mendeley. There is an additional and traditional tool I use with them when doing LaTeX-work: JabRef. I discuss pro's and cons, so you should understand why I choose for Zotero. Both are excellent research tools, but the functionality sticks to managing references. There may be broader tools to manage all of your research, such as One Note or Citavi. I don't know these programs and I am not a big believer.

Zotero

This program meets your needs. It integrates seamlessly with Word 2007 and syncs its catalogue (the references) with your free account at the Zotero server. Data can be synced with the Zotero server or your WebDAV server of choice. I use 4shared.com.

The good

• Elegantly exports to many formats, including the files in a nice way. As a consequence, you can always return on your steps and use your old reference manager.
• Neat integration in all major webbrowsers
• BibTeX can be synced using the AutoZotBib plugin and the Spartan or the RobinTan translator.
• It is open source

The bad

• Each file has its folder and folders have nonsensical names, ruling out the use of Explorer
• Interface is old fashioned, ineffective
• Automatic indexing is lagging pdf import and unintuitive to turn of
• Doesn't sync with Mendeley: you should work via RIS files that include the file path.

Mendeley

A proprietary copy of Zotero, that should sync with it, as well as with a BibTex-file, zo it could act as a bridge between those programs. The file manager is neat, quick and accurate. I regret Zotero doesn't sync back, so I could do part of the job in Mendeley. Mendely offers 1000 MB free cloud storage, which is nice. Prices go up after that, but for lightweight users, it may be a good deal.

The good

• It syncs with Zotero. However, for large sqlite.data files, this becomes cumbersome and slow, as the syncing is continuous.
• It natively syncs with a BibTex file, which is very good
• The interface is nice and let's you read pdfs in the left pane, while having the reference column to the left.
• You can always revert your decision, via RIS files as said before
• Search results go quite deep into the references and are neatly shown

The bad

• The browser integration is limited to a bookmarklet. This means you have to press and see whether you can import straight from the browser. If you do, you only download to your Mendeley account. Importing to your desktop program is a second step. I understand the cloud approach, but soon you'll leave free territory (considering a HD as free storage).
• A deal breaker: there is no way to sort search results! What if you want a chronological overview by author? What if you want to see what journals were published in? These are common desires!
• The thing with syncing large libraries.
• It's proprietary and they've slowed down on updates.

JabRef

JabRef is a totally different breed from the first two. It is to Mendeley/Zotero what TexMaker is to Word. You basically get a list with references, screen wide, optionally linked to fixed folder paths.

The good

• It's blazing fast to open and quick to search through.
• Your database is a text-file, there is nothing to slow it down.
• It's a bibtex file, which all software can read and what you need in LaTex.
• Put it on Dropbox, google Drive, and the like, and you are always in sync.
• You choose an appropriate bibtex key you will remember.

The bad

• It doesn't auto-catalog, manage, or rename pdf files.
• If you use several bibtex files, it is not obvious to move references from one to the other, except by export/import.
• It doesn't auto-create the bibtex keys.
• It doesn't ocr for references.

Workflow

I use Zotero and JabRef. Zotero manages my literature in the same way iTunes manages my music collection. It is useful though, to make/export a small bibtex file when you finished a paper. It's faster and it secures your references. Also, sometimes Zotero skrews up the references (say, names with multiple uppercase characters), and you can solve this in JabRef.

A few ways to make the most use of Zotero:

• Make a dump folder for new documents. I do this by quarter.
• Use three kinds of tags:
• Some generic terms: TO DO, CLASSIC, STARS
• The paper's keywords or theme
• Some nickname, or the project or institue the paper comes from
• Use the notes, but do not overinvest in this, because it is too software specific and you'll lose notes and folders one day for sure. I generally give up why I downloaded a paper or who sent it to me.
• Do not catalog other things than literature. It could replace explorer, but you'll waste your time.
• Make a folder for each project, with two subfolders: a) literature, and b) references. In references, you keep what you reference to in the paper. 
• If you write several papers, make several references folders.
• Export the references folders to bibtex for survival. Polish with JabRef, and edit the bibtex files when you later pick up the work on the paper. By then, your library will have changed and will mess up your paper.
• Example of the latter: Zotero auto-assigns bibtex keys, say AuthorYearA/B/C. If more articles are imported, those will change and you'll be miserable.

Some non-workflow related hints:

• Use a cheap WebDAV server to sync. It works well, won't mess up your database like dropbox would.
• Go through the pain of setting up Firefox if you're on mac.
• Solve the Bibtex export problems.
• Spent your free time tidying up your database. It's your comparative advantage.

Online sources

• Wikipedia [-] http://en.wikipedia.org/wiki/Comparison_of_reference_management_software
• Zotero [-] http://forums.zotero.org/discussion/6174/mendeley/
• Zotero [-] http://forums.zotero.org/discussion/6527/
• Mendeley [-] http://www.mendeley.com/blog/tag/zotero/
• Blog [2011-02-02] http://nakhmani.wordpress.com/2011/02/02/mendeley-vs-zotero-comparison/ (about the notes editor)
• Blog [2012-02-12] http://onid.chrislott.org/2012/in-brief-mendeley-vs-zotero-for-citation-management/ (about pricing)
• Blog [-] http://jodischneider.com/blog/2009/08/27/organizing-a-pdf-library-mendeley-for-information-extraction-zotero-for-open-source-goodness/ (fouten bij 'retrieve metadata' in beide programma's)+
• Blog [-] http://earlycj5.wordpress.com/2009/03/20/zotero-vs-mendeley-initial-thoughts/
• Blog [-] http://dave.langers.nl/index.php?/archives/408-Zotero-vs.-Mendeley.html
• http://groups.google.com/group/latexusersgroup/browse_thread/thread/ecef859dd30e306c?pli=1 (metadata toevoegen in LaTeX)
• http://www.tumblr.com/tagged/zotero+mendeley
• http://alternativeto.net/software/mendeley/comments
• http://ubuntuforums.org/archive/index.php/t-1067681.html
• http://infopolitics.net/2010/07/things-i-want-in-an-academic-writing-workflow/
• http://hlwiki.slais.ubc.ca/index.php/Zotero_vs._Mendeley
• http://www.slideshare.net/giustinid/ref-works-mendeley-zotero

LaTeX

Update 20-06-2013

Probleem

Na heel wat uren turen onder de Office-motorkap blijven veel problemen onopgelost. Vooral Word werkt soms tegen:

• Nummering van hoofdstukken en secties
• Insluiten van vectorafbeeldingen
• Dimensies van tabellen
• Cross references naar tabellen en grafieken
• Inhoudstabellen
• Paginanummering, first pages en secties
• Paginadimensies, illustraties
• Compatibiliteit illustraties in Excel, Powerpoint en Word
• ...

Met andere woorden, het is een boeltje. Ondertussen hoor je dat er een markuptaal bestaat die al die zaken onder controle houdt, LaTeX. Ik experimenteer daar ondertussen al even mee.

Het systeem

Zoals veel dingen uit de alternatieve wereld van computernerds zijn de interfaces van de programma's onoverzichtelijk en is de installatie al meteen problematisch. In essentie heb je twee programma's nodig.

Eén: een 'parser', een programma dat de code omzet in - laten we zeggen - een pdf'je. Dat kan MikTeX zijn of TexLive. Het komt allemaal op hetzelfde neer. Je moet wel de toepassing tex.exe weten te localiseren (onder Windows). Ik heb TexLive geïnstalleerd om alternatief te doen.

Twee: een frontend of editor. Dat kan bij wijze van spreken kladblok zijn, maar het is interessanter om een programma te gebruiken waar bijvoorbeeld knoppen met shortcuts voor bepaalde commando's reeds in aanwezig zijn en waar je met een muisklik het document kunt naar de parser sturen. Ik gebruik hiervoor TexMaker. Meer populair is TexnicCenter, en voor sommige mensen de tussenslag LyX, die reeds een indruk geeft van je output. Ter vergelijking: in Word zie je quasi exact de uiteindelijke output.

Mijn ervaring:

• LyX: nutteloos, je kan de LaTeX code niet wijzigen (!)
• TechnicCenter: oeverloos, er komt geen einde aan de foutmeldingen, zelfs voor een goede file
• TexMaker: heel erg goed, overschrijft je pdf's en je opent ze met de interne viewer in no time

Je kan ook alles online laten geschieden. Een briljant idee, maar het werkt nog niet zo goed. Zie:

• http://docs.latexlab.org
• http://www.scribtex.com/

Voordelen

• Het ziet er goed uit - je hebt standaard een heel wetenschappelijke stijl, en met XeTeX wordt het zelfs artistiek.
• Systematiek is heilzaam.

Nadelen

Eerste grote nadeel: samenwerken. Iets als track changes bestaat wel, maar ik durf mij er eerlijk gezegd niet aan wagen, laat staan om iemand anders te dwingen LaTeX te begrijpen.

Tweede nadeel: cite while you write blijft een beetje klungelig, want je moet in de .bibtex-file keys bepalen voor de referenties. Vanuit Zotero wordt dit automatisch gedaan, maar afhankelijk van de gebruikte plugin krijg je andere keys. Die zijn te manipuleren in JabRef, maar dit kan in feite enkel op het laatste moment wanneer je een definitieve, en paper specifieke referentielijst hebt, zoniet wordt je werk toch telkens overschreven.

Derde gigantische nadeel: tabellen. Probeer in HTML een tabel te maken: dat gaat niet. In LaTeX is het net zo. Je doet er dan ook best aan om te werken via Excel en een plug-in. Dat voorspelt wel problemen, uiteraard. Enkele links:

• http://librecono.wordpress.com/2006/12/27/using-spreadsheets-to-create-latex-tables/
• http://www.ece.cmu.edu/~pueschel/teaching/guides/guide-tables.pdf
• http://blog.dreasgrech.com/2010/02/converting-excel-tables-to-latex-tables.html
• http://www.ctan.org/tex-archive/macros/latex/contrib/booktabs/booktabs.pdf
• http://tug.ctan.org/tex-archive/info/lshort/english/lshort.pdf
• LaTeX & Stata: http://privatewww.essex.ac.uk/~griene/StataLatex.html
• Workflow: http://tex.stackexchange.com/questions/1517/workflow-for-reviewing-pdfs-generated-from-tex

Voor het gebruik van booktabs moet je in de 'preamble' of 'head' de volgende lijn toevoegen:

\usepackage{booktabs}

Vierde nadeel: als er een fout in de code zit, krijg je geen output. Begin dan maar te debuggen.

Nog kritiek:

• http://www.9lives.be/forum/natuur-wetenschap-technologie/690835-latex-3.html

Links

• http://www.math.duke.edu/computing/tex/templates.html
• http://happymutant.com/latex/ - a quick and dirty guide to LaTeX
• http://people.cs.kuleuven.be/~dirk.nuyens/thesislayout/ - een thesis maken in LaTeX (waarschuwt voor a4wide en raadt geometry aan)
• http://latex.ugent.be/ - fantastische latex site van de Ugent
• http://www.andy-roberts.net/misc/ - man met cursussen
• http://www.andy-roberts.net/misc/latex/latexvsword.html - zinloze bijdrage
• http://happymutant.com/latex/index.html#fonts - A Quick & Dirty Draft Course