Software

Software and computer programs have taken an important place in my research in ecology and evolutionary biology: research in these fields requires a lot of statistical and computing analyses, I needed to write papers with some mathematical formulas, and I have always been attracted to use free software. Below I share some of my experiences in the use of R, LaTeX, and Linux.

R

R is a computer language for statistics and graphics. It includes many computing tools (matrix computation, optimisation, ...) as well as a simple interface for compiled code (e.g., C, C++, Fortran). Thousands of contributed packages on CRAN (Comprehensive R Archive Network) and other repositories over the Internet provide a vast number of possibilities for statistics, graphics, and computing. An ambivalent feature of R is that it is software for a very wide range of users: this may be confusing for beginnners who just want to do their analysis of variance or t-test and have heard that R is free. To help newbies in R, I have written a document available in several languages: I am the maintainer and main author of three packages available on CRAN: My teaching page contains several documents and slides related to R.

LaTeX

I use LaTeX to write all my documents as well as slides for my talks. Though LaTeX is extremely attractive, at least three facts limit a more widespread use:
  1. It is almost impossible to start with LaTeX without learning a minimum on class definition, the preamble, special characters, compilation, etc.
  2. LaTeX is not WYSIWYG (what you see is what you get).
  3. Some formattings, layouts, settings, etc., are hard to find.
I wrote an introductory document for LaTeX (26 pages): it is available in French and in English.

Another major difficulty with LaTeX is writing appropriate BiBTeX style files (.bst) to format your bibliography accordingly to the journal where you want to submit your papers. However, the situation has improved remarkably in the past few years. Several publishers provide templates, including examples and .bst files. Tom Schneider maintains a very useful (and very long) page on LaTeX and BiBTeX:

http://www-lmmb.ncifcrf.gov/~toms/latex.html

The top of this page has tables listing .bst files and publishers accepting LaTeX submission (be aware that you submit directly the .tex files, not the PDF). In all cases, check-out the web site where you intend to submit your work (preferably before writing you paper).

Finally, if you are brave enough to hack .bst files (or write your own), you can find some useful tricks in these PDF slides by Piet van Oostrum:

http://www.ntg.nl/bijeen/pdf-s.20031113/BibTeX-tutorial.pdf

I use PPower4 for my slides. Though this package is relatively old, it is still available (though apparently no more supported). I found it to be more flexible than more recent packages for slides (e.g., Beamer). The 'pgf' package helps to insert pictures in a more flexible way than the traditional \includegraphics. See the page of PPower4 on CTAN:

http://www.ctan.org/tex-archive/help/Catalogue/entries/ppower4.html

And finally, the indispensable (and regularly updated) ``The Comprehensive LaTeX Symbol List'':

http://www.ctan.org/tex-archive/info/symbols/comprehensive/symbols-a4.pdf

Linux

I first tried Linux in 2000 (Debian on a Pentium II) at the time when many configurations needed to be done manually. I decided to adopt definitely Linux in 2004 when I discovered Live CDs which allow a smooth installation (and to try Linux without installing it). After using Knoppix with KDE during several years, I switched to Ubuntu with Gnome in June 2009. The installation of the latter is the smoothest I could imagine, and the system is very easy to use. Almost no manual configuration is necessary. Though KDE has its strenghts (flexibility and some development tools, e.g., subversion, are well integrated in Konqueror), the Gnome interface has the advantage of simplicity.
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