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 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
I am the maintainer and main author of three packages available on CRAN:
My teaching page contains several documents
and slides related to R.
- ape (Analysis of Phylogenetics and Evolution)
- pegas (Population and Evolutionary Genetics Analysis System)
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:
I wrote an introductory document for LaTeX (26 pages): it is available
in French and in English.
- It is almost impossible to start with LaTeX without learning a
minimum on class definition, the preamble, special characters,
- LaTeX is not WYSIWYG (what you see is what you get).
- Some formattings, layouts, settings, etc., are hard to find.
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:
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
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:
And finally, the indispensable (and regularly updated) ``The Comprehensive LaTeX Symbol List'':
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
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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