Reconstructing phylogenies is an interesting task, sadly one that often requires to navigate between a multitude of software. To add an unnecessary layer of complexity to the whole thing, most of these softwares speaks different languages, and requires the user to do endless conversions from fasta to phylip to nexus ... [Read more...]

GoogleReader allows you to track your activity, by representing the number of news items read and published by day and by hour. I use it quite a lot to stay up to date with the scientific literature (I subscribed to probably over 30 journals) and a bunch of other feeds. Stuff ... [Read more...]

One of the challenges for ecologists working with trophic/interaction networks is to understand their organization. One of the possible approaches is to compare them across a random model, with more or less constraints, in order to estimate the departure from randomness. To this effect, null models have been developed. ... [Read more...]

I’m starting to get familiar with ggplot2, and I really like it. I just found a very quick way to use several dataframes within the same plot, provided that the dataframes share columns names. One obvious application is the production (…)Read the rest of this entry » [Read more...]

A few weeks ago, a paper on which I am a co-author was accepted for publication in the french ecological journal Life & Environment. In this paper, we evaluate the consequences of recreative harvesting on three populations of sea urchins (…)Read the rest of this entry » [Read more...]

Hic sunt dracones used to be placed on maps, as a way to denote a dangerous or otherwise unexplored territory. We might as well write it all over R-related material used in introductory classes, because students seems to be really (…)Read the rest of this entry » [Read more...]

I’m currently planning my wedding, and my fiancée and I were discussing wether there were more or less couples getting married over time. It turns out that this information is quite easy to get via INSEE, a french institute that (…)Read the rest of this entry » [Read more...]

While reading a paper on mutualistic networks in press at Ecology, by Jimena Dorado et al., I found the following sentence in the Materials & methods section: Correlation analyses were done using the cor.test function in the basepackage of R (…)Read the rest of this entry » [Read more...]

A short modification of a function to draw bipartite networks in matrix form, with sorting of the network to reflect its nestedness. [Read more...]

Basically every function you use in R is part of a package (often the base or stats one). Most of the advances routines, such as the differential equations solvers in simecol are brought to R in the form of Fortran (…)Read the rest of this entry » [Read more...]

A short code to launch R documents from Smultron / Fraise [Read more...]

A little piece of code dealing with the subsampling of matrices, in R. Useful if you want to use something akin to bootstrap, or just check the size of your sample with regard to various statistics. [Read more...]

Following discussion on the comments of the previous post, I thought about how it was possible to draw links going in several directions (i.e. there are no ‘clear’ differences between the levels, and species from level n can interact with species of level n, n+1, n-1, n±k, etc). ... [Read more...]

I published a short function to draw trophic networks with several levels, with links going from level n+1 to level n only. It will only be of interest for people working in ecology (but if you see another possible use, please let me know). It is available here – with examples. ... [Read more...]

Hi there! This blog will be dedicated to data visualization in R. Why? Two reasons. First, when it comes to statistics, I am always starting by some exploratory analyses, mostly with plots. And when I handle large quantities of data, it’s nice to make some graphs to get a ... [Read more...]