Blog Archives

Model for nothing – and the bootstrap for free

January 21, 2011
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Model for nothing – and the bootstrap for free

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 to whatever new format they

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Did what you write drive what I read?

September 16, 2010
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Did what you write drive what I read?

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 tend to accumulate faster

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A (fast!) null model of bipartite networks

September 12, 2010
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A (fast!) null model of bipartite networks

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. The basic idea behind a null

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A quick ggplot2 hack (multiple dataframes)

September 9, 2010
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A quick ggplot2 hack (multiple dataframes)

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 »

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A small and lonely sea urchin…

August 22, 2010
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A small and lonely sea urchin…

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 »

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R be dragons

August 18, 2010
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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 »

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A quick analysis of the trends in the number of weddings in France (1975–2010)

August 15, 2010
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A quick analysis of the trends in the number of weddings in France (1975–2010)

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 »

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R helps reproducible research

August 5, 2010
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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 »

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Viewing a bipartite network

July 30, 2010
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Viewing a bipartite network

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

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Why building R packages is good for you

July 23, 2010
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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 »

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