Publications by Timothée
Getting data from an image (introductory post)
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 grasp about what is going on. Second, I have been a teacher as part of my...
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Draw a trophic network with n levels
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. If I continue to publish at this rhythm, expect a brand new post ar...
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Drawing a trophic network (part 2)
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). This is now done, with a code that is as inelegant as humanly ...
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Subsampling for dummies
A couple months ago, I was writing code for a paper that required some intense subsampling (something along the lines of several thousands of replicates on several thousands matrices). I decided to do the whole thing in R (I must confess that I don’t know how to live without it…), and as you can guess, it is really simple. The whole idea was ...
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Launch R document from Smultron / Fraise
Perhaps you know of the defunct Smultron, a lightweight editor for Mac OS X. There exists a new version called Fraise, with the same features. Among them, R syntax highlighting and the possibility to interact with the R Gui console. To do so, when in Fraise, just push Cmd-B to open the Commands window, then create a new command, and type #!/bin/b...
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Why building R packages is good for you
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 or C code. It is not, however, required to learn any other language that R to contribute a package to the community. There is a great...
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Viewing a bipartite network
I published two functions to visualize trophic networks with three or n levels, although most of my work consists in dealing with two-mode (bipartite) networks. The R library bipartite provides two functions to visualize such webs (plotweb and visweb), and I am generally happy with the results of the latter. However, I sometimes find it difficult...
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R helps reproducible research
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 statistical software (https://www.r-project.org/) Shortly followed by It is implemented in the nestednof f...
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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 deals with all demographic and economic questions. Additionally, they provide a csv file with monthly data, so we ca...
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R be dragons
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 afraid of what they will find. Last year, I had the chance to teach a bunch of master students some fundamentals of R...
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