Subsetting made easy

February 27, 2012 | Gregor

Calculating characteristics such as median, mean,… of a subset of data is quite straightforward in R: For a data set containing results from several “models”, a subset for the model “base” is created by Then, the median of the variable … Continue reading → [Read more...]

Boxplots without boxes

June 14, 2011 | Gregor

Let’s say you have several categories with multiple data points each that you would like to plot as individual points. Even if you have only a single point, the R graphics package will plot a line (without a box for … Continue reading → [Read more...]

R in a nutshell

June 1, 2011 | Gregor

I got this book as a reference for my work with R and do like it. Just after browsing the chapters I already found some useful hints about loading and manipulating data, e.g., loading of fixed-width data files! [Read more...]

More fun with boxplots

May 19, 2011 | Gregor

Here are a few more plotting options for boxplots: Let’s start plotting the full set plot(b$mod, b$x) Plot labels for a subset in full set plot (label all points x __ -1) text(subset(b$mod, b$x __ -1), subset(b$x, b$x __ -1), … Continue reading → [Read more...]

Mapping points

May 16, 2011 | Gregor

Since I look at mercury concentrations at different measurement stations in North America, visualization using a map with values (of your favourite parameter) plotted as colour-coded circles is quite useful. After some trial & error, here is some very basic code … Continue reading → [Read more...]

More fun with sed

March 18, 2011 | Gregor

So I have this strange date and time string, which I would like to convert to a “useable” date, i.e., something that a spreadsheet programme or R can work with. It looks like this (MON has 3 chars): ddMONyr:hh:mm:ss The … Continue reading → [Read more...]

Converting text files with sed

March 3, 2011 | Gregor

Sed is my friend to change fixed-width text files (e.g., from an R screen output) to a comma delimited file using sed 's/ */,/g' file1 __file2.csv Note the two spaces between s/ and */. [Read more...]

Model for nothing – and the bootstrap for free

January 21, 2011 | Timothée

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...]

A (fast!) null model of bipartite networks

September 12, 2010 | Timothée

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...]

A small and lonely sea urchin…

August 22, 2010 | Timothée

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...]
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