New website

I created my former website ( in late 2010, when I was starting my first postdoc at the lovely University of Cambridge. After 10 years, it was about time to revamp it!


The MEDECOS-AEET conference on Mediterranean Ecology will be next week here in Sevilla. The programme looks really exciting - I’m looking forward to it. Here is what we are bringing to the meeting:

New Ecoinformatics working group

Earlier this year a few colleagues (Ignasi Bartomeus, Sara Varela, Antonio J. Pérez-Luque, and myself) created a new working group on Ecoinformatics within the Spanish Terrestrial Ecology Association (AEET). Our main goals are to promote knowledge and training and exchange experiences on all aspects of ecoinformatics, including data management, statistical modelling, programming, etc.

Reproducible Science: What, Why, How

Reproducibility is a hot topic in science nowadays (e.g. see this Nature special). Some argue that we are in the middle of a ‘reproducibility crisis’, and thus scientists are being strongly encouraged to increase the reproducibility of their research.

Reproducible workflows

As a side product (or trailer) of our paper on reproducible science, we made a video promoting reproducible workflows. Particularly, showing how using Git and Rmarkdown make your research and scientific collaboration way much easier and better, compared to a typical (non-reproducible) workflow involving Excel, Word, some figure production software, and a lot of manual steps.

Writing papers in Rmarkdown

Rmarkdown is a great tool for reproducible science. You can combine text and code to produce dynamic reports that generate updated results with a single click, as in the example below.

New paper out in Nature Plants

We have a new paper out in Nature Plants: De Frenne P, Rodríguez-Sánchez F, De Schrijver A, Coomes DA, Hermy M, Vangansbeke P & Verheyen K. 2015. Light accelerates plant responses to warming.

Should supervisors review their students' code?

I have supervised my first master project this year. The project is coming to an end, and I am very happy with the results as well as the fully reproducible workflow we have followed: all developed on GitHub using R package structure and Rmarkdown.

Toward a more reproducible ecology: calculating plant cover in vegetation transects in R

Science has a big reproducibility problem: hardly anyone can reproduce (i.e. re-run, re-obtain) the results of most published papers (including authors themselves!). That is a big problem not only for science as a collective enterprise but also for scientists’ everyday life (‘how did I do this?

Spatial data in R: using R as a GIS (new version)

Roughly one year ago, I posted here a tutorial on how to make basic GIS operations in R like importing, analysing, exporting and mapping spatial data, both raster and vectorial (i.