Posts

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.
29 August 2016 1 min read

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.
12 May 2016 2 min read

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.
25 October 2015 2 min read

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.
9 September 2015 2 min read

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?
8 July 2015 2 min read

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.
26 February 2013 1 min read

First citation to our letter in Nature Climate Change: can we use a simple indicator to assess community responses to climate?

Google Scholar informed me today that our commentary in Nature Climate Change about the complexities involved in assessing community responses to climate change just got its first citation, six months after being published.
21 February 2013 1 min read

Climate refugia: from the Last Glacial Maximum to the 21st century

A report of the wonderful workshop held in Eugene, OR last summer about climate refugia has now appeared in New Phytologist. There we summarise the interesting discussions we had between a varied group of palaeoecologists, climatologists, modellers, phylogeographers and geneticists.
28 November 2012 1 min read

Palaeo50: The Pressing Questions in Palaeoecology

In December 2012 there will be a two-day workshop in Oxford (UK) to discuss the 50 most pressing questions in palaeoecology. I am really fortunate to having been selected to participate and share two days with eminent palaeoecologists and scientists from related disciplines.
29 October 2012 1 min read

Seeing red: Decoding the hidden information on robins' feathers

New publication: Age-related sexual plumage dimorphism and badge framing in the European Robin Erithacus rubecula. Ibis Red breasted robins are a classic symbol of the winter months and have adorned Christmas cards for over a century.
15 December 2011 3 min read