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.
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.
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.
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?
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.
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.
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.
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.
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.
NOTE: This is an old version. The tutorial has been updated. You can find the new version HERE.
In a previous post I pointed out several free alternatives for Geographical Information Systems (GIS).