R

I attended the recent useR 2016 conference at Stanford, USA, where I presented a talk on the technologies for building and distributing the Biomass And Allometry Database. All talks were recorded (see also below) and slides are available here. The talk compliments a post on the ropensci blog and our 2015 data paper in Ecology. Aside from the conference, a highlight of the trip for me was doing a bit of Ecotourism with Dr Will Cornwell in redwood forests and Californian chaparral.

In this post on the methods blog Rich FitzJohn and I describe the key technologies used to build our recently published package for R called plant – an individual-based simulation model that simulates the growth of individual trees, stands of competing plants, or entire metacommunities under a disturbance regime, using common physiological rules and trait-based functional trade-offs to capture differences among species. Link: https://methodsblog.wordpress.com/2016/02/23/plant/

Our latest paper describes an R package called plant – an individual-based simulation model that simulates the growth of individual trees, stands of competing plants, or entire metacommunities under a disturbance regime, using common physiological rules and trait-based functional trade-offs to capture differences among species. Falster DS, FitzJohn RG, Brännström Å, Dieckmann U, Westoby M (2016) plant: A package for modelling forest trait ecology & evolution. Methods in Ecology and Evolution 7: 136-146.

Together with 92 other co-authors, we recently published the Biomass And Allometry Database (BAAD) as a data paper in the journal Ecology, combining data from 176 different scientific studies into a single unified database. Proud to present "BAAD: a biomass and allometry database for woody plants". http://t.co/9dEQAeaoSK Warm thanks to all contributors #data — Daniel Falster (@adaptive_plant) May 7, 2015 We built BAAD for several reasons: we needed it for our own work we perceived a strong need within the vegetation modelling community for such a database, and because it allowed us to road-test some new methods for building and maintaining a database.

In this post on the ropensci blog we discuss some of the challenges we had to overcome in combining data from 176 different scientific studies to the Biomass And Allometry Database (BAAD), recently published as a data paper in the journal Ecology.

In preparation for running a “software carpentry bootcamp” I participated in the Software Carpentry Foundation (SCF)’s “Instructor training course”. The course takes 2-4 hours/week for 12 weeks and covers the basics of educational psychology, instructional design, and how to apply both to teach programming to adults. These two posts contain some reflections on my experience from the course, the first on a lesson about repeating thing, and the second on the course as a whole.

I originally posted this article on the niceRcode blog. Writing code is fast becoming a key - if not the most important - skill for doing research in the 21st century. As scientists, we live in extraordinary times. The amount of data (information) available to us is increasingly exponentially, allowing for rapid advances in our understanding of the world around us. The amount of information contained in a standard scientific paper also seems to be on the rise.