research

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.

The purpose of this post is to consider how researchers using process-based models can best describe their methods, assuming that a given base model may be used in a series of papers. A common situation in the current literature is that a full description of any particular model is given in the first paper where it is used, and then in subsequent papers we say something like “For full details of the model see Falster et al (2011).

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.

Here is a talk I presented at the workshop “Trait-based approaches to Ocean Life”, held in Copenhagen (Denmark) from 26-28 August 2013 at the Royal Danish Academy of Sciences and Letters (H.C. Andersens Boulevard 35, Copenhagen, Denmark). The workshop was organised by the Centre for Ocean Life. I was invited to give an overview of trait based approaches in plant ecology. Here’s the slides from my talk:

This post previous appeared here UPDATE (2020.01.20): The most recent release of the TRY database has been released with an open source license (CC-BY). Great news!!! In the first week of September 2013, members of the TRY trait database consortium are meeting to discuss the future of TRY, including whether TRY should revise their model of data sharing. TRY is a community initiative aiming to Provide a global archive of plant traits, and Promote trait-based approaches in ecology and biodiversity science.