plant: A package for modelling forest trait ecology and evolution

Falster, D.S., FitzJohn, R.G., Brännström, Å., Dieckmann, U. ORCID: https://orcid.org/0000-0001-7089-0393, Westoby, M., & McMahon, S. (2016). plant: A package for modelling forest trait ecology and evolution. Methods in Ecology and Evolution 7 (2) 136-146. 10.1111/2041-210X.12525.

Other (Trait-Driven Models of Ecology and Evolution) plant-master.zip - Supplemental Material Available under License Creative Commons Attribution. Download (687kB)

Abstract

1. Population dynamics in forests are strongly size-structured: larger plants shade smaller plants while also expending proportionately more energy on building and maintaining woody stems. Although the importance of size structure for demography is widely recognized, many models either omit it entirely or include only coarse approximations.

2. Here, we introduce the plant package, an extensible framework for modelling size- and trait-structured demography, ecology and evolution in simulated forests. At its core, plant is an individual-based model where plant physiology and demography are mediated by traits. Individual plants from multiple species can be grown in isolation, in patches of competing plants or in metapopulations under a disturbance regime. These dynamics can be integrated into metapopulation-level estimates of invasion fitness and vegetation structure. Because fitness emerges as a function of traits, plant provides a novel arena for exploring eco-evolutionary dynamics.

3. plant is an open source R package and is available at github.com/traitecoevo/plant. Accessed from R, the core routines in plant are written in C++. The package provides for alternative physiologies and for capturing trade-offs among parameters. A detailed test suite is provided to ensure correct behaviour of the code.

4.plant provides a transparent platform for investigating how physiological rules and functional trade-offs interact with competition and disturbance regimes to influence vegetation demography, structure and diversity.

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