Implementation of the perfect plasticity approximation with biogeochemical compartments in R

Abstract

Modeling forest ecosystems is a landmark challenge in science, due to the complexity of the processes involved and their importance in predicting future planetary conditions. While there are a number of open‐source forest biogeochemistry models, few papers exist detailing the software development approach used to develop these models. This has left many forest biogeochemistry models large, opaque and/or difficult to use, typically implemented in compiled languages for speed. Here, we present a forest biogeochemistry model from the SORTIE‐PPA class of models, PPA‐SiBGC. Our model is based on the perfect plasticity approximation with simple biogeochemistry compartments and uses empirical vegetation dynamics rather than detailed prognostic processes to drive the estimation of carbon and nitrogen fluxes. This allows our model to be used with traditional forest inventory data, making it widely applicable and simple to parameterize. We detail the conceptual design of the model as well as the software implementation in the R language for statistical computing. Our aim is to provide a useful tool for the biogeochemistry modeling community that demonstrates the importance of vegetation dynamics in biogeochemical models.