TY - JOUR
T1 - ACGCA
T2 - An R package for simulating tree growth and mortality based on functional traits
AU - Fell, Michael
AU - Barber, Jarrett
AU - Ogle, Kiona
N1 - Funding Information:
This work was partially supported by a National Science Foundation Advances in Biological Informatics award ( DBI#1458867 ). The authors acknowledge the contributions of Darren Gemoets who translated the original Matlab version of the ACGCA model into C.
Publisher Copyright:
© 2022
PY - 2022/7
Y1 - 2022/7
N2 - The Allometrically Constrained Growth and Carbon Allocation (ACGCA) model is an individual-based model of tree growth and mortality, and it is a unique tool for investigating how tree functional traits influence growth and mortality. Several studies have used the ACGCA model to investigate tree traits, but the model is not readily accessible to the wider scientific community. Thus, we developed an R package that provides a greatly simplified interface to the ACGCA model. The package contains a single function, runacgca, with the capability of simulating tree growth under constant light conditions, variable light, or within a simple forest gap dynamics scenario. The ACGCA package can accommodate temporally varying parameters (tree traits), and its modular structure allows for users to swap out the current carbon gain (photosynthesis) algorithm for alternative versions that may incorporate more physiological detail. We provide examples demonstrating how the package can be used to investigate the effects of tree traits on growth and survival under constant light and under different gap dynamic scenarios. Though not explicitly shown, this model can be easily adapted to include more mechanistic detail or integrated into larger modeling frameworks.
AB - The Allometrically Constrained Growth and Carbon Allocation (ACGCA) model is an individual-based model of tree growth and mortality, and it is a unique tool for investigating how tree functional traits influence growth and mortality. Several studies have used the ACGCA model to investigate tree traits, but the model is not readily accessible to the wider scientific community. Thus, we developed an R package that provides a greatly simplified interface to the ACGCA model. The package contains a single function, runacgca, with the capability of simulating tree growth under constant light conditions, variable light, or within a simple forest gap dynamics scenario. The ACGCA package can accommodate temporally varying parameters (tree traits), and its modular structure allows for users to swap out the current carbon gain (photosynthesis) algorithm for alternative versions that may incorporate more physiological detail. We provide examples demonstrating how the package can be used to investigate the effects of tree traits on growth and survival under constant light and under different gap dynamic scenarios. Though not explicitly shown, this model can be easily adapted to include more mechanistic detail or integrated into larger modeling frameworks.
KW - Individual-based model
KW - Plant functional traits
KW - R package
KW - Trait trade-offs
KW - Tree growth model
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U2 - 10.1016/j.ecoinf.2022.101605
DO - 10.1016/j.ecoinf.2022.101605
M3 - Article
AN - SCOPUS:85125726909
SN - 1574-9541
VL - 69
JO - Ecological Informatics
JF - Ecological Informatics
M1 - 101605
ER -