rCTOOL
Author
Franca Giannini-Kurina; João Serra; Bent Tolstrup Christensen; Jørgen Eriksen; Nicholas John Hutchings; Jørgen Eivind Olesen; Johannes Lund Jensen
Contact
francagk@agro.au.dk or jlj@agro.au.dk
Website
https://github.com/francagiannini/rCTOOL
https://doi.org/10.1016/j.envsoft.2024.106229
Description
rCTOOL, an open-source R package for carbon (C) turnover modelling, featuring comprehensive documentation and a user-friendly interface. As an enhanced version of the widely used Danish C-TOOL model, rCTOOL maintains minimal input data requirements and reliable performance, while addressing the original model's limitations in openness and documentation.
The model is set up to simulate monthly SOC turnover in two depth layers, topsoil from 0 to 25 cm and subsoil from 26 to 100 cm. In each depth layer, the initial C content is assumed to be partitioned into three pools according to turnover rates, i.e. the stability of the soil C. These three pools are Fresh Organic Matter (FOM), which is assumed to decompose rapidly, Humidified Pool (HUM), which is assumed to decompose on a decadal time scale, and finally a Resistant Organic Matter pool, which is assumed to decompose on a time scale of centuries. During the simulation period, C inputs can be added to the FOM pool in the topsoil or subsoil by plant inputs (below-ground biomass from roots, rhizodeposition and above-ground plant residues incorporated into the soil). Other sources of C inputs can come from organic fertilisation, in which case a part of the C input in the topsoil can be allocated to the FOM pool and a part to the HUM pool, depending on the origin of the added material. The monthly turnover of C in each pool is regulated by a linear function depending on a decomposition rate, which can be modified by the soil temperature. The soil temperature is estimated by a pedotransfer heat function depending on soil properties, monthly daily mean air temperature, and monthly daily amplitude air temperature. The decomposed C can be respired, complexed in a more stable state (next pool) or transported to the subsoil from the top layer. We assume that the fraction of decomposed C going to the more complex pool is different according to the step. The fraction of C going from FOM to HUM depends on the clay content, whereas from HUM to ROM it is assumed to be constant. Vertical transport of SOC is unidirectional from topsoil to subsoil between equivalent pools.
Scientific articles
Petersen, B. M., Olesen, J. E., & Heidmann, T. (2002). A flexible tool for simulation of soil carbon turnover. Ecological modelling, 151(1), 1-14. https://doi.org/10.1016/S0304-3800(02)00034-0
Taghizadeh-Toosi, A., Christensen, B. T., Hutchings, N. J., Vejlin, J., Kätterer, T., Glendining, M., & Olesen, J. E. (2014). C-TOOL: A simple model for simulating whole-profile carbon storage in temperate agricultural soils. Ecological Modelling, 292, 11-25. https://doi.org/10.1016/j.ecolmodel.2014.08.016
Giannini-Kurina, Franca, et al. (2025). "Modelling and validating soil carbon dynamics at the long-term plot scale using the rCTOOL R package." Environmental Modelling & Software 183: 106229.
https://doi.org/10.1016/j.envsoft.2024.106229
