Terms of reference

terms_of_reference.md

@@ -0,0 +1,74 @@
+# TROLL individual based model - Terms of Reference
+
+_Document version 1.0_
+
+_Date: 7 July 2026_
+
+## 1. Description
+
+TROLL is a computer simulator written in C++ language. TROLL represents an idealized forest stand with a typical size of 1 to 100 ha within an explicit 3D grid of 1 m³ voxels aboveground, with at most one tree established per 1×1 m ground pixel. Climatic drivers include air temperature, vapour pressure deficit, wind speed, and light intensity above the canopy, as well as precipitation. Depending on the process, TROLL operates at half-hourly temporal resolution or at daily resolution. Forest trees are modelled individually and they are generated as instances of a species, with a set of plant functional traits controlling plant physiology, and especially the carbon and water uptake, as well as demographic processes. This trait-based parameterization, together with the spatial architecture are what lets TROLL jointly track detailed forest structure, carbon fluxes, and species-level biodiversity dynamics within the same simulation.
+
+This code was initiated in 1999 as a research-oriented tropical forest simulator ([Chave 1999](https://doi.org/10.1016/S0304-3800(99)00171-4)), with major subsequent upgrades ([Maréchaux & Chave 2017](https://doi.org/10.1002/ecm.1271), [Maréchaux et al. 2025](https://doi.org/10.5194/gmd-18-5143-2025)). The current computer code is about 10,000 lines stored on https://github.com/troll-model/TROLL. The current version is 4.0, which is delivered in the form of a single file (mainTROLL4.0.cpp). 
+
+Since 2023, a wrapper written in the R language, rcontroll, has been developed to manage the data inputs, run a version of TROLL called by R through the Rcpp language, and manage the data outputs ([Schmitt et al. 2023](https://doi.org/10.1111/2041-210X.14215)). The rcontroll code is available https://github.com/sylvainschmitt/rcontroll. 
+
+The goal of this document is to explain the context and organisation of TROLL. 
+
+## 2. Governance 
+
+The TROLL project is led and managed by a group of five core developers, henceforth the core development team. This team is a self-assembled group of scientists, committed to advancing the scientific research in forest ecology, through the development, applications and delivery of software products. 
+
+The core development team is responsible for reviewing and accepting major merges of the TROLL code. 
+
+They may be contacted via the generic email address: dev@troll-model.org.
+
+**Isabelle Maréchaux**, INRAE — AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, 34000 Montpellier, France
+Ecologist, forest modelling, plant physiology.
+Role: project lead, lead of version 4.0 upgrade (including water module)
+
+**Fabian Jörg Fischer** — School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, United Kingdom
+Ecologist, forest modelling, statistical modeling, remote sensing.
+Role: lead of spatial data integration (ALS), lead of version 3 upgrade (trait variability)
+
+**Sylvain Schmitt**, CIRAD — CIRAD, UPR Forêts et Sociétés, 34398 Montpellier, France
+Ecologist, forest modelling, statistical modeling.
+Role: lead of rcontroll wrapper. 
+
+**Philippe Verley**, IRD — AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, 34000 Montpellier, France
+Computer scientist 
+Role: lead for code factorization and code acceleration; website management
+
+Jérôme Chave, CNRS —  CRBE, Université de Toulouse, CNRS, IRD, Toulouse INP, 118 route de Narbonne, 31062 Toulouse, France
+Ecologist, forest modelling, statistical modeling.
+Role: lead of versions 1.0 and 2.0
+
+The core development team agrees to meet twice a year to explore code updates, improvements, and discuss collaborative projects.
+
+## 3. Licence and intellectual property
+
+TROLL version 4.0 and further developments are publicly available on GitHub as a
+standalone code. TROLL is licensed under the GNU General Public License v3.0 ([GPL3.0](https://github.com/sylvainschmitt/TROLL/blob/main/LICENSE)). “Permissions of this strong copyleft license are conditioned on making available complete source code of licensed works and modifications, which include larger works using a licensed work, under the same license. Copyright and license notices must be preserved. Contributors provide an express grant of patent rights”.
+
+By inheritance, rcontroll is licensed under the GNU General Public License v3.0 (GPL3.0). 
+
+Intellectual property resides with the code developers. 
+
+## 4. Acknowledgements
+
+Invitations to the core development team to collaborate on research projects are welcome.
+
+Users of the TROLL code are encouraged to contact the core development team about any questions and/or feedback (for this, users are encouraged to make use of the “issues” option on github). 
+
+In any case, users are encouraged to acknowledge the contribution 
+
+## 5. References
+
+Chave, J. (1999). Study of structural, successional and spatial patterns in tropical rain forests using TROLL, a spatially explicit forest model. *Ecological modelling*, 124(2-3), 233-254. https://doi.org/10.1016/S0304-3800(99)00171-4
+
+Maréchaux, I., & Chave, J. (2017). An individual‐based forest model to jointly simulate carbon and tree diversity in Amazonia: description and applications. *Ecological Monographs*, 87(4), 632-664.  https://doi.org/10.1002/ecm.1271
+
+Maréchaux, I., Fischer, F. J., Schmitt, S., & Chave, J. (2025). TROLL 4.0: representing water and carbon fluxes, leaf phenology, and intraspecific trait variation in a mixed-species individual-based forest dynamics model–Part 1: Model description. *Geoscientific Model Development*, 18(16), 5143-5204. https://doi.org/10.5194/gmd-18-5143-2025
+
+Schmitt, S., Salzet, G., Fischer, F. J., Maréchaux, I., & Chave, J. (2023). rcontroll: An R interface for the individual‐based forest dynamics simulator TROLL. *Methods in Ecology and Evolution*, 14(11), 2749-2757. https://doi.org/10.1111/2041-210X.14215
+
+