the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
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
Abstract. TROLL 4.0 is an individual-based forest dynamics model that is capable of jointly simulating forest structure, diversity and ecosystem functioning, including the ecosystem water balance and productivity, leaf area dynamics and the tree community functional and taxonomic composition. It represents ecosystem flux processes in a manner similar to dynamic global vegetation models, while adopting a representation of plant community structure and diversity at a resolution consistent with that used by field ecologists. Specifically, trees are modeled as three-dimensional individuals with a metric-scale spatial representation, providing a detailed description of ecological processes such as competition for resources and tree demography. Carbon assimilation and plant water loss are explicitly represented at tree level using coupled photosynthesis and stomatal conductance models, depending on the micro-environmental conditions experienced by trees. Soil water uptake by trees is also modelled. Physiological and demographic processes are parameterized using plant functional traits measured in the field. Here we provide a detailed description and discussion of the implementation of TROLL 4.0. An evaluation of the model at two tropical forest sites is provided in a companion paper (Schmitt et al., submitted companion paper). TROLL 4.0’s representation of processes reflects the state of the art, and we discuss possible developments to improve its predictive capability and its capacity to address challenges in forest monitoring, forest dynamics and carbon cycle research.
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CEC1: 'Comment on egusphere-2024-3104: No compliance with the policy of the journal', Juan Antonio Añel, 30 Oct 2024
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Dear authors,
Unfortunately, after checking your manuscript, it has come to our attention that it does not comply with our "Code and Data Policy".
https://www.geoscientific-model-development.net/policies/code_and_data_policy.htmlYou have archived your code on GitHub. However, GitHub is not a suitable repository for scientific publication. GitHub itself instructs authors to use other long-term archival and publishing alternatives, such as Zenodo. Therefore, the current situation with your manuscript is irregular, as no manuscript can be accepted in Discussions without fully comply with the code policy of the journal. Statements like the one you include in your manuscript, saying that the code will be stored after acceptance of the manuscript for publication, are not acceptable. Therefore, you must publish your code in one of the appropriate repositories and reply to this comment with the relevant information (link and a permanent identifier for it (e.g. DOI)) as soon as possible, as we can not accept manuscripts in Discussions that do not comply with our policy.
Please, note that if you do not fix this problem, we will have to reject your manuscript for publication in our journal.
Also, you must include the modified 'Code and Data Availability' section in a potentially reviewed manuscript, the DOI of the code.
Moreover, I have found that only one of your posted git has a license (GPLv3); for the other no license is listed. If you do not include a license the code remains your property and nobody can use it. Therefore, when uploading the model's code to new repositories, you could want to choose a free software/open-source (FLOSS) license. We recommend the GPLv3, which you already uses for the part of the code you have posted in GitHub.
Juan A. Añel
Geosci. Model Dev. Executive EditorCitation: https://doi.org/10.5194/egusphere-2024-3104-CEC1 -
AC1: 'Reply on CEC1', Isabelle Maréchaux, 31 Oct 2024
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Dear Editor,
We are sorry that the way we archived the code associated to our two submitted companion manuscripts did not comply with the code policy of Geoscientific Model Development.
We have solved this issue by creating three new Zenodo repositories:
1. A first one for the C++ code of TROLL 4.0:
Maréchaux, I., Fischer, F. J., Schmitt, S., & Chave, J. (2024). TROLL-code/TROLL: GMD preprint (4.0.0-GMD). Zenodo. https://doi.org/10.5281/zenodo.14013147
2. A second one for the R wrapper of this C++ code, rcontroll:
Schmitt, S., Salzet, G., Fischer, F.J., Maréchaux, I., & Chave, J. (2024). sylvainschmitt/rcontroll: GMD preprint (v0.2.0). Zenodo. https://doi.org/10.5281/zenodo.14012116
3. A third one for the R scripts used to perform all the simulations and analyses of our evaluation manuscript:
Schmitt, S. (2024). sylvainschmitt/troll_eval: GMD preprint (0.1.0). Zenodo. https://doi.org/10.5281/zenodo.14012085
The three citations and associated DOI will be added to any future revised version of our two manuscripts, in the “Code and Data Availability” section, as well as in the reference lists.
The three repositories have a GPLv3 license as recommended.
We hope that these modifications will make our manuscripts appropriate for publication in Geoscientific Model Development.
Yours sincerely,
Isabelle Maréchaux & Sylvain Schmitt, on behalf of all co-authors
Citation: https://doi.org/10.5194/egusphere-2024-3104-AC1 -
CEC2: 'Reply on AC1', Juan Antonio Añel, 31 Oct 2024
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Dear authors,
Thanks for addressing this issue so quickly. I have checked the repositories and we can consider now the current version of your manuscript in compliance with the code policy of the journal.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2024-3104-CEC2
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CEC2: 'Reply on AC1', Juan Antonio Añel, 31 Oct 2024
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AC1: 'Reply on CEC1', Isabelle Maréchaux, 31 Oct 2024
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