the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 01 Apr 2025
rsofun v5.0: A model-data integration framework for simulating ecosystem processes
Abstract. Mechanistic vegetation models serve to estimate terrestrial carbon fluxes and climate impacts on ecosystems across diverse biotic and abiotic conditions. Systematically informing them with data is key for enhancing their predictive accuracy and estimating uncertainty. Here we present the Simulating Optimal FUNctioning {rsofun} R package, providing a computationally efficient and parallelizable implementation of the P-model for site-scale simulations of ecosystem photosynthesis, complemented with functionalities for Bayesian model-data integration and estimation of parameters and uncertainty. We describe a use case to demonstrate the package functionalities for modelling ecosystem gross CO2 uptake at one flux measurement site, including model sensitivity analysis, Bayesian parameter calibration, and prediction uncertainty estimation. {rsofun} lowers the bar of entry to ecosystem modelling and model-data integration and serves as an open-access resource for model development and dissemination.
Status: open (until 27 May 2025)
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CEC1: 'Comment on egusphere-2025-1260 - No compliance with the policy of the journal and stop of peer-review', Juan Antonio Añel, 09 Apr 2025
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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.htmlFirst, you have not published with your manuscript the data used for your work. For example, you state you use "ecosystem flux measurements taken at one site" and Fluxnet2015 data. However, you do not provide such data in a repository (see our policy). Also, I have not found information about the output data produced for the work that you present here.
Additionally, you point out to a site that does not comply with our policy for the publication of calibration diagnostics: https://geco178 bern.github.io/rsofun/articles/sensitivity_analysis.html. You should have included this information in the Code and Data Availability section. Moreover, this is a Git site, which is not acceptable according to our policy, but also, the link is broken and does not provide any information. This is exactly the proof of why such sites are not acceptable for scientific publication. The site https://geco-bern.github.io/rsofun/articles/new_cost_function.html which you mention later works, but again, is not acceptable and should be listed in the Code and Data Availability section.
As the Topical Editor mentioned you after submitting your manuscript, it does not comply with our policy, and therefore it should not be in Discussions or under review. At this point, given the lack of critical information to replicate your work, namely the data (something which we failed to spot before), the sensible thing to do is to stop inviting reviewers for your manuscript, if it applies, until your manuscript is deemed in compliance with the policy of the journal.
To continue the evaluation of your work, you must reply to this comment with the information for the requested repositories for data, code and diagnostics, including their links and permanent identifiers (e.g. DOI), and a new text for the Code and Data Availability section in your manuscript that could substitute the exiting one. After it, we will check it and will decide on how to proceed with your manuscript, namely if the review process can continue.
Please, note that if you do not comply with this request, we will have to reject your manuscript for publication in our journal.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-1260-CEC1 -
CC1: 'Reply on CEC1', Benjamin Stocker, 10 Apr 2025
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Dear Editor
First of all, please accept our apologies that we hadn’t answered the comment by the Editor Carlos Sierra from 31 March. It had slipped our attention.
Second, we sincerely apologise for the lack of reader guidance in describing code and data availability. Reproducibility, open access, and transparency are central for our research and we have designed the repository referred to in the code availability statement in accordance with these standards. Apparently, we have not sufficiently described locations of published code (also in the permanent repository Zenodo), data files of model forcing, evaluation, and output data. In fact, these points had all been covered by our published repository.
Thanks to your message, we have realised that code and data provision through an R package may obscure access and the “physical” location (in file form) of data provided along with the package. Indeed, data files were provided in our package in an R-specific format, and are thus not readable across platforms. To resolve this point and the point of a lack of reader guidance, we have now implemented the following changes in the published repository and propose to implement the following changes in the manuscript. Please advise us how to proceed. We are ready to submit a revised version of our manuscript to biorxiv.
Changes in the published repository
- We added a section to the README file providing details that correspond to the Data availability and the Code availability Sections.
- We added a human-readable CSV version of the model forcing and evaluation data files.
- To clarify the origin of these files, we added two data processing scripts data-raw/generate_pmodel_drivers.R and data-raw/generate_pmodel_drivers-csv.Ras a documentation how the input data was generated based on the publicly available FLUXNET data.
- These changes were marked as model version v.5.0.1 and our published repository and Zenodo was updated accordingly (https://doi.org/10.5281/zenodo.15189864). Please note that the changes between v.5.0.0 and v.5.0.1 are only related to these auxiliary files, but do not affect the model outputs and results shown in the paper.
Proposed changes in the manuscript
- The Section on Code availability will be changed to:
The {rsofun} R package can be installed from CRAN (https://cran.r-project.org/package=rsofun) or directly from its source code on GitHub (publicly available at https://github.com/geco-bern/rsofun under an AGPLv3 licence). Versioned releases of the GitHub repository are deposited on Zenodo (https://doi.org/10.5281/zenodo.15189864*). Code to reproduce the analysis and plots presented here is contained in the repository (subdirectory ‘analysis/’) and is demonstrated on the model documentation website (https://geco-bern.github.io/rsofun/, article ‘Sensitivity analysis and calibration interpretation’). - The Section Data availability will be changed to:
The model forcing and evaluation data is based on the publicly available FLUXNET2015 data for the site FR-Pue, prepared by FluxDataKit v3.4.2 (10.5281/zenodo.14808331), taken here as a subset of the originally published data for years 2007-2012. It is accessible through the {rsofun} R package and contained as part of the repository (subdirectory ‘data/’) as CSV and as files. Outputs of the analysis presented here are archived in the ‘analysis/paper_results_files/’ subfolder. - URLs will be removed from Section 4.2
Failure on our side to more clearly describe relevant information already at an earlier stage may have given the impression of a lack of transparency and open access. Specifically, the following information and data had already been published before, along with our initial submission, and address several of the points you raised:
- The code and data contained in the repo makes all published analyses fully reproducible and is also deposited on Zenodo (https://doi.org/10.5281/zenodo.15189864). The link to Zenodo is provided in the README of the Github repository. Please accept our apologies that we forgot to include it in the Code and Data Availability statements.
- The URL of the GitHub repository is given in the Code Availability section of our manuscript and the address provided is not broken. The link you referred to must have accidentally included a line number that slipped in while copying text.
- All model forcing, evaluation, and output data is published along with the repository (subdirectory data/ of https://github.com/geco-bern/rsofun and corresponding location on Zenodo).
- All code used for the analysis presented in our manuscript is published along with the repository (subdirectory analysis/ of https://github.com/geco-bern/rsofun and corresponding location on Zenodo).
- The same code is also demonstrated and extensively documented by the vignettes published along with the repository (subdirectory vignettes/ of https://github.com/geco-bern/rsofun). These are the source code for the article ‘Sensitivity analysis and calibration interpretation’ on the model documentation website (https://geco-bern.github.io/rsofun/articles/sensitivity_analysis.html).
- Full reproducible workflows for several basic use cases of the model as implemented in the rsofun R package are extensively documented on the model description website https://geco-bern.github.io/rsofun/. We made great efforts in making these user-friendly and fully transparent.
In designing the repository, we put great attention to making code reproducible and reusable, but not primarily to make data reusable and open access. This is one of the reasons why we have initially decided to keep data accessible just for demonstration purpose within the (open access) package, but not in CSV format.
Sincerely,
Benjamin StockerCitation: https://doi.org/10.5194/egusphere-2025-1260-CC1 -
CC2: 'Reply on CC1', Benjamin Stocker, 14 Apr 2025
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We have now updated the version of the pre-print, published on biorxiv, with the extended information in the Data availability and the Code availability Sections. The DOI of the updated pre-print version is: https://doi.org/10.1101/2023.11.24.568574.
Kind regards,
Benjamin Stocker
Citation: https://doi.org/10.5194/egusphere-2025-1260-CC2 -
CEC2: 'Reply on CC2', Juan Antonio Añel, 14 Apr 2025
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Dear authors,
Many thanks for your detailed reply, and the explanations provided in Zenodo about the code and data that you use in your work. However, there is an outstanding issue that needs to be clarified. Regarding your data you state "The model forcing and evaluation data is based on the publicly available FLUXNET2015 data for the site FR-Pue, prepared by FluxDataKit v3.4.2 (10.5281/zenodo.14808331)." The problem here is that you state "is based on". What is necessary here to reproduce your work is not to know the dataset from which you take the forcing and evaluation data, but the exact data that you use for it. In this regard, it is unclear if somebody trying to replicate your work will have the ability to obtain exactly the data that you use simply accessing to a dataset much bigger. Therefore, instead of linking the full dataset from which you take your input data, you should share the exact input data that you have used, taken from such dataset.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-1260-CEC2 -
CC3: 'Reply on CEC2', Benjamin Stocker, 15 Apr 2025
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Dear Editor,
In our understanding, our reply (https://doi.org/10.5194/egusphere-2025-1260-CC1) and the information given in the Data availability Section address your points. Specifically, you write:
What is necessary here to reproduce your work is [...] to know [...] the exact data that you use for it.
In the Data availability Section, we write:
The model forcing and evaluation data [...] is accessible through the {rsofun} R package and contained as part of the repository (subdirectory ‘data/’) as CSV and as files.
The DOI of the repository containing these files is given in the Code availability Section. Further, in our reply (https://doi.org/10.5194/egusphere-2025-1260-CC1), we wrote:
- We added a human-readable CSV version of the model forcing and evaluation data files.
- To clarify the origin of these files, we added two data processing scripts data-raw/generate_pmodel_drivers.R and data-raw/generate_pmodel_drivers-csv.R as a documentation how the input data was generated based on the publicly available FLUXNET data.
You further write:
[...] if somebody trying to replicate your work will have the ability to obtain exactly the data that you use simply accessing to a dataset much bigger.
In the Data availability statement, we write:
The model forcing and evaluation data is based on the publicly available FLUXNET2015 data for the site FR-Pue, prepared by FluxDataKit v3.4.2 (10.5281/zenodo.14808331), taken here as a subset of the originally published data for years 2007-2012.
This information should be sufficient to reproduce the data preparation. Furthermore, in our reply (https://doi.org/10.5194/egusphere-2025-1260-CC1), we mention that we have added data generation scripts (data-raw/generate_pmodel_drivers.R and data-raw/generate_pmodel_drivers-csv.R) that do just that.
You finally write:
Therefore, instead of linking the full dataset from which you take your input data, you should share the exact input data that you have used, taken from such dataset.
The exact input (and also evaluation) data we have used has been part of the published repository from the start. With our latest version update of the repository, have added that data also in the form of CSV files and we have added scripts for reproducing data generation. And all this information (except pointing to those scripts) is now provided in the revised Data availability Section. Please excuse us, but we are not sure what should still be changed at this point and how our replies and additions to the manuscript and the repository do not yet resolve open points. Please advise us. Thank you.
Beni Stocker
Citation: https://doi.org/10.5194/egusphere-2025-1260-CC3 -
CEC3: 'Reply on CC3', Juan Antonio Añel, 15 Apr 2025
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Dear authors,
Many thanks for the explanation. The current wording of the Code and Data Availability section in your manuscript creates some confusion, and it is not so clear as your reply to my previous comment. It is now clear that it is possible to obtain the exact data used in your study through the use of the software that you provide. I would recommend that in potential reviewed versions of your manuscript you avoid using the expression "based on" and instead you declare in the section the information that you have posted in your reply on how to get the Fluxnet input data.
With this information we can consider your manuscript in compliance with the Code and Data policy of the journal.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-1260-CEC3 -
CC4: 'Reply on CEC3', Benjamin Stocker, 16 Apr 2025
reply
Dear Editor,
Ok, thank you. From your reply I understand that no further changes to the manuscript or the published data and code are needed at this point and that the latest version of the manuscript on biorxiv (https://doi.org/10.1101/2023.11.24.568574) will be considered for the peer-review process at GMD.
Kind regards,
Benjamin Stocker
Citation: https://doi.org/10.5194/egusphere-2025-1260-CC4 -
CEC4: 'Reply on CC4', Juan Antonio Añel, 16 Apr 2025
reply
Dear authors,
Yes, it is correct, no further changes to your manuscript are need at this point.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-1260-CEC4
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CEC4: 'Reply on CC4', Juan Antonio Añel, 16 Apr 2025
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CC4: 'Reply on CEC3', Benjamin Stocker, 16 Apr 2025
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CC3: 'Reply on CEC2', Benjamin Stocker, 15 Apr 2025
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CEC2: 'Reply on CC2', Juan Antonio Añel, 14 Apr 2025
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CC1: 'Reply on CEC1', Benjamin Stocker, 10 Apr 2025
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