Quantitative Sub-Ice and Marine Tracing of Antarctic Sediment Provenance (TASP v0.1)

Marschalek, James W.; Gasson, Edward; van de Flierdt, Tina; Hillenbrand, Claus-Dieter; Siegert, Martin J.; Holder, Liam

doi:https://doi.org/10.5194/gmd-2023-8

Preprints

https://doi.org/10.5194/gmd-2023-8

Preprints

Submitted as: model description paper

17 Mar 2023

Submitted as: model description paper |

| 17 Mar 2023

Status: this preprint was under review for the journal GMD but the revision was not accepted.

Quantitative Sub-Ice and Marine Tracing of Antarctic Sediment Provenance (TASP v0.1)

James W. Marschalek, Edward Gasson, Tina van de Flierdt, Claus-Dieter Hillenbrand, Martin J. Siegert, and Liam Holder

Abstract. Ice sheet models must be able to accurately simulate palaeo ice sheets to have confidence in their predictions of future Antarctic ice mass loss and resulting global sea-level rise, particularly over longer timescales. This requires accurate reconstructions of the extent and flow patterns of palaeo ice sheets using real-world data. Such reconstructions can be achieved by tracing the detrital components of offshore sedimentary records back to their source areas on land. However, sediment provenance data and ice sheet model results have not been directly linked, despite the complimentary information each can provide the other. Here, we present a computational framework (Tracing Antarctic Sediment Provenance, TASP) that predicts marine geochemical sediment provenance data using the output of numerical ice sheet modelling. The ice sheet model is used to estimate the spatial pattern of erosion rates and to trace ice flow pathways. Beyond the ice sheet margin, simple approximations of modern detrital particle transport mechanisms using ocean reanalysis data produce a good agreement between our predictions for the modern ice sheet/ocean system and marine surface sediments. Comparing results for the modern system to seafloor surface sediment measurements will allow application of the method to past ice sheet configurations. TASP currently predicts neodymium isotope compositions using the PSUICE3D ice sheet model, but it has been designed so that it could be adapted to predict other provenance indicators or use outputs of other ice sheet models.

Received: 20 Jan 2023 – Discussion started: 17 Mar 2023

Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims made in the text, published maps, institutional affiliations, or any other geographical representation in this preprint. The responsibility to include appropriate place names lies with the authors.

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James W. Marschalek, Edward Gasson, Tina van de Flierdt, Claus-Dieter Hillenbrand, Martin J. Siegert, and Liam Holder

Status: closed

CEC1:
'Comment on gmd-2023-8', Juan Antonio Añel, 05 May 2023

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.html

First of all, you have archived your data in repositories not suitable for scientific publication. The UCSD library or Copernicus servers are not acceptable. Therefore, you must make a copy of the data that you use in your work in one of the repositories that we can accept (listed in our policy). Also, for the Nd isotope compositions data, the repository (in Zenodo.org) is currently not accessible. This is unacceptable, and our policy is clear about it. All the assets must be open and accessible at the moment of submission, without limitations and without the possibility that the author can delete them. Therefore, you must create a new repository for this data, open and available without restrictions.

Also, in the Zenodo repository for TASP, there is no license listed. If you do not include a license, the code is not "free libre open-source" (FLOSS); it continues to be your property, and nobody can use it. Therefore, you must add a license for the TASP code in Zenodo. We recommend the GPLv3. You only need to include the file 'https://www.gnu.org/licenses/gpl-3.0.txt' as LICENSE.txt with your code. Also, you can choose other options that Zenodo provides: GPLv2, Apache License, MIT License, etc.

I have to highlight that if you do not fix this problem in a prompt manner, we will reject your manuscript for publication in our journal. I should note that, actually, your manuscript should not have been accepted in Discussions, given this lack of compliance with our policy. Therefore, the current situation with your manuscript is irregular.

Therefore, please, publish your data in one of the appropriate repositories and fix the issue with the TASP license, and reply to this comment with the relevant information (link and DOI) as soon as possible, as it should be available for the Discussions stage.

Also, you must include in a potentially reviewed version of your manuscript the modified 'Code Availability' and 'Data Availability' sections, including the DOIs for the new repositories.

Juan A. Añel
Geosci. Model Dev. Exec. Editor

Citation: https://doi.org/10.5194/gmd-2023-8-CEC1
- AC1:
  'Reply on CEC1', Jim Marschalek, 16 May 2023
  
  The two datasets on the UCSD library and Copernicus servers are previously published datasets created by other workers. These are used by TASP (although other equivalent datasets could be used), but were not generated as part of this study. References to these previously published datasets have therefore been removed from the ‘Data Availability’ section.
  The embargo on the Nd isotope composition dataset has been removed.
  We provide an updated DOI for TASP (10.5281/zenodo.7900763), now including the LICENSE.txt, as requested. We also took the opportunity to add example data files and an example ice sheet model output to the repository.
  The updated Code and Data availability sections are as follows:
  Code Availability
  The source code is available on the Git repository https://github.com/jwm17/TASP (DOI: 10.5281/zenodo.7900763). Additional files created for this study and required to execute the code can also be found there, as well as an example ice sheet model file (DeConto et al., 2021).
  Data Availability
  The neodymium isotope composition data published here are available at DOI:10.5281/zenodo.7548284.
  
  Citation: https://doi.org/10.5194/gmd-2023-8-AC1
  - CEC2: 'Reply on AC1', Juan Antonio Añel, 16 May 2023
    
    Dear authors,
    First of all, thanks for your reply. Unfortunately, it does not solve all the issues regarding our policy and the replicability of your work, and several problems should be addressed.
    - First, regarding the UCSD and Copernicus data: the fact that others have produced the datasets does not solve the issue. Those datasets are necessary to replicate your work, and accessibility to them is not assured currently. Therefore, please, take the exact data you use for your work, and store them in one of the repositories listed in our policy.
    - Second, some files in your Zenodo.org repositories (in both) are in .xlsx or .xls format. These formats do not fully comply with the ISO standard for long-term archival and accessibility. Actually, it could be the case that it is possible to read them with a specific version of proprietary software (Microsoft Excel). This way, storing the data in plain ASCII, CSV, or other formats would be better. In your case, saving the data as .ods files (Open Document Format) is probably the best and faster option.
    - In your new text for the code accessibility section, you mention the GitHub repository as if it was the primary one. This is not the case, and it isn't evident. The primary repository, and the only one that needs to be mentioned, is the Zenodo.org one. In this way, you should make clear that the permanent archive for the code used in your work is the one at Zenodo. Then, if you want, you can add a text similar to the one that follows: "A non-permanent version of the code used here can be found in --- GitHub link---".
    - Additionally, you have used MatLab to produce your software. Again, this is proprietary software, and in this way, the replicability of your work is limited to those with a license. Also, compatibility between versions is not assured. Therefore, at minimum, you should specify in your manuscript the version number of MatLab that you have used to run your software. It would be good if you could clarify if your code runs in GNU Octave, a FLOSS alternative to MatLab that also runs M Language scripts.
    Regards,
    Juan A. Añel
    Geosci. Model Dev. Executive Editor
    
    Citation: https://doi.org/10.5194/gmd-2023-8-CEC2
    
    AC2: 'Reply on CEC2', Jim Marschalek, 25 May 2023
    
    We appreciate the editor’s concerns that our results could not be exactly reproduced without the previoulsy published ocean reanalysis and ice shelf melt rate datasets. However, as these two datasets are published with DOIs, we feel it is not good scholarly practise to copy and re-archive them, as this is likely to lead to confusion about the original source of these datasets.
    Your policy states: “Where the authors cannot, for reasons beyond their control, publicly archive part or all of the code and data associated with a paper, they must clearly state the restrictions. They must also provide confidential access to the code and data for the editor and reviewers in order to enable peer review.” We feel the current situation is such a reason beyond our control, as we did not generate and are not the owners of these datasets.
    The MS Excel files have been converted to CSV files and the code has been adjusted to read in this different file type (new TASP doi:10.5281/zenodo.7944862).
    The reference to GitHub has been removed to ensure the Zenodo archive is emphasised as the permanent archive.
    The software was run using MATLAB version R2022a and this is now stated in the ‘Code and Data Availability’ section. The code does not run using GNU Octave.
    Our new Code and Data Availability section is as follows:
    Code and Data Availability
    The TASP code is available under a GPLv3 licence. The version of TASP used to produce the results in this paper was run using MATLAB version R2022a and is archived on Zenodo (Marschalek, 2023; https://doi.org/10.5281/zenodo.7944862). An example ice sheet model output used to produce the results in this paper is also available in the TASP repository (DeConto et al., 2021). The sub-ice shelf melt rate data (Adusumilli et al., 2020) can be found here: https://doi.org/10.6075/J04Q7SHT and the ORAS5 ocean reanalysis product files used (velocity and sea surface temperature) can be downloaded here: https://doi.org/10.24381/cds.67e8eeb7 (Copernicus Climate Data Store, 2021). As these are published datasets, it is not appropriate to copy these data in our TASP repository as it could lead to confusion about the original source of the data. However, the files are freely accessible in these archives or can be provided by the authors on request.
    The neodymium isotope composition data published here are available here: https://doi.org/10.5281/zenodo.7548284.
    
    We hope these changes adequately address your code and data access requirements.
    
    Citation: https://doi.org/10.5194/gmd-2023-8-AC2
RC1:
'Comment on gmd-2023-8', Anonymous Referee #1, 19 May 2023

Please find review attached.

Citation: https://doi.org/10.5194/gmd-2023-8-RC1
- AC3: 'Reply on RC1', Jim Marschalek, 05 Jul 2023
  
  We thank the reviewer for their input and upload our response as a pdf supplement.
  
  Citation: https://doi.org/10.5194/gmd-2023-8-AC3
RC2:
'Comment on gmd-2023-8', Evan Gowan, 29 May 2023

Please see the attached pdf for the review.

Citation: https://doi.org/10.5194/gmd-2023-8-RC2
- AC4: 'Reply on RC2', Jim Marschalek, 05 Jul 2023
  
  We thank the reviewer for their input and upload our response as a pdf supplement.
  
  Citation: https://doi.org/10.5194/gmd-2023-8-AC4

Status: closed

CEC1:
'Comment on gmd-2023-8', Juan Antonio Añel, 05 May 2023

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.html

First of all, you have archived your data in repositories not suitable for scientific publication. The UCSD library or Copernicus servers are not acceptable. Therefore, you must make a copy of the data that you use in your work in one of the repositories that we can accept (listed in our policy). Also, for the Nd isotope compositions data, the repository (in Zenodo.org) is currently not accessible. This is unacceptable, and our policy is clear about it. All the assets must be open and accessible at the moment of submission, without limitations and without the possibility that the author can delete them. Therefore, you must create a new repository for this data, open and available without restrictions.

Also, in the Zenodo repository for TASP, there is no license listed. If you do not include a license, the code is not "free libre open-source" (FLOSS); it continues to be your property, and nobody can use it. Therefore, you must add a license for the TASP code in Zenodo. We recommend the GPLv3. You only need to include the file 'https://www.gnu.org/licenses/gpl-3.0.txt' as LICENSE.txt with your code. Also, you can choose other options that Zenodo provides: GPLv2, Apache License, MIT License, etc.

I have to highlight that if you do not fix this problem in a prompt manner, we will reject your manuscript for publication in our journal. I should note that, actually, your manuscript should not have been accepted in Discussions, given this lack of compliance with our policy. Therefore, the current situation with your manuscript is irregular.

Therefore, please, publish your data in one of the appropriate repositories and fix the issue with the TASP license, and reply to this comment with the relevant information (link and DOI) as soon as possible, as it should be available for the Discussions stage.

Also, you must include in a potentially reviewed version of your manuscript the modified 'Code Availability' and 'Data Availability' sections, including the DOIs for the new repositories.

Juan A. Añel
Geosci. Model Dev. Exec. Editor

Citation: https://doi.org/10.5194/gmd-2023-8-CEC1
- AC1:
  'Reply on CEC1', Jim Marschalek, 16 May 2023
  
  The two datasets on the UCSD library and Copernicus servers are previously published datasets created by other workers. These are used by TASP (although other equivalent datasets could be used), but were not generated as part of this study. References to these previously published datasets have therefore been removed from the ‘Data Availability’ section.
  The embargo on the Nd isotope composition dataset has been removed.
  We provide an updated DOI for TASP (10.5281/zenodo.7900763), now including the LICENSE.txt, as requested. We also took the opportunity to add example data files and an example ice sheet model output to the repository.
  The updated Code and Data availability sections are as follows:
  Code Availability
  The source code is available on the Git repository https://github.com/jwm17/TASP (DOI: 10.5281/zenodo.7900763). Additional files created for this study and required to execute the code can also be found there, as well as an example ice sheet model file (DeConto et al., 2021).
  Data Availability
  The neodymium isotope composition data published here are available at DOI:10.5281/zenodo.7548284.
  
  Citation: https://doi.org/10.5194/gmd-2023-8-AC1
  - CEC2: 'Reply on AC1', Juan Antonio Añel, 16 May 2023
    
    Dear authors,
    First of all, thanks for your reply. Unfortunately, it does not solve all the issues regarding our policy and the replicability of your work, and several problems should be addressed.
    - First, regarding the UCSD and Copernicus data: the fact that others have produced the datasets does not solve the issue. Those datasets are necessary to replicate your work, and accessibility to them is not assured currently. Therefore, please, take the exact data you use for your work, and store them in one of the repositories listed in our policy.
    - Second, some files in your Zenodo.org repositories (in both) are in .xlsx or .xls format. These formats do not fully comply with the ISO standard for long-term archival and accessibility. Actually, it could be the case that it is possible to read them with a specific version of proprietary software (Microsoft Excel). This way, storing the data in plain ASCII, CSV, or other formats would be better. In your case, saving the data as .ods files (Open Document Format) is probably the best and faster option.
    - In your new text for the code accessibility section, you mention the GitHub repository as if it was the primary one. This is not the case, and it isn't evident. The primary repository, and the only one that needs to be mentioned, is the Zenodo.org one. In this way, you should make clear that the permanent archive for the code used in your work is the one at Zenodo. Then, if you want, you can add a text similar to the one that follows: "A non-permanent version of the code used here can be found in --- GitHub link---".
    - Additionally, you have used MatLab to produce your software. Again, this is proprietary software, and in this way, the replicability of your work is limited to those with a license. Also, compatibility between versions is not assured. Therefore, at minimum, you should specify in your manuscript the version number of MatLab that you have used to run your software. It would be good if you could clarify if your code runs in GNU Octave, a FLOSS alternative to MatLab that also runs M Language scripts.
    Regards,
    Juan A. Añel
    Geosci. Model Dev. Executive Editor
    
    Citation: https://doi.org/10.5194/gmd-2023-8-CEC2
    
    AC2: 'Reply on CEC2', Jim Marschalek, 25 May 2023
    
    We appreciate the editor’s concerns that our results could not be exactly reproduced without the previoulsy published ocean reanalysis and ice shelf melt rate datasets. However, as these two datasets are published with DOIs, we feel it is not good scholarly practise to copy and re-archive them, as this is likely to lead to confusion about the original source of these datasets.
    Your policy states: “Where the authors cannot, for reasons beyond their control, publicly archive part or all of the code and data associated with a paper, they must clearly state the restrictions. They must also provide confidential access to the code and data for the editor and reviewers in order to enable peer review.” We feel the current situation is such a reason beyond our control, as we did not generate and are not the owners of these datasets.
    The MS Excel files have been converted to CSV files and the code has been adjusted to read in this different file type (new TASP doi:10.5281/zenodo.7944862).
    The reference to GitHub has been removed to ensure the Zenodo archive is emphasised as the permanent archive.
    The software was run using MATLAB version R2022a and this is now stated in the ‘Code and Data Availability’ section. The code does not run using GNU Octave.
    Our new Code and Data Availability section is as follows:
    Code and Data Availability
    The TASP code is available under a GPLv3 licence. The version of TASP used to produce the results in this paper was run using MATLAB version R2022a and is archived on Zenodo (Marschalek, 2023; https://doi.org/10.5281/zenodo.7944862). An example ice sheet model output used to produce the results in this paper is also available in the TASP repository (DeConto et al., 2021). The sub-ice shelf melt rate data (Adusumilli et al., 2020) can be found here: https://doi.org/10.6075/J04Q7SHT and the ORAS5 ocean reanalysis product files used (velocity and sea surface temperature) can be downloaded here: https://doi.org/10.24381/cds.67e8eeb7 (Copernicus Climate Data Store, 2021). As these are published datasets, it is not appropriate to copy these data in our TASP repository as it could lead to confusion about the original source of the data. However, the files are freely accessible in these archives or can be provided by the authors on request.
    The neodymium isotope composition data published here are available here: https://doi.org/10.5281/zenodo.7548284.
    
    We hope these changes adequately address your code and data access requirements.
    
    Citation: https://doi.org/10.5194/gmd-2023-8-AC2
RC1:
'Comment on gmd-2023-8', Anonymous Referee #1, 19 May 2023

Please find review attached.

Citation: https://doi.org/10.5194/gmd-2023-8-RC1
- AC3: 'Reply on RC1', Jim Marschalek, 05 Jul 2023
  
  We thank the reviewer for their input and upload our response as a pdf supplement.
  
  Citation: https://doi.org/10.5194/gmd-2023-8-AC3
RC2:
'Comment on gmd-2023-8', Evan Gowan, 29 May 2023

Please see the attached pdf for the review.

Citation: https://doi.org/10.5194/gmd-2023-8-RC2
- AC4: 'Reply on RC2', Jim Marschalek, 05 Jul 2023
  
  We thank the reviewer for their input and upload our response as a pdf supplement.
  
  Citation: https://doi.org/10.5194/gmd-2023-8-AC4

James W. Marschalek, Edward Gasson, Tina van de Flierdt, Claus-Dieter Hillenbrand, Martin J. Siegert, and Liam Holder

Data sets

Surface sediment Nd isotope compositions from the Ross Sea, Antarctica Liam Holder and James Marschalek https://doi.org/10.5281/zenodo.7548284

Model code and software

Tracing Antarctic Sediment Provenance (TASP) James Marschalek https://doi.org/10.5281/zenodo.7529996

James W. Marschalek, Edward Gasson, Tina van de Flierdt, Claus-Dieter Hillenbrand, Martin J. Siegert, and Liam Holder

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Short summary

Ice sheet models can help predict how Antarctica’s ice sheets respond to environmental change; such models benefit from comparison to geological data. Here, we use ice sheet model results, plus other data, to predict the erosion of Antarctic debris and trace its transport to where it is deposited on the ocean floor. This allows the results of ice sheet modelling to be directly and quantitively compared to real-world data, helping to reduce uncertainty regarding Antarctic sea level contribution.


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