the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 02 Nov 2023
biospheremetrics v1.0.1: An R package to calculate two complementary terrestrial biosphere integrity indicators: human colonization of the biosphere (BioCol) and risk of ecosystem destabilization (EcoRisk)
Abstract. Ecosystems are under multiple stressors and impacts can be measured with multiple variables. Humans have altered mass and energy flows of basically all ecosystems on Earth towards dangerous levels. However, integrating the data and synthesizing conclusions is becoming more and more complicated. Here we present an automated and easy to apply R package to assess terrestrial biosphere integrity which combines 2 complementary metrics:
The BioCol metric quantifies the human colonization pressure exerted on the biosphere through alteration and extraction (appropriation) of net primary productivity, whereas the EcoRisk metric quantifies biogeochemical and vegetation structural changes as a proxy for the risk of ecosystem destabilization.
Applied to simulations with the dynamic global vegetation model LPJmL5 for 1500–2016, we find that presently (period 2007–2016), large regions show modification and extraction of >25 % of the preindustrial potential net primary production, leading to drastic alterations in key ecosystem properties and suggesting a high risk for ecosystem destabilization. In consequence of these dynamics, EcoRisk shows particularly high values in regions with intense land use and deforestation, but also in regions prone to impacts of climate change such as the arctic and boreal zone.
The metrics presented here enable global-scale, spatially explicit evaluation of historical and future states of the biosphere and are designed for use by the wider scientific community, not only limited to assessing biosphere integrity, but also to benchmark model performance.
The package will be maintained on GitHub and through that we encourage application also to other models and data sets.
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Notice on discussion status
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
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Preprint
(12809 KB)
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The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
- Preprint
(12809 KB) - Metadata XML
- BibTeX
- EndNote
- Final revised paper
Journal article(s) based on this preprint
Interactive discussion
Status: closed
-
RC1: 'Comment on egusphere-2023-2503', Juan Rocha, 16 Dec 2023
Thanks for the opportunity to read your work. The manuscript is set to describe a new R package to calculate metrics of integrity and stability in ecosystems. The paper is clear and methods well explained with some simulation results coming from LPJmL models.
The paper, however, falls short in introducing the software, its requirements and documentation for a larger adoption by the community. If the central goal of the paper is to introduce the `biosphericmetrics` package, more attention should be given to the software documentation. For example, the package does not contain vignettes or demos that help the user understand what are the main functionalities. Since the package is meant to be used as companion of LPJmL model output, the authors should make available a small datasets that the users can test to understand the usage of functions (the equivalent of mtcars in other packages, not the 3GB in Zenodo). The user should be able to install the package, read the help of functions, and be able to run a demo with some results. I understand the output can be large files, but you can get inspiration of other packages such as stars or terra in making available small spatial data cubes (NetCDF files) for testing.
The GitHub repository has some useful information on for example what functions to use when working on small datasets, sending jobs to servers, or plotting. However, the package documentation is not stand alone. For example, it seems one needs json files to use `calc_biocol()`, but that dependency is not documented on the help files of the function. Most functions on the package do not have examples and are not working out of the box, many assumes the user has access to Fabian’s folder structure. Thus I can install the package, but as a reviewer I cannot test if it works. The package also lacks testing and better documentation on scalability.
I strongly recommend to check the standards for software development in specialised journals such as Journal of Open Source Software, and the Journal of Statistical Software (JStatSoft). Both of them recommend the workflow and standards of the rOpenSci consortia: https://stats-devguide.ropensci.org
At minimum the package should contain a vignette explaining its functionality and a demo data that users can use to test its functionality.
Best regards,
Juan
## Specific comments
Line Comment
190 Unfinished sentence
Citation: https://doi.org/10.5194/egusphere-2023-2503-RC1 -
AC1: 'Reply on RC1', Fabian Stenzel, 19 Jan 2024
Dear Juan,
thank you for your review and the positive evaluation of the manuscript.
We appreciate your comments on the package and will incorporate them in
the next package version.
We will:
- add demo data
- add unit tests based on this data
- change the example script to become a vignette and also use the demo data there to make the use of the functions more accessible
- go over all function parameters again and make sure to explain their use and structure
We will additionally incorporate most of the code comments received directly
on github by Guido Kraemer (https://github.com/stenzelf/biospheremetrics/issues).
Best,
Fabian (on behalf of all authors)Citation: https://doi.org/10.5194/egusphere-2023-2503-AC1
-
AC1: 'Reply on RC1', Fabian Stenzel, 19 Jan 2024
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RC2: 'Comment on egusphere-2023-2503', Anonymous Referee #2, 02 Feb 2024
This manuscript presents software that computes two measures of human impact on the terrestrial system, i.e. the human colonization of the biosphere and the risk of ecosystem destabilization.
To my opinion, this is a relevant manuscript, however, I must admit that I am not specialized on this topic. I am in favor in adding the nitrogen components into the assessment.
The preprint is very well written and well-documented, with nice figures and maps.
I only have few minor/textual comments.
- L4: “2” should be “two”; A number smaller or equal to ten should be written fully, if the number is not accompanied with physical units that refer to processes. Check also the reminder of the manuscript (i.e. L65 4/four components; L174 7/seven).
- L5: I should start with (i), and (ii) on line 6;
- L8-10: this sentence is to large and should be split in order to improve readability; the word “extraction” here should be explained here since I did not understand what the authors mean at this stage of the manuscript; Later on, it becomes clearer;
- L19 and elsewhere. References in the text: I am not familiar with the official formats of this journal, but to my opinion it is more logical to range the citations chronologically first and then alphabetically. After all, one refers first to the paper that came first;
- L51: Should be, “HANPP, however, cannot be …”;
- Add reference for Eq. 5:
- Eqs 13-17 are referred from Ostberg et al. (2018)? If not, add reference;
- L190: insert whit space between 1000 and m:
- L223-225: format “th” as superscript;
- Fig 2: Use capital M for “map”;
- L245: Better write: “Values of gi are high in regions …”;
- L272-275: It would be better to use (i), (ii), (iii), when one lists up items;
- L280: Better “Figure 5k,m”;
- L316-318: a list so use (i) and (ii);
Citation: https://doi.org/10.5194/egusphere-2023-2503-RC2
Interactive discussion
Status: closed
-
RC1: 'Comment on egusphere-2023-2503', Juan Rocha, 16 Dec 2023
Thanks for the opportunity to read your work. The manuscript is set to describe a new R package to calculate metrics of integrity and stability in ecosystems. The paper is clear and methods well explained with some simulation results coming from LPJmL models.
The paper, however, falls short in introducing the software, its requirements and documentation for a larger adoption by the community. If the central goal of the paper is to introduce the `biosphericmetrics` package, more attention should be given to the software documentation. For example, the package does not contain vignettes or demos that help the user understand what are the main functionalities. Since the package is meant to be used as companion of LPJmL model output, the authors should make available a small datasets that the users can test to understand the usage of functions (the equivalent of mtcars in other packages, not the 3GB in Zenodo). The user should be able to install the package, read the help of functions, and be able to run a demo with some results. I understand the output can be large files, but you can get inspiration of other packages such as stars or terra in making available small spatial data cubes (NetCDF files) for testing.
The GitHub repository has some useful information on for example what functions to use when working on small datasets, sending jobs to servers, or plotting. However, the package documentation is not stand alone. For example, it seems one needs json files to use `calc_biocol()`, but that dependency is not documented on the help files of the function. Most functions on the package do not have examples and are not working out of the box, many assumes the user has access to Fabian’s folder structure. Thus I can install the package, but as a reviewer I cannot test if it works. The package also lacks testing and better documentation on scalability.
I strongly recommend to check the standards for software development in specialised journals such as Journal of Open Source Software, and the Journal of Statistical Software (JStatSoft). Both of them recommend the workflow and standards of the rOpenSci consortia: https://stats-devguide.ropensci.org
At minimum the package should contain a vignette explaining its functionality and a demo data that users can use to test its functionality.
Best regards,
Juan
## Specific comments
Line Comment
190 Unfinished sentence
Citation: https://doi.org/10.5194/egusphere-2023-2503-RC1 -
AC1: 'Reply on RC1', Fabian Stenzel, 19 Jan 2024
Dear Juan,
thank you for your review and the positive evaluation of the manuscript.
We appreciate your comments on the package and will incorporate them in
the next package version.
We will:
- add demo data
- add unit tests based on this data
- change the example script to become a vignette and also use the demo data there to make the use of the functions more accessible
- go over all function parameters again and make sure to explain their use and structure
We will additionally incorporate most of the code comments received directly
on github by Guido Kraemer (https://github.com/stenzelf/biospheremetrics/issues).
Best,
Fabian (on behalf of all authors)Citation: https://doi.org/10.5194/egusphere-2023-2503-AC1
-
AC1: 'Reply on RC1', Fabian Stenzel, 19 Jan 2024
-
RC2: 'Comment on egusphere-2023-2503', Anonymous Referee #2, 02 Feb 2024
This manuscript presents software that computes two measures of human impact on the terrestrial system, i.e. the human colonization of the biosphere and the risk of ecosystem destabilization.
To my opinion, this is a relevant manuscript, however, I must admit that I am not specialized on this topic. I am in favor in adding the nitrogen components into the assessment.
The preprint is very well written and well-documented, with nice figures and maps.
I only have few minor/textual comments.
- L4: “2” should be “two”; A number smaller or equal to ten should be written fully, if the number is not accompanied with physical units that refer to processes. Check also the reminder of the manuscript (i.e. L65 4/four components; L174 7/seven).
- L5: I should start with (i), and (ii) on line 6;
- L8-10: this sentence is to large and should be split in order to improve readability; the word “extraction” here should be explained here since I did not understand what the authors mean at this stage of the manuscript; Later on, it becomes clearer;
- L19 and elsewhere. References in the text: I am not familiar with the official formats of this journal, but to my opinion it is more logical to range the citations chronologically first and then alphabetically. After all, one refers first to the paper that came first;
- L51: Should be, “HANPP, however, cannot be …”;
- Add reference for Eq. 5:
- Eqs 13-17 are referred from Ostberg et al. (2018)? If not, add reference;
- L190: insert whit space between 1000 and m:
- L223-225: format “th” as superscript;
- Fig 2: Use capital M for “map”;
- L245: Better write: “Values of gi are high in regions …”;
- L272-275: It would be better to use (i), (ii), (iii), when one lists up items;
- L280: Better “Figure 5k,m”;
- L316-318: a list so use (i) and (ii);
Citation: https://doi.org/10.5194/egusphere-2023-2503-RC2
Peer review completion
Journal article(s) based on this preprint
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Johanna Braun
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Dieter Gerten
Jens Heinke
Sarah Matej
Sebastian Ostberg
Sibyll Schaphoff
Wolfgang Lucht
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
- Preprint
(12809 KB) - Metadata XML