PONE-D-19-21282

PyLandStats: An open-source Pythonic library to compute landscape metrics

PLOS ONE

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1. Thank you fo rincluding the following funding information within your acknowledgements section; "This research has been supported by the Ecole Polytechnique Federale de Lausanne 397

(EPFL). The Corine Land Cover inventory used for the example data were produced 398

with funding by the European Union."

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Reviewer #2: Yes

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Reviewer #1: N/A

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: This article introduces PyLandStats, a definitely needed Python-based alternative to other patch metrics packages.

General comments:

* I would prefer having the patch metrics listed in the article rather than refer to the documentation, it seems like important information readers would want to see right away. How were these metrics selected? (around line 70)

* I miss benchmark to see how much memory and time is required. What are the limitations, I assume everything is in memory? It could be also useful to see how demanding are individual metrics.

* Did you compare the results with other packages? Do the automated tests actually test the correctness of the computations (e.g. compare with manually verified values)?

* The quality of the figures is really bad, I wonder if the submission system messed that up?

Software comments:

* why there are functions for computing metrics for Landscape, but only properties for spatio-temporal and buffer analysis? Seems to be inconsistent, if possible comment on that.

* how are dates specified, could it be e.g. DateTime object as well?

* you call it gradient analysis, however, especially the generic case sounds more like zonal analysis in GIS terms, perhaps worth clarifying that in the manuscript.

* L152: might be better to mention matplotlib as the library used for plotting in the beginning of the section

* L112: perhaps clarify when the metrics are computed, if I understood correctly, it's not during the initialization but once you get the property.

Typos:

L20: missing 'and'

L125: the the

L138: skip 'probably'

L146: slug?

Figure 1 caption: metric

L159: consists of

L192: across

L195: missing space

L196: I would add space between number and unit

L203: weird formulation

L211: skip 'really'

L263: scope of this article

L268: in a GitHub repository

L276: dependencies

L282: are

L300: neighbor

L300: inter-patch (or one word), see also other places

L324: of adjacency matrix

L335: software packages

L368:object-oriented what?

in references there are multiple places where it needs upper case in titles

Reviewer #2: In this study the author introduce PyLandStats, a new Python library to compute and quantify landscapes spatial patterns.

I’ve found the paper interesting and the library really useful, especially because before the recent Hesselbarth et al. (2019) there were not (to the best of my knowledge) R packages or Python libraries to efficiently compute a whole set of landscape statistics without relying to standalone GIS software.

The figures provided have a low quality, I recommend the author to improve them. The palette of Fig 3,5,7,8 could also be improved to increase the readability of the figure.

It would be nice to see some comparison between the proposed packaged and the R pkg landscapemetrics, as well as for FRAGSTATS and LecoS QGIS plugin, in term of both accuracy and precision of the measures and time computation.

I cannot access to the GitHub repository, something went wrong with the link?

Personal curiosity: the library relies on rasterio, have you found some issues regarding the incompatibility between rasterio and gdal python libraries ? (e.g. https://rasterio.readthedocs.io/en/stable/topics/switch.html).

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Reviewer #1: No

Reviewer #2: No

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PyLandStats: An open-source Pythonic library to compute landscape metrics

PONE-D-19-21282R1

Dear Dr. Bosch,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

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With kind regards,

Duccio Rocchini, PhD

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Thank you for addressing my comments and putting the effort into reproducible research. I am looking forward to using the library. Found just couple small typos, which could be fixed:

L119: Likewise Landscape instances ('Similarly to' would be better)

L154: follow -> following

L330: is scales

Reviewer #2: the author has answered to all the comments and provided an updated version of the manuscript. I would recommend to accept the paper. Well done!

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Reviewer #1: No

Reviewer #2: No