PONE-D-20-15404

Preparing GIS data for analysis of stream monitoring data: The R package openSTARS

PLOS ONE

Dear Mira Kattwinkel

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. 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

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

Reviewer #1: No

Reviewer #2: Yes

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3. 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

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4. 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

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5. 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: The submitted text "Preparing GIS data for analysis of stream monitoring data: The R package openSTARS" by Mira Kattwinkel at.al. describes a complete working licenses free library named "openStars" for R statistical environment. The software is dedicated on pre-processing of stream monitoring data for further statistical analysis, mainly by SSN. The tool is already available online and free for use. There is a manual which is easy to understand and reproduce. However, I didn't succeeded to reproduce provided example in Supporting_Information_S2. There are computational error with derive_streams(accum_threshold = 100, condition = T, clean = TRUE, burn = 10) when accum_threshold is equal to 100, failing to execute correctly calc_edges() and calc_sites(), mainly producing missing values for locID, pid and netID. The error does not exist for accum_threshold bigger than 170, but the results are different than those in supporting information. The used version of GRASS is 7.6 on R version 3.6.3 for Fedora 31.

2.The text have to be revisited because the existence of non-clear statements, such as at p.8, line 170 where the following text exists "openSTARS and STARS yielded very similar results (2)", where reference to some index (2) is confusing. Another example is the sentence on p. 9, line 182, starting with "The major conceptional difference..." where it is claimed "that the STARS derives the stream network from a DEM, whereas openSTARS relies on an existing stream network in vector format", which is opposite to the previous text.

3.According the statistical part in Paragraph 3, I think that is too brief and incomplete. Secondly, it is not clear a correlation of what and how is computed. I only could guess that outliers are removed from computation, because it is very suspicious to have r bigger that 0.98 with so large outliers. Moreover, the correlation is not suitable because samples in poor agreement may have high correlation. Likewise, the study of possible bias is also missing. As an option for revision the authors could consider any parametric or non-parametric test or at least a graphical tools, such as widely used in medicine Bland-Altman plots.

Reviewer #2: The submission itself is more or less ready to go, and explains workflow variants, and in the supplementary materials also analysis in the SSD package. The points that I feel deserve attention are that GRASS is now 7.8.3, R 4.0.2, and some of the package code is showing its age. For example, check_compl_confluences() now reports: "The command: v.to.db --quiet map=streams_v option=length type=line columns=length_new produced an error (1) during execution: ERROR: Column <length_new> exists. To overwrite, use the --overwrite flag". This may have subsequent consequences. Another is in calc_edges(), where: "Error in .prepareFastSubset(isub = isub, x = x, enclos = parent.frame(), : RHS of == is length 2 which is not 1 or nrow (1197). For robustness, no recycling is allowed (other than of length 1 RHS). Consider %in% instead. In addition: Warning message: In if (dt[stream == id, prev_str01, ] == 0) { : the condition has length > 1 and only the first element will be used" which I believe occurs from R 4.0.0, because the lengths of compared objects are now checked. These are minor issues, but would trip up users of the R package. I feel that the writing of CI code for the package code on Github with the latest released versions of R, this package and the packages it depends on, GRASS, and the GRASS extensions.

A possible vulnerability is that both GRASS and R (sp and sf packages) have adapted to changes in PROJ and GDAL, so that the handling of coordinate reference systems across the boundary between the two interfaces software systems needs checking, and relying on PROJ strings may not be as reliable as it has. So when checking the software and provided scripts for changes from version changes in R and GRASS, it would be very sensible to check whether any vulnerabilities are present as R moves from Proj4 to WKT2 string representations.</length_new>

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Preparing GIS data for analysis of stream monitoring data: The R package openSTARS

PONE-D-20-15404R1

Dear Dr. Kattwinkel,

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

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Kind regards,

Stoyan Nedkov

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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: All comments have been addressed

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: N/A

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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

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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: Finally, I successfully replicated the whole process as it is shown in Supporting Information 2.

The main reason for the previous issues was partly my failure - I was set different geographical projections in GRASS software. However, the error messages was completely useless and their revisions must be considered. In my opinion, the reliance on GRASS settings must be explained explicitly in the manual.

Note, that it is a technical remark for further developments and it does not impact my decision.

Reviewer #2: (No Response)

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Reviewer #1: No

Reviewer #2: No