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[REVIEW]: SSN2: The next generation of spatial stream network modeling in R #6389

Closed editorialbot closed 4 months ago

editorialbot commented 9 months ago

Submitting author: !--author-handle-->@michaeldumelle<!--end-author-handle-- (Michael Dumelle) Repository: https://github.com/USEPA/SSN2 Branch with paper.md (empty if default branch): develop Version: v0.2.0(JOSS) Editor: !--editor-->@mikemahoney218<!--end-editor-- Reviewers: @fernandomayer, @k-doering-NOAA, @fawda123 Archive: 10.5281/zenodo.12770259

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/66fd932526762f8ccd8bd9c3954e0e3d"><img src="https://joss.theoj.org/papers/66fd932526762f8ccd8bd9c3954e0e3d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/66fd932526762f8ccd8bd9c3954e0e3d/status.svg)](https://joss.theoj.org/papers/66fd932526762f8ccd8bd9c3954e0e3d)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@fernandomayer & @k-doering-NOAA, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mikemahoney218 know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @k-doering-NOAA

📝 Checklist for @fawda123

📝 Checklist for @fernandomayer

editorialbot commented 9 months ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 9 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.23 s (888.3 files/s, 208289.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            65           2240            198          14898
R                              117           1673           5470           9003
JavaScript                       4           2099           1928           7019
Markdown                         6            223              0            929
TeX                              2             94              0            782
XML                              2              0              2            639
Rmd                              2            171            561            216
C                                2             12             22             45
YAML                             3             12              2             44
SVG                              1              0              1             11
CSS                              1              0              5              1
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           206           6524           8189          33588
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 9 months ago

Wordcount for paper.md is 1982

editorialbot commented 9 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mikemahoney218 commented 9 months ago

👋🏼 @michaeldumelle, @fernandomayer, @k-doering-NOAA, @fawda123: this is the review thread for the paper. Just about all of our communications will happen here from now on. :smile:

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread. For best results, don't include anything else in the comment!

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6389 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if you require some more time.

Please feel free to ping me (@mikemahoney218) if you have any questions/concerns. Thanks again so much for agreeing to review!

editorialbot commented 9 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1371/journal.pone.0282524 is OK
- 10.32614/RJ-2018-009 is OK

MISSING DOIs

- 10.1002/2015wr018349 may be a valid DOI for title: Spatial statistical network models for stream and river temperature in New England, USA
- 10.1016/j.jtherbio.2021.103028 may be a valid DOI for title: Integrating thermal infrared stream temperature imagery and spatial stream network models to understand natural spatial thermal variability in streams
- 10.1111/rec.13626 may be a valid DOI for title: Riparian vegetation shade restoration and loss effects on recent and future stream temperatures
- 10.1111/1752-1688.12372 may be a valid DOI for title: The Stream-Catchment (StreamCat) Dataset: A database of watershed metrics for the conterminous United States
- 10.1139/cjfas-2016-0247 may be a valid DOI for title: Scalable population estimates using spatial-stream-network (SSN) models, fish density surveys, and national geospatial database frameworks for streams
- 10.1371/journal.pone.0239237 may be a valid DOI for title: Preparing GIS data for analysis of stream monitoring data: The R package openSTARS
- 10.1086/710340 may be a valid DOI for title: Variation in stream network relationships and geospatial predictions of watershed conductivity
- 10.1016/j.scitotenv.2017.08.151 may be a valid DOI for title: Using spatial-stream-network models and long-term data to understand and predict dynamics of faecal contamination in a mixed land-use catchment
- 10.1371/journal.pone.0238422 may be a valid DOI for title: SSNdesign — An R package for pseudo-Bayesian optimal and adaptive sampling designs on stream networks
- 10.1016/j.cageo.2004.03.012 may be a valid DOI for title: Multivariable geostatistics in S: the gstat package
- 10.1890/08-1668.1 may be a valid DOI for title: A mixed-model moving-average approach to geostatistical modeling in stream networks
- 10.1038/s41598-019-43132-7 may be a valid DOI for title: A spatial stream-network approach assists in managing the remnant genetic diversity of riparian forests
- 10.1007/s10021-018-0311-8 may be a valid DOI for title: Estimating ecosystem metabolism to entire river networks
- 10.1111/1752-1688.12543 may be a valid DOI for title: Improving predictive models of in-stream phosphorus concentration based on nationally-available spatial data coverages
- 10.1111/1365-2664.13997 may be a valid DOI for title: Dendritic prioritization through spatial stream network modeling informs targeted management of Himalayan riverscapes under brown trout invasion
- 10.1016/j.cageo.2014.02.009 may be a valid DOI for title: rtop: An R package for interpolation of data with a variable spatial support, with an example from river networks
- 10.1198/jasa.2009.ap08248 may be a valid DOI for title: A moving average approach for spatial statistical models of stream networks

INVALID DOIs

- None
michaeldumelle commented 9 months ago

Thank you @mikemahoney218 , @fernandomayer, and @k-doering-NOAA ! If anyone has any questions that come up that I can help with, please don't hesitate to reach out.

mikemahoney218 commented 9 months ago

@editorialbot add @fawda123 as reviewer

All three reviewers I reached out to accepted, which is fantastic! While we can have a review with 2 reviewers, 3 is ideal, so I'm going ahead and adding @fawda123 as a reviewer as well. Thanks again so much for agreeing to review!

editorialbot commented 9 months ago

@fawda123 added to the reviewers list!

michaeldumelle commented 9 months ago

Thank you @fawda123 !

mikemahoney218 commented 8 months ago

Hi all! Just wanted to bump this thread now that we're about two weeks into the review window.

@fernandomayer, @k-doering-NOAA, @fawda123 : note that when you post this comment on this thread: @editorialbot generate my checklist

You'll get a checklist generated containing all the elements we're asking you to look over as part of your review. Please let me know if you've got any questions/comments/concerns regarding the review!

@michaeldumelle , I should have mentioned this earlier, but if you want to take a look at those "MISSING DOIs" in the Editorialbot message above -- assuming those DOIs correspond to your actual citations, please go ahead and add them to your bibtex file (eg doi = "10.1002/2015wr018349"). No rush, but they'll need to get fixed before we'd accept the paper.

michaeldumelle commented 8 months ago

@mikemahoney218 I updated the bibtex file, incorporating the aforementioned DOIs and adding a few more. I pushed the changes to the joss branch, and you can review the commit here. Please let me know when you need anything else from me. Thank you!

mikemahoney218 commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-1-4614-7618-4 is OK
- 10.1002/9781119115151 is OK
- 10.1002/2015wr018349 is OK
- 10.1371/journal.pone.0282524 is OK
- 10.1016/j.jtherbio.2021.103028 is OK
- 10.1111/rec.13626 is OK
- 10.1111/1752-1688.12372 is OK
- 10.1002/2017WR020969 is OK
- 10.1139/cjfas-2016-0247 is OK
- 10.1371/journal.pone.0239237 is OK
- 10.18637/jss.v063.i19 is OK
- 10.1086/710340 is OK
- 10.1016/j.scitotenv.2017.08.151 is OK
- 10.1016/j.cageo.2004.03.012 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1890/08-1668.1 is OK
- 10.18637/jss.v056.i02 is OK
- 10.1111/j.1523-1739.2012.01897.x is OK
- 10.1038/s41598-019-43132-7 is OK
- 10.1007/s10021-018-0311-8 is OK
- 10.48550/arxiv.2110.02507 is OK
- 10.1111/1752-1688.12543 is OK
- 10.1111/1365-2664.13997 is OK
- 10.1016/j.cageo.2014.02.009 is OK
- 10.1198/jasa.2009.ap08248 is OK
- 10.18637/jss.v056.i03 is OK
- 10.1007/978-0-387-98141-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None
fawda123 commented 8 months ago

Review checklist for @fawda123

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

fawda123 commented 8 months ago

@michaeldumelle I've finished my initial review of the package and paper, nice work! These package updates are critical to maintain relevancy of "legacy" software as R continues to develop. It's nice to see the effort put into this work. I've added a few issues (https://github.com/USEPA/SSN2/issues/11, https://github.com/USEPA/SSN2/issues/12, https://github.com/USEPA/SSN2/issues/13, https://github.com/USEPA/SSN2/issues/14, https://github.com/USEPA/SSN2/issues/15) in the main repo for your consideration. I think the biggest ask is updates to your unit tests. Let me know if you have any questions!

michaeldumelle commented 8 months ago

@fawda123 thank you so much for the kind words about the software and for the thorough and helpful review! I really appreciate the time you put into this, and I look forward to incorporating all of your feedback once the remaining reviews come in. I will reach out if I have any clarifying questions.

@mikemahoney218 SSN2 currently has three branches: 1) main, which is up to date with CRAN; 2) which is the development version that is ahead of CRAN; and 3) joss, which is up to date with main but has the joss paper in it. When incorporating feedback on the software, can I push changes to the development branch with the understanding that the changes will be merged into main alongside the next CRAN update? And when incorporating feedback on the paper, can I push changes to the joss branch?

mikemahoney218 commented 8 months ago

Life will be easier if you can merge the development branch into the JOSS branch -- in particular, I think it will be easier for reviewers if there's one branch containing all of the most up-to-date revisions to the code and the paper (and it will also be better when we move to accepting the package and need an archive and DOI). Is that possible?

michaeldumelle commented 8 months ago

@mikemahoney218 definitely! How does this plan sound? Once I get reviews, I will address code feedback in the development branch and paper feedback in the joss branch. Once I am done addressing code and paper feedback, I will merge the development branch into the JOSS branch so the joss branch has the most up-to-date revisions to both code and the paper.

mikemahoney218 commented 8 months ago

So long as you can make it clear to reviewers what's living where -- especially as @fernandomayer and @k-doering-NOAA are still going to do their initial pass. It's normal for these reviews to involve a lot of back and forth and conversation, much much more so than a traditional peer review where the reviewers only look at the document when you're done working on it. We're fully expecting something closer to a co-production workflow, where reviewers are looking at your code while you're incorporating changes from their reviews and the other reviewers!

That's why I think it'd be better if you can have one branch that's up to date, rather than splitting changes out across branches. I'm not sure what advantage separating code and paper changes has, though!

michaeldumelle commented 8 months ago

@mikemahoney218 I had planned to leave the joss branch frozen with the software version at the time of the article's (hopeful) publication, which is why all the hassle with the separate branches (as the development branch will eventually be merged into main/CRAN). Do you recommend I add all the joss files to the development branch and eventually merge it into main, placing all the joss files in .Rbuildignore? Then I can delete the joss branch?

mikemahoney218 commented 8 months ago

I personally think that will be the easiest for everyone to follow. We'll be capturing the software at time of acceptance as a Zenodo archive from your repository (associated with a new GH release), so you'll need to have everything in one place by then anyway, and will have the release tag as a permanent record on your repository of "the software as accepted by JOSS". So I think having everything in one branch, with the paper in .Rbuildignore, makes the most sense.

michaeldumelle commented 8 months ago

@mikemahoney218 Sounds like a plan, and I appreciate the advice! I will start on these changes once I have the initial round of reviews back from everyone.

k-doering-NOAA commented 8 months ago

Review checklist for @k-doering-NOAA

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

k-doering-NOAA commented 8 months ago

@mikemahoney218 I wanted to report one potential COI: Jay Ver Hoef and I are both employed by NOAA Fisheries, although at different offices (I'm at the Office of Science and Technology, while Jay is at the Alaska Fisheries Science Center). To my knowledge, we've never collaborated or even met.

Is it ok to continue my review?

mikemahoney218 commented 8 months ago

I think so! The JOSS documentation says that we can waive a COI if:

you and a submitter are both employed by the same very large organization but in different units without any knowledge of each other.

This sounds like a clearcut case of that to me! If you're still able to make an impartial assessment of the work, then I think it makes total sense for you to continue your review.

k-doering-NOAA commented 8 months ago

@mikemahoney218 thanks - I thought it could be waived as well upon seeing that line in the JOSS documentation, but wanted to report just in case. I am able to make an impartial assessment of the work. I'll continue reviewing, then, thanks for confirming!

mikemahoney218 commented 8 months ago

Fantastic! Thanks for reporting 😄

k-doering-NOAA commented 8 months ago

@michaeldumelle et al., fantastic work! A nicely written article and R package. I just completed the first pass through my checklist.

I did feel there were two small pieces of documentation missing, so I postponed checking 2 of the checkboxes for now. Once the missing documentation has been added, I can check them off.

I added edits to the paper and one suggestion, but these are non-blocking. I also made a few comments on issues posted by @fawda123, in case they can be of some help.

michaeldumelle commented 8 months ago

@k-doering-NOAA thanks so much for the kind words and the helpful feedback! I really appreciate your hard work on this and will start incorporating your suggestions once I get the final review back. I will reach out if I have any clarifying questions.

mikemahoney218 commented 8 months ago

Howdy everyone! Checking in as we're now about a month into the review.

@fawda123 and @k-doering-NOAA , thank you so much again for your initial reviews here!

@fernandomayer , do you know when you're expecting to start your review?

@michaeldumelle , it's probably a good idea to start working on the issues raised by the other reviewers now.

Thanks again everyone, and let me know if you have any questions/comments/concerns :smile:

fernandomayer commented 8 months ago

Review checklist for @fernandomayer

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

mikemahoney218 commented 7 months ago

@fernandomayer , do you know when you're expecting to finish your review?

@michaeldumelle , have you made any progress on addressing the completed reviews?

michaeldumelle commented 7 months ago

@mikemahoney218 I feel comfortable addressing all reviewer comments but wanted to wait until all reviews are complete to formally get started. If you think it is best to formally get started now, I am happy to do so!

mikemahoney218 commented 7 months ago

I think it would make sense to get started! Especially here where neither completed review is asking for fundamental functionality changes (I think), it's unlikely that you're going to get asked to change anything back. Ideally JOSS reviews are a bit more like ongoing discussions than the typical long-term back-and-forth of other journals, so it's fine for you to get started even with one review still outstanding.

k-doering-NOAA commented 7 months ago

@mikemahoney218 and @michaeldumelle, just wanted to point out that @michaeldumelle made changes that allowed me to check off all the checklist items on my review. Thanks!

mikemahoney218 commented 7 months ago

Thank you so much @k-doering-NOAA -- and thank you so much for reviewing for JOSS!

fernandomayer commented 7 months ago

@mikemahoney218 I've just finished my review. Sorry for taking so long.

@michaeldumelle et al: congratulations for the nice work.

mikemahoney218 commented 7 months ago

Thank you @fernandomayer !

michaeldumelle commented 7 months ago

Thank you very much @fawda123 , @k-doering-NOAA , and @fernandomayer for the thoughtful reviews, and I appreciate your contributions to the software and article. @mikemahoney218 , I am working on these and plan to be done within a few weeks -- I will reach out if any questions come up. If anyone has any additional thoughts/recommendations, please don't hesitate to reach out!

fawda123 commented 7 months ago

Same @michaeldumelle, just respond in the issues if you have any questions about my comments.

mikemahoney218 commented 6 months ago

@michaeldumelle , I just wanted to reach out to ask you how things are going -- how you're doing addressing reviewer comments, if you've got any questions or concerns, and when we might expect you to have addressed everything!

michaeldumelle commented 6 months ago

@mikemahoney218 thank you for reaching out! Things are going great; I don't have any questions/concerns at the moment, but will reach out if any come up. Things have just been particularly busy (out on work/personal travel 6 of 8 weeks from mid-April to mid-June). I expect to have addressed everything by the end of June, and hopefully much sooner. If this timeline does not work for you, please let me know and we can work something out.

mikemahoney218 commented 6 months ago

Safe travels! That timeline should be fine.

mikemahoney218 commented 6 months ago

Just as a quick note: I'm going to be traveling and generally less available until May 20th. I'll still be checking GitHub and email intermittently, but apologies if it takes me a bit longer to respond than usual!

michaeldumelle commented 6 months ago

No problem @mikemahoney218 and enjoy your travels!

mikemahoney218 commented 5 months ago

@michaeldumelle , as we're approaching mid-June, I wanted to bump this thread again, to make sure it doesn't slip through the cracks! Hope your leave went (is going?) well. Let me know if you're still expecting to address all comments by the end of the month!

michaeldumelle commented 5 months ago

Thank you @mikemahoney218 ! I am finally back from leave, which was great (thanks for asking). Lots of fun work-related and personal travel 😄 . I am hoping to have all comments addressed by the end of the month, but it may take until the early part of July. Apologies for the delays and thanks so much for your patience/understanding. I will reach out if I have any questions/comments/concerns and notify you when all comments are addressed.

michaeldumelle commented 4 months ago

@mikemahoney218 There is just one GitHub issue left to address, so we are almost there! It is a substantive one (updating unit testing), so it may take a few days. Then we will be ready to proceed here.

mikemahoney218 commented 4 months ago

Sounds good, and thanks for the update! I'll be largely offline this week (happy 4th!) but will be back next week (and intermittently online this week as well)