Closed editorialbot closed 1 year ago
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.29 s (450.2 files/s, 57502.0 lines/s)
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Language files blank comment code
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R 92 2012 2045 8221
TeX 3 170 8 1274
Markdown 4 134 0 1051
Rmd 4 296 325 363
Bourne Shell 25 74 468 76
YAML 2 12 4 71
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SUM: 130 2698 2850 11056
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gitinspector failed to run statistical information for the repository
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1093/biostatistics/kxu058 is OK
- 10.1097/01.ee9.0000606120.58494.9d is OK
- 10.1073/pnas.1510489113 is OK
- 10.1515/ijb-2015-0013 is OK
- 10.2202/1557-4679.1217 is OK
- 10.1111/j.1541-0420.2011.01685.x is OK
- 10.1002/sim.5907 is OK
- 10.1007/978-3-319-65304-4_14 is OK
- 10.1007/978-1-4419-9782-1 is OK
- 10.1007/978-3-319-65304-4 is OK
- 10.2202/1557-4679.1356 is OK
- 10.1111/rssb.12362 is OK
- 10.1111/biom.13375 is OK
- 10.21105/joss.02526 is OK
- 10.5281/zenodo.1342293 is OK
- 10.5281/zenodo.3558313 is OK
- 10.5281/zenodo.3698329 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Wordcount for paper.md
is 1295
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
👋🏼 @blind-contours, @mhu48, @lucasmiranda42 - this is the review thread for the submission. All of our communications will happen here from now on.
Please check the post at the top of the issue for instructions on how to generate your own review checklist. As you go over the submission, please check any items that you feel have been satisfied. There are also 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 directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.
Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!
Hi! First impressions on my side.
1) The paper is well written: it clearly states how the package fits in the field, and the problems it intends to solve. My only concern is regarding the references: in the README file of the main repo there are several other references that are not mentioned in the manuscript. I would suggest either adding them or justifying why this is not the case :)
2) The package installs without problems. I filed an issue with a minor concern regarding how the instructions are documented, but overall everything seems to work properly. The example provided in the README file does however not work. It seems to be due to an undocumented change in the API; I filed an issue accordingly.
3) While automatic tests are provided, the CI pipeline seems to be failing at the moment. I would suggest inspecting why and fixing the failing tests.
4) Lastly, while the provided example seems well documented (I haven't gone fully through it yet due to the issue mentioned above) I couldn't find a link to more extensive documentation of the package capabilities and functions. In case it indeed does not exist, I would suggest expanding here!
I will for now wait until (2) is clarified and/or fixed, and fully test functionality then.
Best, and looking forward! Lucas
Hi,
I have reviewed your paper titled "Package X for Statistical Analysis" submitted to the Journal of Open Statistical Software. Overall, the paper is well written and clearly articulates the purpose and scope of the proposed package. However, I do have some concerns and suggestions that I would like to share with you.
Firstly, I recommend that you either include some more references in the manuscript to support this research project, or justify why the current two listed are sufficient for the paper.
Secondly, I successfully installed the package without any issues. However, I encountered similar problems with the example provided in the README file and the CI pipeline. It would be a good idea if you could investigate and address the issues causing the failures to ensure that the package is reliable and robust. I look forward to reviewing the full functionality and performance of the package once this is resolved. I also suggest adding one or two more alternative examples so the new user could more easily understand the different ways to apply this package.
Lastly, I would appreciate more details discussing the potential scope and usage of the package in the second paragraph under the secion, "SuperNOVA ’s Scope".
Overall, I believe that the package has the potential to be a valuable contribution to the field.
Best regards,
Ming
👋🏻 Just wanted to check in here. @blind-contours - please have a look at the comments from the reviewers above, and let us know if you have any questions or when you are ready for the reviewers to take another look. Thanks!
👋🏻 @blind-contours - could you give us an update on how things are going here? Don't hesitate to let us know if you have any questions. Thanks!
@csoneson, thank you for your patience. I have re-written the paper based on the comments from @mhu48. I need to run some additional checks to ensure functionality as I have done some considerable updates and also included data-adaptive mediation analysis to the package. Let me run my checks and get back to you in a couple days. Thank you for your review.
👋🏻 @blind-contours - could you provide an update on how things are going here? Thanks!
Almost done! At JSM now presenting the method. I'll reach out shortly when I'm finished.
@csoneson, @mhu48, @lucasmiranda42 -- I've fixed the example in the readme introduction and re-written the readme to be clearer and include mediation. I've also updated the paper. The current CI is still broken because SL3 has an imputation dependency that isn't on CRAN anymore so the install fails at the moment. I'm trying to figure out how to fix this in the YML script. But for now, everything in the package should work. Please let me know what other comments/suggestions you have and I'll update the package.
The package passes all green on my end with no notes or anything.
Thanks @blind-contours - @mhu48, @lucasmiranda42, when you have a chance, could you take a look at the modified submission and let us know what you think. Thanks!
👋🏻 @mhu48, @lucasmiranda42 - just wanted to check in to see if you have an estimate of when you might be able to take another look at this submission. Thanks a lot in advance!
Thanks for the reminder. I will try to find some time over this weekend to review this revision.
On Sat, Sep 16, 2023 at 8:02 AM Charlotte Soneson @.***> wrote:
👋🏻 @mhu48 https://github.com/mhu48, @lucasmiranda42 https://github.com/lucasmiranda42 - just wanted to check in to see if you have an estimate of when you might be able to take another look at this submission. Thanks a lot in advance!
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5422#issuecomment-1722225856, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKGGVY4IKSUN7QENPKJYQL3X2WPP5ANCNFSM6AAAAAAXQBEYBI . You are receiving this because you were mentioned.Message ID: @.***>
Thanks @mhu48 - @lucasmiranda42, do you have an estimate of when you think you will be able to take another look? Thanks.
Hi Charlotte,
Thanks for the reminder, I forgot to click send on the email last night.
I reviewed the revised submission this weekend and feel that it is ready for publication.
Thank you for the opportunity to contribute.
Best,
Ming
On Mon, Sep 25, 2023 at 11:10 AM Charlotte Soneson @.***> wrote:
Thanks @mhu48 https://github.com/mhu48 - @lucasmiranda42 https://github.com/lucasmiranda42, do you have an estimate of when you think you will be able to take another look? Thanks.
— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5422#issuecomment-1734059852, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKGGVY36LPSOFHH5VOQSGBTX4GUJDANCNFSM6AAAAAAXQBEYBI . You are receiving this because you were mentioned.Message ID: @.***>
Thanks @mhu48 - could you please also tick the remaining boxes in your review checklist above?
👋🏻 @lucasmiranda42 - could you let us know when you think you would be able to take a look at the revised version of this submission? Thanks in advance!
Dear all, the package now runs smoothly on my end and fulfils all functionality claims. My only concern is regarding documentation, which I couldn't find (other than the README). @blind-contours could you elaborate on whether this is intended and why API docs may not be needed? With this, the paper would have green light on my side as well. Best! Lucas
@lucasmiranda42 there should be a detailed vignette that accompanies the package. Let me ensure that it is compiling properly. Was it not showing up on your version when you did testing?
I've added a new directory /doc that should have an html file that brings up the vignette. I'm going to make some edits to it now but it should be available for users.
@lucasmiranda42 - just wanted to check whether the additional information provided by @blind-contours allowed you to access the vignette?
Perfect! All set on my side, then :)
Thank you @lucasmiranda42! @blind-contours - I will also take a quick look through the submission, and will get back to you shortly with the next steps.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1515/ijb-2015-0013 is OK
- 10.2202/1557-4679.1217 is OK
- 10.1111/j.1541-0420.2011.01685.x is OK
- 10.1002/sim.5907 is OK
- 10.1007/978-3-319-65304-4_14 is OK
- 10.1007/978-1-4419-9782-1 is OK
- 10.1007/978-3-319-65304-4 is OK
- 10.2202/1557-4679.1356 is OK
- 10.1111/rssb.12362 is OK
- 10.1111/biom.13375 is OK
- 10.21105/joss.02526 is OK
- 10.5281/zenodo.1342293 is OK
- 10.5281/zenodo.3558313 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@blind-contours I have gone through the submission and overall it looks good. Just a couple of points, mostly related to the bibliography - could you please:
{}
as appropriate to make the representation of Mark van der Laan's name consistent across bibliography items superNOVA
and package on line 100In addition, the sentence starting on line 51 and ending on line 57 is very long, and I would suggest splitting it up to increase readability.
You can generate a new proof with @editorialbot generate pdf
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@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
@editorialbot generate pdf
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@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Zenodo DOI: 10.5281/zenodo.10038794
Link here: https://zenodo.org/records/10038794
I think I've made the suggested changes and also created the release version and upload to Zenodo correctly - if there are issues do please let me know.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1111/rssb.12362 is OK
- 10.5281/zenodo.1342293 is OK
- 10.1515/ijb-2015-0013 is OK
MISSING DOIs
- None
INVALID DOIs
- https://doi.org/10.48550/arXiv.2305.01849 is INVALID because of 'https://doi.org/' prefix
- 10.1111/j.1541-0420 is INVALID
Thanks @blind-contours - a couple of things remain:
Thanks!
Sorry about that. Everything should be fixed now.
@editorialbot generate pdf
@editorialbot check references
Submitting author: !--author-handle-->@blind-contours<!--end-author-handle-- (David McCoy) Repository: https://github.com/blind-contours/SuperNOVA Branch with paper.md (empty if default branch): main Version: v1.0.0-JOSS Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @mhu48, @lucasmiranda42 Archive: 10.5281/zenodo.10038794
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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.)
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