[REVIEW]: oce: an R package for Oceanographic Analysis

whedon commented 3 years ago

Submitting author: !--author-handle-->@dankelley@kthyng<!--end-editor-- Reviewers: @gonzalobravoargentina, @patrickcgray Archive: 10.5281/zenodo.6325185

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Reviewer instructions & questions

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Review checklist for @gonzalobravoargentina

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@dankelley) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] #3726
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @patrickcgray

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@dankelley) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @gonzalobravoargentina, @diodon it looks like you're currently assigned to review this paper :tada:.

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kthyng commented 3 years ago

@gonzalobravoargentina, @diodon here is where the review actually takes place, along with issues in the software repo as needed. Thanks!

whedon commented 3 years ago

Wordcount for paper.md is 1379

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=3.97 s (239.7 files/s, 74475.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           574          30744           7802         126495
R                              232           2524          31144          44109
SQL                              1              0              0          15232
PO File                          4           6250            681          14182
C++                             29            298            874           3414
C                                8            158            501           1732
Markdown                        31            556              0           1680
XML                              4              0              2           1371
Fortran 77                       4              8            198           1248
Rmd                              8            464           1711            455
CSS                              3             99             48            428
YAML                             9             49             14            276
JavaScript                       4             64             34            266
make                            33             34              2            243
TeX                              1             13              0            142
MATLAB                           1             17             41             87
C/C++ Header                     1              8              0             43
Python                           1              6              5             24
SVG                              1              0              1             11
Bourne Shell                     3              3             23              8
-------------------------------------------------------------------------------
SUM:                           952          41295          43081         211446
-------------------------------------------------------------------------------

Statistical information for the repository 'e0c9b797f9eac537f34892f6' was
gathered on 2021/08/09.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Clark Richards                   5           406             49            0.68
Dan Kelley                     414         29260          24020           79.80
Dan.Kelley@Dal.Ca               38          2380           1117            5.24
Dirk Eddelbuettel                1            39             39            0.12
dan.kelley@dal.ca                2             2             13            0.02
dankelley                       84          5177           4267           14.14

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Clark Richards              352           86.7         14.2                9.09
Dan Kelley                    9            0.0        135.6               11.11
Dan.Kelley@Dal.Ca           736           30.9        144.7               20.11
Dirk Eddelbuettel            39          100.0          2.1                0.00
dankelley                  6351          122.7         57.6               22.26

whedon commented 3 years ago

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

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/wics.1212 is OK
- 10.1175/2008JTECHO615.1 is OK
- 10.1016/S0098-3004(02)00013-4 is OK
- 10.5670/oceanog.2010.21 is OK
- 10.3389/fmars.2021.635922 is OK
- 10.1080/07055900.2012.707610 is OK

MISSING DOIs

- 10.1002/wics.1212 may be a valid DOI for title: The Comprehensive R Archive Network

INVALID DOIs

- None

whedon commented 3 years ago

:wave: @diodon, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @gonzalobravoargentina, please update us on how your review is going (this is an automated reminder).

kthyng commented 3 years ago

@gonzalobravoargentina Thanks for your effort on your review! Do you have some specific comments as to anything that has come up during your review, and what is preventing you from checking the final boxes? Just a reminder to open issues in the software repo and link back to this review as issues arise.

@diodon Will you be able to work on your review soon?

kthyng commented 3 years ago

@gonzalobravoargentina and @diodon Can we get an update on your status here? Hoping to finish and start/finish reviews as soon as possible. Thanks.

kthyng commented 3 years ago

I just emailed @gonzalobravoargentina to touch base and I cannot find an email address for @diodon.

@diodon Are you still interested in doing this review? Please get back to me here with a timeline when you can work on your review, or just to let me know you can't do it anymore (no problem!). Since I haven't heard from you since mid-August, we'll move on to finding a new reviewer in a week if I haven't heard from you yet by then.

diodon commented 3 years ago

Hi Kristen,

Sorry, things have been quite hectic on my side. Sadly, I must have to withdraw my intentions of evaluating the package as I will be very busy until the end of the year.

Cheers, EKS

On Wed, 27 Oct 2021 at 08:06, Kristen Thyng @.***> wrote:

I just emailed @gonzalobravoargentina https://github.com/gonzalobravoargentina to touch base and I cannot find an email address for @diodon https://github.com/diodon.

@diodon https://github.com/diodon Are you still interested in doing this review? Please get back to me here with a timeline when you can work on your review, or just to let me know you can't do it anymore (no problem!). Since I haven't heard from you since mid-August, we'll move on to finding a new reviewer in a week if I haven't heard from you yet by then.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3594#issuecomment-952363403, or unsubscribe https://github.com/notifications/unsubscribe-auth/AATPAD5PPHIULM3IQQ3GOTTUI4Q4ZANCNFSM5B2ILCNA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

kthyng commented 3 years ago

@diodon Ok, thanks for letting me know!

@dankelley I'll search for a replacement reviewer now.

kthyng commented 3 years ago

@SeascapeScience Any chance you are still interested in reviewing this JOSS submission? We need a replacement reviewer for it! Thanks for your consideration.

SeascapeScience commented 3 years ago

Hi Kristen,

Yes, I’m interested. What’s the timeline for review?

Nick

——————————————— Nicholas Record, Ph.D.

Senior Research Scientist, Bigelow Laboratory for Ocean Sciences Director, Tandy Center for Ocean Forecasting Director, Sea Change Semester Program he/him

207-315-2567 x316 @SeascapeScience ———————————————

On Oct 27, 2021, at 11:14 AM, Kristen Thyng @.***> wrote:

@SeascapeScience https://github.com/SeascapeScience Any chance you are still interested in reviewing this JOSS submission? We need a replacement reviewer for it! Thanks for your consideration.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3594#issuecomment-953030993, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ3XN3IINCLA4V6O3BD7NDUJAJPBANCNFSM5B2ILCNA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

kthyng commented 3 years ago

@SeascapeScience Normally 4-6 weeks but given that this review was already underway I'd appreciate it if you could do more like 2-4 weeks if possible. Would that work for you?

SeascapeScience commented 3 years ago

I’ll do my best.

——————————————— Nicholas Record, Ph.D.

Senior Research Scientist, Bigelow Laboratory for Ocean Sciences Director, Tandy Center for Ocean Forecasting Director, Sea Change Semester Program he/him

207-315-2567 x316 @SeascapeScience ———————————————

On Oct 27, 2021, at 12:20 PM, Kristen Thyng @.***> wrote:

@SeascapeScience https://github.com/SeascapeScience Normally 4-6 weeks but given that this review was already underway I'd appreciate it if you could do more like 2-4 weeks if possible. Would that work for you?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3594#issuecomment-953088930, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ3XN34OGSIVIDNDE2CDRLUJARDPANCNFSM5B2ILCNA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

kthyng commented 3 years ago

Thank you @SeascapeScience! I will modify the issue now to make you a reviewer.

kthyng commented 3 years ago

@whedon remove @diodon as reviewer

whedon commented 3 years ago

OK, @diodon is no longer a reviewer

kthyng commented 3 years ago

@whedon add @SeascapeScience as reviewer

whedon commented 3 years ago

OK, @SeascapeScience is now a reviewer

kthyng commented 3 years ago

@SeascapeScience you should be good to go now. Thanks again.

kthyng commented 3 years ago

@gonzalobravoargentina replied by email and said he can finish the review this week. @gonzalobravoargentina just let me know if you have any questions about the review process!

gonzalobravoargentina commented 2 years ago

I have not many comments about the software because is continuously improving and all the basic tools for oceanographic analysis are cover. This paper will increase the visibility of OCE package and more users will contribute for upgrading the quality of the codes.

The list of available R packages for Oceanographic data is not so long but, in my opinion, Oce is the most complete and user friendly See: https://hafezahmad.medium.com/popular-r-packages-used-in-oceanography-fisheries-and-environmental-science-e3fbf0805f1a

I would like to add some comments regarding the statement of need of software paper and State of the field of the software paper.

In the marine biology community, R is one of the most popular software and a great number of people are used to this language. In many cases marine biologists need to process oceanographic data for their studies and the OCE package is a great option to avoid learning new languages (e.g. MATLAB, Python). The R oce package was an excellent tool during my studies and the support of the authors was excellent.

@dankelleyDo you think that a short list of advantages and disadvantages of R vs MATLAB or others in the oceanographic field could be added?

dankelley commented 2 years ago

@gonzalobravoargentina that's a good idea about R vs Matlab. I talk about R, Matlab and others in my textbook Oceanographic Analysis with R. I think I will follow your advice, and write a paragraph about this for the README file on the landing page for github/dankelley/R.

And many thanks for mentioning biological oceanography. I have also found, in my teaching of undergraduates, that R is very popular in that community.

Again, thanks for the review.

Dan

dankelley commented 2 years ago

@gonzalobravoargentina I have added the following paragraph to the README. I hope it gets close to what you were thinking of. Thanks again. Dan.

Why use R for oceanographic analysis?

The R language is popular in many branches of science, and Oceanography is not an exception. Perhaps because of its broad statistical support, R is especially popular in Biological Oceanography, and its popularity seems to be growing also among Chemical and Geological Oceanographers. In the remaining subdiscipline of Physical Oceanography, many researchers remain attached to Matlab, which was the strongest choice for interactive work in the late 1900s. However, the commercial and closed-source nature of Matlab is a problem in the eyes of many people, and so open-source alternatives have become increasingly popular. Of these, Python and R are the most popular languages at the moment, and many Oceanographers are conversant with each, switching between the two according to the task at hand. A strength of R in this regard is the availability of well-vetted and well-documented packages for handling a wide spectrum of specialized tasks. Of these, the oce package is particularly important.

gonzalobravoargentina commented 2 years ago

Great !