[REVIEW]: mde: An R package to ease missing dat exploration and handling
editorialbot opened this issue · comments
Submitting author: @Nelson-Gon (Nelson Gonzabato)
Repository: https://github.com/Nelson-Gon/mde
Branch with paper.md (empty if default branch): joss_submission
Version: v0.3.2
Editor: @cheginit
Reviewers: @roualdes, @JerryChiaRuiChang
Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/d4b8b71c7a822d1050dba722370a4a63"><img src="https://joss.theoj.org/papers/d4b8b71c7a822d1050dba722370a4a63/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/d4b8b71c7a822d1050dba722370a4a63)
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Reviewer instructions & questions
@roualdes & @JerryChiaRuiChang, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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Checklists
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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.18637/jss.v105.i07 is OK
- 10.21105/joss.00355 is OK
- 10.18637/jss.v045.i03 is OK
MISSING DOIs
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: dplyr: A Grammar of Data Manipulation
- No DOI given, and none found for title: tidyr: Tidy Messy Data
INVALID DOIs
- https://doi.org/10.1016/j.jsp.2009.10.001 is INVALID because of 'https://doi.org/' prefix
Software report:
github.com/AlDanial/cloc v 1.90 T=0.05 s (2320.6 files/s, 247177.6 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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HTML 36 1050 129 6388
R 40 500 460 1240
Markdown 25 353 0 956
CSS 3 98 52 442
JavaScript 5 65 37 277
YAML 5 27 0 197
XML 1 0 0 111
TeX 1 4 0 64
SVG 1 0 1 11
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SUM: 117 2097 679 9686
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Commit count by author:
282 Nelson-Gon
5 jordanjenkins
4 NelsonGon
2 Ronak Shah
Paper file info:
📄 Wordcount for paper.md is 606
✅ The paper includes a Statement of need section
License info:
🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)
@roualdes & @JerryChiaRuiChang, thanks again for accepting to review this submission. This is the review thread for the submission. All of our communications will happen here from now on.
First, please follow the instructions in the first comment of this thread to create your review checklists.
These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied by editing your checklist comment that our EditorBot will create for you.
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#6697 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 reach out to me if you need more time. You can also use @EditorialBot to set automatic reminders if you know you'll be away for a known period of time.
Please don't hesitate to ping me (@cheginit) with any questions or concerns.
Hi @roualdes, @JerryChiaRuiChang, just a friendly reminder for the review.
Review checklist for @roualdes
Conflict of interest
- 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
- I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- Repository: Is the source code for this software available at the https://github.com/Nelson-Gon/mde?
- License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
- Contribution and authorship: Has the submitting author (@Nelson-Gon) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
- Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
- Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.
Functionality
- Installation: Does installation proceed as outlined in the documentation?
- Functionality: Have the functional claims of the software been confirmed?
- 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
- A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- 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
- Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- 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, who the target audience is, and its relation to other work?
- State of the field: Do the authors describe how this software compares to other commonly-used packages?
- Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- 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?
A good idea here, to provide some helper functions for working with and understanding the scope of missing data within data frames. I'm just a little hung up on the Substantial scholarly effort checkbox.
For instance, cloc counts roughly 650 lines of code (excluding tests, blank lines, comments, and doc strings).
On the positive side of things, for sure some functions look like re-usable patterns and combinations of dplyr tooling.
On the negative side of things, however, some of the functions are wrappers around pretty standard patterns in R, e.g. sum(is.na(x)) for counting NAs, and other functions are just catching errors that dplyr already catches.
Somewhere in between positive and negative, many of these functions could be cleaned up.
drop_all_na.data.framedrops columns or rows of the user supplied data frame depending on second argument. The doc however suggests only columns will be dropped. From a user's perspective, this seems to break POLA.recode_as_na_for.data.frameis pretty computationally inefficient, performing way too much work. Most of this function could be reduced to just a couple of lines of code abusing the fact that R can pass operators as function arguments, see?match.fun.- Comments like "This is currently not the best way, a prototype that JustWorks^^TM" aren't very encouraging.
- The code is oddly formatted, with the body of functions sometimes being indented, sometimes not. And an inconsistent use of assignment operators, e.g. <-, =, ->.
I'll stop here for now and ask for guidance on how best to proceed. Please advise @cheginit. Thanks.
Thanks @Nelson-Gon for letting us know about your decision. Also, thanks to @roualdes and @JerryChiaRuiChang for agreeing to review.
@crvernon The author decided to withdraw their submission.
@editorialbot withdraw
Per:
Thanks @Nelson-Gon for letting us know about your decision. Also, thanks to @roualdes and @JerryChiaRuiChang for agreeing to review.
@crvernon The author decided to withdraw their submission.
Paper withdrawn.