[REVIEW]: home2park: An R package to assess the spatial provision of urban parks

[whedon]

Submitting author: @xp-song (Xiao Ping Song)
Repository: https://github.com/ecological-cities/home2park
Version: v0.1.1
Editor: @martinfleis
Reviewer: @aelissa, @nickbearman
Archive: 10.5281/zenodo.5516698

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/16d81fa40c903d4cd5dfa91900b55bb0"><img src="https://joss.theoj.org/papers/16d81fa40c903d4cd5dfa91900b55bb0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/16d81fa40c903d4cd5dfa91900b55bb0/status.svg)](https://joss.theoj.org/papers/16d81fa40c903d4cd5dfa91900b55bb0)

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

@aelissa & @nickbearman, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @aelissa

✨ 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

• 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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@xp-song) 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

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 and who the target audience is?
• 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?

Review checklist for @nickbearman

✨ 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

• 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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@xp-song) 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

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 and who the target audience is?
• 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?

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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

@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 678

[whedon]

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

OK DOIs

- 10.2478/quageo-2019-0008 is OK
- 10.1016/j.apgeog.2015.06.008 is OK
- 10.1007/s10708-009-9303-8 is OK
- 10.1016/j.landurbplan.2016.11.001 is OK
- 10.1038/s41598-020-57864-4 is OK
- 10.3390/ijerph14121521 is OK
- 10.1016/j.landurbplan.2020.103908 is OK
- 10.1088/1748-9326/abb396 is OK
- 10.1016/j.ufug.2020.126689 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.21 s (423.5 files/s, 105467.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            34           1805            484           6890
JavaScript                      12            797            543           3866
Markdown                         6            307              0           1077
CSS                              6            157             77           1045
R                               19            596           1601           1032
XML                              2              0              2            525
Rmd                              4            351            398            307
YAML                             4             15              2            142
TeX                              1              0              0            134
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                            89           4028           3108          15029
-------------------------------------------------------------------------------


Statistical information for the repository 'ffd94db9aa3d6b4dddb864de' was
gathered on 2021/08/12.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
xpsong                           2          5242             24          100.00

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
xpsong                     5218           99.5          0.0               10.44

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[martinfleis]

👋 @xp-song @aelissa @nickbearman this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. 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 and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3609 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 any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@martinfleis) if you have any questions/concerns.

[whedon]

👋 @nickbearman, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @aelissa, please update us on how your review is going (this is an automated reminder).

[nickbearman]

Hi all, I am having a look at this now.
For the record, as it is a Saturday:
My working pattern is probably not the same as your working pattern, therefore
you may get (GitHub notifications) from me outside of normal working hours. Please do not feel any
pressure to respond outside of your own working pattern.

[nickbearman]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[nickbearman]

@martinfleis I think my invitation has expired, I can't edit the checklist and when I click the link https://github.com/openjournals/joss-reviews/invitations GitHub said the invitation had expired. Thanks!

[martinfleis]

@whedon re-invite @nickbearman as reviewer

[whedon]

OK, the reviewer has been re-invited.

@nickbearman please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[martinfleis]

@nickbearman I have invited you again. Let me know if the issue persists. Thanks!

[nickbearman]

@martinfleis Thanks very much, it works now!

[nickbearman]

I have a query reinstallation.
On my own PC I had to install Rtools (which was fine) and then reinstall a couple of specific packages (ellipsis and backports) but I think this is just the usual R package fiddling around with that we need to do. I did get the package working on my PC.

To verify that it should do a clean install, I tried installing it on RStudio.Cloud. That, however, did not work:
`Installing package into ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)

• installing source package ‘home2park’ ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  Killed
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmpDVcFS8/filee043922ee/home2park_0.1.0.tar.gz’ had non-zero exit status`

Given this needs to be complied, does anyone know if that should be possible on RStudio.Cloud?
I have no other way of testing install on a 'clean' environment! Thanks

[nickbearman]

Currently I can't really test the software without a link to the 'Get started' tutorial.
I have run through the README instructions, but they are quite high-level.
The paper could expand slightly on the statistic the library generates - this is not 100% clear. Possibly a list of statistics it generates might be useful? I'm not sure currently, maybe the tutorial will help. I will revisit this in a few days time and see if it is any clearer.

[xp-song]

Currently I can't really test the software without a link to the 'Get started' tutorial.
I have run through the README instructions, but they are quite high-level.

Thanks for pointing out the dead link, I've amended it in commit 91e1f09. The website also contains more detailed explanations of the package: https://ecological-cities.github.io/home2park/

I'll have a look at testing the installation on other environments and see if it works, perhaps using conda

[xp-song]

I have a query reinstallation.
On my own PC I had to install Rtools (which was fine) and then reinstall a couple of specific packages (ellipsis and backports) but I think this is just the usual R package fiddling around with that we need to do. I did get the package working on my PC.

To verify that it should do a clean install, I tried installing it on RStudio.Cloud. That, however, did not work:
`Installing package into ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)

• installing source package ‘home2park’ ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  Killed
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmpDVcFS8/filee043922ee/home2park_0.1.0.tar.gz’ had non-zero exit status`

Given this needs to be complied, does anyone know if that should be possible on RStudio.Cloud?
I have no other way of testing install on a 'clean' environment! Thanks

I'm not too experienced with testing with 'clean' installation myself (other than the R-CMD-Check, which works fine), but based on this post, I managed to install it using a new conda environment:

In my command line (Mac Terminal):

conda create -n r-dev -c r r-essentials
conda activate r-dev

To install packages from github, install R package devtools:

conda install r-devtools

To ensure that dependency R package units installs properly, particularly for a conda environment:

conda install -c conda-forge udunits2

Load R, and run the following:

devtools::install_github("ecological-cities/home2park@main")

---

sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS 10.16

Matrix products: default
BLAS/LAPACK: /Users/xpsong/opt/anaconda3/envs/r-dev/lib/R/lib/libRblas.dylib

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] compiler_3.6.1

[nickbearman]

Thanks @xp-song for the notes re installation. I'm happy with this. @martinfleis any comments?

[martinfleis]

Thank you @nickbearman!

@xp-song The submission is now almost ready to be published.

The next steps you need to do now:

• Make a new tagged release of the software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service
• Check that the archival deposit (e.g., in Zenodo) has the correct metadata. In particular, the title and author list should be identical to those of the paper.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[xp-song]

@nickbearman @aelissa @martinfleis Thank you very much for your thoughtful review and comments. Here are requested information (I'm not able to edit your post directly):

• Make a new tagged release of the software, and list the version tag of the archived version here.

https://github.com/ecological-cities/home2park/releases/tag/v0.1.1

• Archive the reviewed software in Zenodo or a similar service

https://zenodo.org/record/5516698#.YUfmNi0RppQ

• Check that the archival deposit (e.g., in Zenodo) has the correct metadata. In particular, the title and author list should be identical to those of the paper.

• Please list the DOI of the archived version here.

10.5281/zenodo.5516698

[martinfleis]

@whedon set 10.5281/zenodo.5516698 as archive

[whedon]

OK. 10.5281/zenodo.5516698 is the archive.

[martinfleis]

@whedon set v0.1.1 as version

[whedon]

OK. v0.1.1 is the version.

[martinfleis]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[martinfleis]

Thank you @xp-song. I'm going to hand this over now to the associate EiC on rotation for the final steps.

[martinfleis]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.2478/quageo-2019-0008 is OK
- 10.1016/j.apgeog.2015.06.008 is OK
- 10.1007/s10708-009-9303-8 is OK
- 10.1016/j.landurbplan.2016.11.001 is OK
- 10.1038/s41598-020-57864-4 is OK
- 10.3390/ijerph14121521 is OK
- 10.1016/j.landurbplan.2020.103908 is OK
- 10.1088/1748-9326/abb396 is OK
- 10.1016/j.ufug.2020.126689 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2594

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2594, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[xp-song]

@whedon accept deposit=true

[whedon]

I'm sorry @xp-song, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

[xp-song]

whoops, embarrassing mistake.

[kthyng]

@xp-song Don't worry, it happens all the time! It doesn't say who should input that command, after all!

[kthyng]

I see your zenodo archive is made and in place, your version is up to date, and your paper looks great! We can proceed!

[kthyng]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03609 joss-papers#2595
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03609
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[martinfleis]

Congratulations @xp-song!

Thank you again @aelissa and @nickbearman for you valuable reviews!

[kthyng]

Thanks all, especially for your reviews @aelissa and @nickbearman and for being so thorough as handling editor @martinfleis!

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03609/status.svg)](https://doi.org/10.21105/joss.03609)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03609">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03609/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03609/status.svg
   :target: https://doi.org/10.21105/joss.03609

This is how it will look in your documentation:

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